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Zou Z, Zheng Y, Chang L, Zou L, Zhang L, Min Y, Zhao Y. TIP aquaporins in Cyperus esculentus: genome-wide identification, expression profiles, subcellular localizations, and interaction patterns. BMC PLANT BIOLOGY 2024; 24:298. [PMID: 38632542 PMCID: PMC11025170 DOI: 10.1186/s12870-024-04969-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 03/31/2024] [Indexed: 04/19/2024]
Abstract
BACKGROUND Tonoplast intrinsic proteins (TIPs), which typically mediate water transport across vacuolar membranes, play an essential role in plant growth, development, and stress responses. However, their characterization in tigernut (Cyperus esculentus L.), an oil-bearing tuber plant of the Cyperaceae family, is still in the infancy. RESULTS In this study, a first genome-wide characterization of the TIP subfamily was conducted in tigernut, resulting in ten members representing five previously defined phylogenetic groups, i.e., TIP1-5. Although the gene amounts are equal to that present in two model plants Arabidopsis and rice, the group composition and/or evolution pattern were shown to be different. Except for CeTIP1;3 that has no counterpart in both Arabidopsis and rice, complex orthologous relationships of 1:1, 1:2, 1:3, 2:1, and 2:2 were observed. Expansion of the CeTIP subfamily was contributed by whole-genome duplication (WGD), transposed, and dispersed duplications. In contrast to the recent WGD-derivation of CeTIP3;1/-3;2, synteny analyses indicated that TIP4 and - 5 are old WGD repeats of TIP2, appearing sometime before monocot-eudicot divergence. Expression analysis revealed that CeTIP genes exhibit diverse expression profiles and are subjected to developmental and diurnal fluctuation regulation. Moreover, when transiently overexpressed in tobacco leaves, CeTIP1;1 was shown to locate in the vacuolar membrane and function in homo/heteromultimer, whereas CeTIP2;1 is located in the cell membrane and only function in heteromultimer. Interestingly, CeTIP1;1 could mediate the tonoplast-localization of CeTIP2;1 via protein interaction, implying complex regulatory patterns. CONCLUSIONS Our findings provide a global view of CeTIP genes, which provide valuable information for further functional analysis and genetic improvement through manipulating key members in tigernut.
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Affiliation(s)
- Zhi Zou
- National Key Laboratory for Tropical Crop Breeding/Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Institute of Tropical Biosciences and Biotechnology/Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, 571101, P. R. China.
| | - Yujiao Zheng
- National Key Laboratory for Tropical Crop Breeding/Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Institute of Tropical Biosciences and Biotechnology/Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, 571101, P. R. China
| | - Lili Chang
- National Key Laboratory for Tropical Crop Breeding/Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Institute of Tropical Biosciences and Biotechnology/Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, 571101, P. R. China
| | - Liangping Zou
- National Key Laboratory for Tropical Crop Breeding/Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Institute of Tropical Biosciences and Biotechnology/Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, 571101, P. R. China
| | - Li Zhang
- Hubei Provincial Key Laboratory for Protection and Application of Special Plants in Wuling Area of China, College of Life Science, South-Central Minzu University, Wuhan, Hubei, 430074, P. R. China
| | - Yi Min
- Hainan University, Haikou, Hainan, 570228, P. R. China.
| | - Yongguo Zhao
- National Key Laboratory for Tropical Crop Breeding/Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Institute of Tropical Biosciences and Biotechnology/Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, 571101, P. R. China.
- College of Biology and Food Engineering, Guangdong University of Petrochemical Technology, Maoming, Guangdong, 525000, P. R. China.
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Zhang F, Ma J, Liu Y, Fang J, Wei S, Xie R, Han P, Zhao X, Bo S, Lu Z. A Multi-Omics Analysis Revealed the Diversity of the MYB Transcription Factor Family's Evolution and Drought Resistance Pathways. Life (Basel) 2024; 14:141. [PMID: 38255756 PMCID: PMC10820167 DOI: 10.3390/life14010141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 01/15/2024] [Accepted: 01/15/2024] [Indexed: 01/24/2024] Open
Abstract
The MYB transcription factor family can regulate biological processes such as ABA signal transduction to cope with drought stress, but its evolutionary mechanism and the diverse pathways of response to drought stress in different species are rarely reported. In this study, a total of 4791 MYB family members were identified in 908,757 amino acid sequences from 12 model plants or crops using bioinformatics methods. It was observed that the number of MYB family members had a linear relationship with the chromosome ploidy of species. A phylogenetic analysis showed that the MYB family members evolved in subfamily clusters. In response to drought stress, the pathways of MYB transcription factor families exhibited species-specific diversity, with closely related species demonstrating a higher resemblance. This study provides abundant references for drought resistance research and the breeding of wheat, soybean, and other plants.
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Affiliation(s)
- Fan Zhang
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China; (F.Z.); (J.M.); (Y.L.); (J.F.); (S.W.); (R.X.); (P.H.)
- Key Laboratory of Black Soil Protection and Utilization, Ministry of Agriculture and Rural Areas, Hohhot 010031, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Remediation and Pollution Control, Hohhot 010031, China
- Inner Mongolia Conservation Tillage Engineering Technology Research Center, Hohhot 010031, China
| | - Jie Ma
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China; (F.Z.); (J.M.); (Y.L.); (J.F.); (S.W.); (R.X.); (P.H.)
- Key Laboratory of Black Soil Protection and Utilization, Ministry of Agriculture and Rural Areas, Hohhot 010031, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Remediation and Pollution Control, Hohhot 010031, China
- Inner Mongolia Conservation Tillage Engineering Technology Research Center, Hohhot 010031, China
- School of Life Science, Inner Mongolia University, Hohhot 010030, China
- Key Laboratory of Herbage & Endemic Crop Biotechnology, Ministry of Education, Hohhot 010030, China
| | - Ying Liu
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China; (F.Z.); (J.M.); (Y.L.); (J.F.); (S.W.); (R.X.); (P.H.)
- Key Laboratory of Black Soil Protection and Utilization, Ministry of Agriculture and Rural Areas, Hohhot 010031, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Remediation and Pollution Control, Hohhot 010031, China
- Inner Mongolia Conservation Tillage Engineering Technology Research Center, Hohhot 010031, China
- School of Life Science, Inner Mongolia University, Hohhot 010030, China
- Key Laboratory of Herbage & Endemic Crop Biotechnology, Ministry of Education, Hohhot 010030, China
| | - Jing Fang
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China; (F.Z.); (J.M.); (Y.L.); (J.F.); (S.W.); (R.X.); (P.H.)
- Key Laboratory of Black Soil Protection and Utilization, Ministry of Agriculture and Rural Areas, Hohhot 010031, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Remediation and Pollution Control, Hohhot 010031, China
- Inner Mongolia Conservation Tillage Engineering Technology Research Center, Hohhot 010031, China
- School of Life Science, Inner Mongolia University, Hohhot 010030, China
- Key Laboratory of Herbage & Endemic Crop Biotechnology, Ministry of Education, Hohhot 010030, China
| | - Shuli Wei
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China; (F.Z.); (J.M.); (Y.L.); (J.F.); (S.W.); (R.X.); (P.H.)
- Key Laboratory of Black Soil Protection and Utilization, Ministry of Agriculture and Rural Areas, Hohhot 010031, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Remediation and Pollution Control, Hohhot 010031, China
- Inner Mongolia Conservation Tillage Engineering Technology Research Center, Hohhot 010031, China
- School of Life Science, Inner Mongolia University, Hohhot 010030, China
- Key Laboratory of Herbage & Endemic Crop Biotechnology, Ministry of Education, Hohhot 010030, China
| | - Rui Xie
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China; (F.Z.); (J.M.); (Y.L.); (J.F.); (S.W.); (R.X.); (P.H.)
- Key Laboratory of Black Soil Protection and Utilization, Ministry of Agriculture and Rural Areas, Hohhot 010031, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Remediation and Pollution Control, Hohhot 010031, China
- Inner Mongolia Conservation Tillage Engineering Technology Research Center, Hohhot 010031, China
| | - Pingan Han
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China; (F.Z.); (J.M.); (Y.L.); (J.F.); (S.W.); (R.X.); (P.H.)
- Key Laboratory of Black Soil Protection and Utilization, Ministry of Agriculture and Rural Areas, Hohhot 010031, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Remediation and Pollution Control, Hohhot 010031, China
- Inner Mongolia Conservation Tillage Engineering Technology Research Center, Hohhot 010031, China
| | - Xiaoqing Zhao
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China; (F.Z.); (J.M.); (Y.L.); (J.F.); (S.W.); (R.X.); (P.H.)
- Key Laboratory of Black Soil Protection and Utilization, Ministry of Agriculture and Rural Areas, Hohhot 010031, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Remediation and Pollution Control, Hohhot 010031, China
- Inner Mongolia Conservation Tillage Engineering Technology Research Center, Hohhot 010031, China
- School of Life Science, Inner Mongolia University, Hohhot 010030, China
- Key Laboratory of Herbage & Endemic Crop Biotechnology, Ministry of Education, Hohhot 010030, China
| | - Suling Bo
- College of Computer Information, Inner Mongolia Medical University, Hohhot 010110, China
| | - Zhanyuan Lu
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China; (F.Z.); (J.M.); (Y.L.); (J.F.); (S.W.); (R.X.); (P.H.)
- Key Laboratory of Black Soil Protection and Utilization, Ministry of Agriculture and Rural Areas, Hohhot 010031, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Remediation and Pollution Control, Hohhot 010031, China
- Inner Mongolia Conservation Tillage Engineering Technology Research Center, Hohhot 010031, China
- School of Life Science, Inner Mongolia University, Hohhot 010030, China
- Key Laboratory of Herbage & Endemic Crop Biotechnology, Ministry of Education, Hohhot 010030, China
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3
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S V, M G, K R, S M, V G S, Boopathi N M. Floral volatile composition of Jasminum sambac variants developed through colchicine. Nat Prod Res 2024:1-9. [PMID: 38163992 DOI: 10.1080/14786419.2023.2298723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 12/18/2023] [Indexed: 01/03/2024]
Abstract
Jasmines are commercially grown for their fragrant flowers and essential oil. The present study investigates the composition of the volatile compounds from flowers of Jasminum sambac cv. Ramanthapuram Gundumalli and its variants that were evolved through colchicine. GC-MS analysis revealed that the flowers possessed major terpenes and sesquiterpenes such as Linalool, α-farnesene, germacrene-D, geranyl Linalool and D-Limonene as well as benzenoids (including benzyl acetate, benzyl alcohol and (Z)-Cinnamyl benzoate). The relative abundance of these volatile compounds in the variants have shown higher percentages than their wild-type (parent) which indicates that the variants possessed enhanced volatile composition. The new variations generated in floral volatile composition of J. sambac through polyploidisation are likely to have significant impact on the loose flower and perfume industries. Besides, the identified unique compounds can also be used as metabolic signatures to characterise the novel variants.
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Affiliation(s)
- Vishnupandi S
- Department of Floriculture and Landscape Architecture, Tamil Nadu Agricultural University, Coimbatore, India
| | - Ganga M
- Department of Floriculture and Landscape Architecture, Tamil Nadu Agricultural University, Coimbatore, India
| | - Rajamani K
- Department of Floriculture and Landscape Architecture, Tamil Nadu Agricultural University, Coimbatore, India
| | - Manonmani S
- Department of Rice, Tamil Nadu Agricultural University, Coimbatore, India
| | - Shobhana V G
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, India
| | - Manikanda Boopathi N
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, India
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4
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Kong X, Zhang Y, Wang Z, Bao S, Feng Y, Wang J, Yu Z, Long F, Xiao Z, Hao Y, Gao X, Li Y, Ding Y, Wang J, Lei T, Xu C, Wang J. Two-step model of paleohexaploidy, ancestral genome reshuffling and plasticity of heat shock response in Asteraceae. HORTICULTURE RESEARCH 2023; 10:uhad073. [PMID: 37303613 PMCID: PMC10251138 DOI: 10.1093/hr/uhad073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 04/10/2023] [Indexed: 06/13/2023]
Abstract
An ancient hexaploidization event in the most but not all Asteraceae plants, may have been responsible for shaping the genomes of many horticultural, ornamental, and medicinal plants that promoting the prosperity of the largest angiosperm family on the earth. However, the duplication process of this hexaploidy, as well as the genomic and phenotypic diversity of extant Asteraceae plants caused by paleogenome reorganization, are still poorly understood. We analyzed 11 genomes from 10 genera in Asteraceae, and redated the Asteraceae common hexaploidization (ACH) event ~70.7-78.6 million years ago (Mya) and the Asteroideae specific tetraploidization (AST) event ~41.6-46.2 Mya. Moreover, we identified the genomic homologies generated from the ACH, AST and speciation events, and constructed a multiple genome alignment framework for Asteraceae. Subsequently, we revealed biased fractionations between the paleopolyploidization produced subgenomes, suggesting the ACH and AST both are allopolyplodization events. Interestingly, the paleochromosome reshuffling traces provided clear evidence for the two-step duplications of ACH event in Asteraceae. Furthermore, we reconstructed ancestral Asteraceae karyotype (AAK) that has 9 paleochromosomes, and revealed a highly flexible reshuffling of Asteraceae paleogenome. Of specific significance, we explored the genetic diversity of Heat Shock Transcription Factors (Hsfs) associated with recursive whole-genome polyploidizations, gene duplications, and paleogenome reshuffling, and revealed that the expansion of Hsfs gene families enable heat shock plasticity during the genome evolution of Asteraceae. Our study provides insights on polyploidy and paleogenome remodeling for the successful establishment of Asteraceae, and is helpful for further communication and exploration of the diversification of plant families and phenotypes.
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Affiliation(s)
| | | | | | | | - Yishan Feng
- Department of Bioinformatics, School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei 063000, China
| | - Jiaqi Wang
- Department of Bioinformatics, School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei 063000, China
| | - Zijian Yu
- Department of Bioinformatics, School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei 063000, China
| | - Feng Long
- Department of Bioinformatics, School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei 063000, China
| | - Zejia Xiao
- Department of Bioinformatics, School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei 063000, China
| | - Yanan Hao
- Department of Bioinformatics, School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei 063000, China
| | - Xintong Gao
- Department of Bioinformatics, School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei 063000, China
| | - Yinfeng Li
- Department of Bioinformatics, School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei 063000, China
| | - Yue Ding
- Department of Bioinformatics, School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei 063000, China
| | - Jianyu Wang
- Department of Bioinformatics, School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei 063000, China
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5
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Wang J, Yuan M, Feng Y, Zhang Y, Bao S, Hao Y, Ding Y, Gao X, Yu Z, Xu Q, Zhao J, Zhu Q, Wang P, Wu C, Wang J, Li Y, Xu C, Wang J. A common whole-genome paleotetraploidization in Cucurbitales. PLANT PHYSIOLOGY 2022; 190:2430-2448. [PMID: 36053177 PMCID: PMC9706448 DOI: 10.1093/plphys/kiac410] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 08/10/2022] [Indexed: 06/01/2023]
Abstract
Cucurbitales are an important order of flowering plants known for encompassing edible plants of economic and medicinal value and numerous ornamental plants of horticultural value. By reanalyzing the genomes of two representative families (Cucurbitaceae and Begoniaceae) in Cucurbitales, we found that the previously identified Cucurbitaceae common paleotetraploidization that occurred shortly after the core-eudicot-common hexaploidization event is shared by Cucurbitales, including Begoniaceae. We built a multigenome alignment framework for Cucurbitales by identifying orthologs and paralogs and systematically redating key evolutionary events in Cucurbitales. Notably, characterizing the gene retention levels and genomic fractionation patterns between subgenomes generated from different polyploidizations in Cucurbitales suggested the autopolyploid nature of the Begoniaceae common tetraploidization and the allopolyploid nature of the Cucurbitales common tetraploidization and the Cucurbita-specific tetraploidization. Moreover, we constructed the ancestral Cucurbitales karyotype comprising 17 proto-chromosomes, confirming that the most recent common ancestor of Cucurbitaceae contained 15 proto-chromosomes and rejecting the previous hypothesis for an ancestral Cucurbitaceae karyotype with 12 proto-chromosomes. In addition, we found that the polyploidization and tandem duplication events promoted the expansion of gene families involved in the cucurbitacin biosynthesis pathway; however, gene loss and chromosomal rearrangements likely limited the expansion of these gene families.
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Affiliation(s)
- Jiaqi Wang
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
| | - Min Yuan
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
| | - Yishan Feng
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
| | - Yan Zhang
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
| | - Shoutong Bao
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
| | - Yanan Hao
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
| | - Yue Ding
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
| | - Xintong Gao
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
| | - Zijian Yu
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
| | - Qiang Xu
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
| | - Junxin Zhao
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
| | - Qianwen Zhu
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
| | - Ping Wang
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
| | - Chunyang Wu
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
| | - Jianyu Wang
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
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6
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Henry CN, Piper K, Wilson AE, Miraszek JL, Probst CS, Rong Y, Liberles DA. WGDTree: a phylogenetic software tool to examine conditional probabilities of retention following whole genome duplication events. BMC Bioinformatics 2022; 23:505. [PMID: 36434497 PMCID: PMC9701042 DOI: 10.1186/s12859-022-05042-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 11/08/2022] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Multiple processes impact the probability of retention of individual genes following whole genome duplication (WGD) events. In analyzing two consecutive whole genome duplication events that occurred in the lineage leading to Atlantic salmon, a new phylogenetic statistical analysis was developed to examine the contingency of retention in one event based upon retention in a previous event. This analysis is intended to evaluate mechanisms of duplicate gene retention and to provide software to generate the test statistic for any genome with pairs of WGDs in its history. RESULTS Here a software package written in Python, 'WGDTree' for the analysis of duplicate gene retention following whole genome duplication events is presented. Using gene tree-species tree reconciliation to label gene duplicate nodes and differentiate between WGD and SSD duplicates, the tool calculates a statistic based upon the conditional probability of a gene duplicate being retained after a second whole genome duplication dependent upon the retention status after the first event. The package also contains methods for the simulation of gene trees with WGD events. After running simulations, the accuracy of the placement of events has been determined to be high. The conditional probability statistic has been calculated for Phalaenopsis equestris on a monocot species tree with a pair of consecutive WGD events on its lineage, showing the applicability of the method. CONCLUSIONS A new software tool has been created for the analysis of duplicate genes in examination of retention mechanisms. The software tool has been made available on the Python package index and the source code can be found on GitHub here: https://github.com/cnickh/wgdtree .
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Affiliation(s)
- C. Nicholas Henry
- grid.264727.20000 0001 2248 3398Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA 19122 USA
| | - Kathryn Piper
- grid.264727.20000 0001 2248 3398Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA 19122 USA ,grid.265850.c0000 0001 2151 7947Present Address: Department of Biological Sciences, University at Albany, Albany, NY 12222 USA
| | - Amanda E. Wilson
- grid.264727.20000 0001 2248 3398Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA 19122 USA
| | - John L. Miraszek
- grid.264727.20000 0001 2248 3398Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA 19122 USA ,grid.134936.a0000 0001 2162 3504Present Address: Genetics Area Program, University of Missouri, Columbia, MO 65211 USA
| | - Claire S. Probst
- grid.264727.20000 0001 2248 3398Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA 19122 USA
| | - Yuying Rong
- grid.264727.20000 0001 2248 3398Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA 19122 USA ,grid.256868.70000 0001 2215 7365Department of Biology, Haverford College, Haverford, PA 19041 USA ,grid.4830.f0000 0004 0407 1981Present Address: Groningen Institute for Evolutionary Life Sciences, University of Groningen, 9747 AG Groningen, The Netherlands
| | - David A. Liberles
- grid.264727.20000 0001 2248 3398Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA 19122 USA
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7
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Zhang Y, Zhang L, Xiao Q, Wu C, Zhang J, Xu Q, Yu Z, Bao S, Wang J, Li Y, Wang L, Wang J. Two independent allohexaploidizations and genomic fractionation in Solanales. FRONTIERS IN PLANT SCIENCE 2022; 13:1001402. [PMID: 36212355 PMCID: PMC9538396 DOI: 10.3389/fpls.2022.1001402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 08/29/2022] [Indexed: 06/16/2023]
Abstract
Solanales, an order of flowering plants, contains the most economically important vegetables among all plant orders. To date, many Solanales genomes have been sequenced. However, the evolutionary processes of polyploidization events in Solanales and the impact of polyploidy on species diversity remain poorly understood. We compared two representative Solanales genomes (Solanum lycopersicum L. and Ipomoea triloba L.) and the Vitis vinifera L. genome and confirmed two independent polyploidization events. Solanaceae common hexaploidization (SCH) and Convolvulaceae common hexaploidization (CCH) occurred ∼43-49 and ∼40-46 million years ago (Mya), respectively. Moreover, we identified homologous genes related to polyploidization and speciation and constructed multiple genomic alignments with V. vinifera genome, providing a genomic homology framework for future Solanales research. Notably, the three polyploidization-produced subgenomes in both S. lycopersicum and I. triloba showed significant genomic fractionation bias, suggesting the allohexaploid nature of the SCH and CCH events. However, we found that the higher genomic fractionation bias of polyploidization-produced subgenomes in Solanaceae was likely responsible for their more abundant species diversity than that in Convolvulaceae. Furthermore, through genomic fractionation and chromosomal structural variation comparisons, we revealed the allohexaploid natures of SCH and CCH, both of which were formed by two-step duplications. In addition, we found that the second step of two paleohexaploidization events promoted the expansion and diversity of β-amylase (BMY) genes in Solanales. These current efforts provide a solid foundation for future genomic and functional exploration of Solanales.
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Affiliation(s)
- Yan Zhang
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, China
| | - Lan Zhang
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, China
| | - Qimeng Xiao
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, China
| | - Chunyang Wu
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, China
| | - Jiaqi Zhang
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, China
| | - Qiang Xu
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, China
| | - Zijian Yu
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, China
| | - Shoutong Bao
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, China
| | - Jianyu Wang
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, China
| | - Yu Li
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, China
| | - Li Wang
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, China
| | - Jinpeng Wang
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, China
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
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8
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Yang Q, Liu T, Wu T, Lei T, Li Y, Wang X. GGDB: A Grameneae genome alignment database of homologous genes hierarchically related to evolutionary events. PLANT PHYSIOLOGY 2022; 190:340-351. [PMID: 35789395 PMCID: PMC9434254 DOI: 10.1093/plphys/kiac297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 06/01/2022] [Indexed: 06/15/2023]
Abstract
The genomes of Gramineae plants have been preferentially sequenced owing to their economic value. These genomes are often quite complex, for example harboring many duplicated genes, and are the main source of genetic innovation and often the result of recurrent polyploidization. Deciphering these complex genome structures and linking duplicated genes to specific polyploidization events are important for understanding the biology and evolution of plants. However, efforts have been hampered by the complexity of analyzing these genomes. Here, we analyzed 29 well-assembled and up-to-date Gramineae genome sequences by hierarchically relating duplicated genes in collinear regions to specific polyploidization or speciation events. We separated duplicated genes produced by each event, established lists of paralogous and orthologous genes, and ultimately constructed an online database, GGDB (http://www.grassgenome.com/). Homologous gene lists from each plant and between plants can be displayed, searched, and downloaded from the database. Interactive comparison tools are deployed to demonstrate homology among user-selected plants and to draw genome-scale or local alignment figures and gene-based phylogenetic trees corrected by exploiting gene collinearity. Using these tools and figures, users can easily detect structural changes in genomes and explore the effects of paleo-polyploidy on crop genome structure and function. The GGDB will provide a useful platform for improving our understanding of genome changes and functional innovation in Gramineae plants.
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Affiliation(s)
- Qihang Yang
- School of Life Science, North China University of Science and Technology, Tangshan, Hebei 063210, China
- Center for Genomics and Bio-computing, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Tao Liu
- School of Life Science, North China University of Science and Technology, Tangshan, Hebei 063210, China
- College of Sciences, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Tong Wu
- School of Life Science, North China University of Science and Technology, Tangshan, Hebei 063210, China
- Center for Genomics and Bio-computing, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Tianyu Lei
- School of Life Science, North China University of Science and Technology, Tangshan, Hebei 063210, China
- Center for Genomics and Bio-computing, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Yuxian Li
- School of Life Science, North China University of Science and Technology, Tangshan, Hebei 063210, China
- Center for Genomics and Bio-computing, North China University of Science and Technology, Tangshan, Hebei 063210, China
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9
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Wang J, Zhang L, Wang J, Hao Y, Xiao Q, Teng J, Shen S, Zhang Y, Feng Y, Bao S, Li Y, Yan Z, Wei C, Wang L, Wang J. Conversion between duplicated genes generated by polyploidization contributes to the divergence of poplar and willow. BMC PLANT BIOLOGY 2022; 22:298. [PMID: 35710333 PMCID: PMC9205023 DOI: 10.1186/s12870-022-03684-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 06/06/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Gene conversion has an important effect on duplicate genes produced by polyploidization. Poplar (Populus trichocarpa) and willow (Salix brachista) are leading models and excellent green plants in the Salicaceae. Although much attention has been paid to the evolution of duplicated genes in poplar and willow, the role of conversion between duplicates generated from polyploidization remains poorly understood. RESULTS Here, through genomic synteny analyses, we identified duplicate genes generated by the Salicaceae common tetraploidization (SCT) in the poplar and willow genomes. We estimated that at least 0.58% and 0.25% of poplar and willow duplicates were affected by whole-gene conversion after the poplar-willow divergence, with more (5.73% and 2.66%) affected by partial-gene conversion. Moreover, we found that the converted duplicated genes were unevenly distributed on each chromosome in the two genomes, and the well-preserved homoeologous chromosome regions may facilitate the conversion of duplicates. Notably, we found that conversion maintained the similarity of duplicates, likely contributing to the conservation of certain sequences, but is essentially accelerated the rate of evolution and increased species divergence. In addition, we found that converted duplicates tended to have more similar expression patterns than nonconverted duplicates. We found that genes associated with multigene families were preferentially converted. We also found that the genes encoding conserved structural domains associated with specific traits exhibited a high frequency of conversion. CONCLUSIONS Extensive conversion between duplicate genes generated from the SCT contributes to the diversification of the family Salicaceae and has had long-lasting effects on those genes with important biological functions.
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Affiliation(s)
- Jianyu Wang
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Lan Zhang
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Jiaqi Wang
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Yanan Hao
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Qimeng Xiao
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Jia Teng
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Shaoqi Shen
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Yan Zhang
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Yishan Feng
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Shoutong Bao
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Yu Li
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Zimo Yan
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Chendan Wei
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Li Wang
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China.
| | - Jinpeng Wang
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Science, Beijing, 100093, China.
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10
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Zhou Y, Zhang C, Zhang L, Ye Q, Liu N, Wang M, Long G, Fan W, Long M, Wing RA. Gene fusion as an important mechanism to generate new genes in the genus Oryza. Genome Biol 2022; 23:130. [PMID: 35706016 PMCID: PMC9199173 DOI: 10.1186/s13059-022-02696-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 05/30/2022] [Indexed: 11/16/2022] Open
Abstract
Background Events of gene fusion have been reported in several organisms. However, the general role of gene fusion as part of new gene origination remains unknown. Results We conduct genome-wide interrogations of four Oryza genomes by designing and implementing novel pipelines to detect fusion genes. Based on the phylogeny of ten plant species, we detect 310 fusion genes across four Oryza species. The estimated rate of origination of fusion genes in the Oryza genus is as high as 63 fusion genes per species per million years, which is fixed at 16 fusion genes per species per million years and much higher than that in flies. By RNA sequencing analysis, we find more than 44% of the fusion genes are expressed and 90% of gene pairs show strong signals of purifying selection. Further analysis of CRISPR/Cas9 knockout lines indicates that newly formed fusion genes regulate phenotype traits including seed germination, shoot length and root length, suggesting the functional significance of these genes. Conclusions We detect new fusion genes that may drive phenotype evolution in Oryza. This study provides novel insights into the genome evolution of Oryza. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02696-w.
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Affiliation(s)
- Yanli Zhou
- Germplasm Bank of Wild species, Kunming Institute of Botany, Chinese Academy of Science, Kunming, Yunnan, 650201, China
| | - Chengjun Zhang
- Germplasm Bank of Wild species, Kunming Institute of Botany, Chinese Academy of Science, Kunming, Yunnan, 650201, China. .,Department of Ecology and Evolution, The University of Chicago, 1101 E. 57th Street, Chicago, IL, 60637, USA.
| | - Li Zhang
- Department of Ecology and Evolution, The University of Chicago, 1101 E. 57th Street, Chicago, IL, 60637, USA.,Chinese Institute for Brain Research, (CIBR), Beijing, 102206, China
| | - Qiannan Ye
- Germplasm Bank of Wild species, Kunming Institute of Botany, Chinese Academy of Science, Kunming, Yunnan, 650201, China
| | - Ningyawen Liu
- Germplasm Bank of Wild species, Kunming Institute of Botany, Chinese Academy of Science, Kunming, Yunnan, 650201, China
| | - Muhua Wang
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA.,State Key Laboratory for Biocontrol, School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519000, China
| | - Guangqiang Long
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Wei Fan
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Manyuan Long
- Department of Ecology and Evolution, The University of Chicago, 1101 E. 57th Street, Chicago, IL, 60637, USA.
| | - Rod A Wing
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA. .,Center for Desert Agriculture, King Abdullah University of Science & Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia.
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11
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Teng J, Wang J, Zhang L, Wei C, Shen S, Xiao Q, Yue Y, Hao Y, Ge W, Wang J. Paleopolyploidies and Genomic Fractionation in Major Eudicot Clades. FRONTIERS IN PLANT SCIENCE 2022; 13:883140. [PMID: 35712579 PMCID: PMC9194900 DOI: 10.3389/fpls.2022.883140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 04/27/2022] [Indexed: 06/15/2023]
Abstract
Eudicots account for ~75% of living angiosperms, containing important food and energy crops. Recently, high-quality genome sequences of several eudicots including Aquilegia coerulea and Nelumbo nucifera have become available, providing an opportunity to investigate the early evolutionary characteristics of eudicots. We performed genomic hierarchical and event-related alignments to infer homology within and between representative species of eudicots. The results provide strong evidence for multiple independent polyploidization events during the early diversification of eudicots, three of which are likely to be allopolyploids: The core eudicot-common hexaploidy (ECH), Nelumbo-specific tetraploidy (NST), and Ranunculales-common tetraploidy (RCT). Using different genomes as references, we constructed genomic alignment to list the orthologous and paralogous genes produced by polyploidization and speciation. This could provide a fundamental framework for studying other eudicot genomes and gene(s) evolution. Further, we revealed significantly divergent evolutionary rates among these species. By performing evolutionary rate correction, we dated RCT to be ~118-134 million years ago (Mya), after Ranunculales diverged with core eudicots at ~123-139 Mya. Moreover, we characterized genomic fractionation resulting from gene loss and retention after polyploidizations. Notably, we revealed a high degree of divergence between subgenomes. In particular, synonymous nucleotide substitutions at synonymous sites (Ks) and phylogenomic analyses implied that A. coerulea might provide the subgenome(s) for the gamma-hexaploid hybridization.
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Affiliation(s)
- Jia Teng
- Department of Bioinformatics, School of Life Sciences and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Jianyu Wang
- Department of Bioinformatics, School of Life Sciences and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Lan Zhang
- Department of Bioinformatics, School of Life Sciences and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Chendan Wei
- Department of Bioinformatics, School of Life Sciences and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Shaoqi Shen
- Department of Bioinformatics, School of Life Sciences and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Qimeng Xiao
- Department of Bioinformatics, School of Life Sciences and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Yuanshuai Yue
- Department of Bioinformatics, School of Life Sciences and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Yanan Hao
- Department of Bioinformatics, School of Life Sciences and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Weina Ge
- Department of Bioinformatics, School of Life Sciences and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Jinpeng Wang
- Department of Bioinformatics, School of Life Sciences and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Science, Beijing, China
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12
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Wang ZH, Wang XF, Lu T, Li MR, Jiang P, Zhao J, Liu ST, Fu XQ, Wendel JF, Van de Peer Y, Liu B, Li LF. Reshuffling of the ancestral core-eudicot genome shaped chromatin topology and epigenetic modification in Panax. Nat Commun 2022; 13:1902. [PMID: 35393424 PMCID: PMC8989883 DOI: 10.1038/s41467-022-29561-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 03/23/2022] [Indexed: 12/21/2022] Open
Abstract
All extant core-eudicot plants share a common ancestral genome that has experienced cyclic polyploidizations and (re)diploidizations. Reshuffling of the ancestral core-eudicot genome generates abundant genomic diversity, but the role of this diversity in shaping the hierarchical genome architecture, such as chromatin topology and gene expression, remains poorly understood. Here, we assemble chromosome-level genomes of one diploid and three tetraploid Panax species and conduct in-depth comparative genomic and epigenomic analyses. We show that chromosomal interactions within each duplicated ancestral chromosome largely maintain in extant Panax species, albeit experiencing ca. 100–150 million years of evolution from a shared ancestor. Biased genetic fractionation and epigenetic regulation divergence during polyploidization/(re)diploidization processes generate remarkable biochemical diversity of secondary metabolites in the Panax genus. Our study provides a paleo-polyploidization perspective of how reshuffling of the ancestral core-eudicot genome leads to a highly dynamic genome and to the metabolic diversification of extant eudicot plants. The role of polyploidization generated genomic diversity in shaping the hierarchical genome architecture remains unclear. Here, the authors show that repatterning of the ancestral eudicot genome has resulted in multi-dimensional genome plasticity and secondary metabolite diversification via comparisons of Panax genomes.
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Affiliation(s)
- Zhen-Hui Wang
- Faculty of Agronomy, Jilin Agricultural University, 130118, Changchun, China.,Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, 200438, Shanghai, China.,Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, 130024, Changchun, China
| | - Xin-Feng Wang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, 200438, Shanghai, China
| | - Tianyuan Lu
- McGill University and Genome Quebec Innovation Center, Montreal, QC, H3A 0G1, Canada
| | - Ming-Rui Li
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, 200438, Shanghai, China
| | - Peng Jiang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, 130024, Changchun, China
| | - Jing Zhao
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, 130024, Changchun, China
| | - Si-Tong Liu
- School of Life Sciences, Jilin University, 130061, Changchun, China
| | - Xue-Qi Fu
- School of Life Sciences, Jilin University, 130061, Changchun, China
| | - Jonathan F Wendel
- Department of Ecology, Evolution & Organismal Biology, Iowa State University, Ames, IA, 50011, USA
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University and VIB Center for Plant Systems Biology, Gent, Belgium. .,Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa. .,College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, 210095, Nanjing, China.
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, 130024, Changchun, China.
| | - Lin-Feng Li
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, 200438, Shanghai, China.
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13
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Singh R, Saripalli G, Gautam T, Kumar A, Jan I, Batra R, Kumar J, Kumar R, Balyan HS, Sharma S, Gupta PK. Meta-QTLs, ortho-MetaQTLs and candidate genes for grain Fe and Zn contents in wheat ( Triticum aestivum L.). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:637-650. [PMID: 35465199 PMCID: PMC8986950 DOI: 10.1007/s12298-022-01149-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 02/09/2022] [Accepted: 02/15/2022] [Indexed: 05/06/2023]
Abstract
Majority of cereals are deficient in essential micronutrients including grain iron (GFe) and grain zinc (GZn), which are therefore the subject of research involving biofortification. In the present study, 11 meta-QTLs (MQTLs) including nine novel MQTLs for GFe and GZn contents were identified in wheat. Eight of these 11 MQTLs controlled both GFe and GZn. The confidence intervals of the MQTLs were narrower (0.51-15.75 cM) relative to those of the corresponding QTLs (0.6 to 55.1 cM). Two ortho-MQTLs involving three cereals (wheat, rice and maize) were also identified. Results of MQTLs were also compared with the results of earlier genome wide association studies (GWAS). As many as 101 candidate genes (CGs) underlying MQTLs were also identified. Twelve of these CGs were prioritized; these CGs encoded proteins with important domains (zinc finger, RING/FYVE/PHD type, flavin adenine dinucleotide linked oxidase, etc.) that are involved in metal ion binding, heme binding, iron binding, etc. qRT-PCR analysis was conducted for four of these 12 prioritized CGs using genotypes which have differed for GFe and GZn. Significant differential expression in these genotypes was observed at 14 and 28 days after anthesis. The MQTLs/CGs identified in the present study may be utilized in marker-assisted selection (MAS) for improvement of GFe/GZn contents and also for understanding the molecular basis of GFe/GZn homeostasis in wheat. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-022-01149-9.
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Affiliation(s)
- Rakhi Singh
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, 250 004 Meerut, U.P India
| | - Gautam Saripalli
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, 250 004 Meerut, U.P India
- Department of Plant Science and Landscape Architecture, University of Maryland College Park, MD-20742 College Park, MD United States
| | - Tinku Gautam
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, 250 004 Meerut, U.P India
| | - Anuj Kumar
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, 250 004 Meerut, U.P India
| | - Irfat Jan
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, 250 004 Meerut, U.P India
| | - Ritu Batra
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, 250 004 Meerut, U.P India
| | - Jitendra Kumar
- Dept. of Biotechnology, Govt. of India, National Agri-Food Biotechnology Institute (NABI), Sector 81 (Knowledge City), S.A.S. Nagar, 140306 Mohali, Punjab India
| | - Rahul Kumar
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, 250 004 Meerut, U.P India
| | - Harindra Singh Balyan
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, 250 004 Meerut, U.P India
| | - Shailendra Sharma
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, 250 004 Meerut, U.P India
| | - Pushpendra Kumar Gupta
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, 250 004 Meerut, U.P India
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14
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Tomar S, Subba A, Bala M, Singh AK, Pareek A, Singla-Pareek SL. Genetic Conservation of CBS Domain Containing Protein Family in Oryza Species and Their Association with Abiotic Stress Responses. Int J Mol Sci 2022; 23:ijms23031687. [PMID: 35163610 PMCID: PMC8836131 DOI: 10.3390/ijms23031687] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/01/2022] [Accepted: 01/04/2022] [Indexed: 01/27/2023] Open
Abstract
Crop Wild Relatives (CWRs) form a comprehensive gene pool that can answer the queries related to plant domestication, speciation, and ecological adaptation. The genus ‘Oryza’ comprises about 27 species, of which two are cultivated, while the remaining are wild. Here, we have attempted to understand the conservation and diversification of the genes encoding Cystathionine β-synthase (CBS) domain-containing proteins (CDCPs) in domesticated and CWRs of rice. Few members of CDCPs were previously identified to be stress-responsive and associated with multiple stress tolerance in rice. Through genome-wide analysis of eleven rice genomes, we identified a total of 36 genes encoding CDCPs in O. longistaminata, 38 in O. glaberrima, 39 each in O. rufipogon, O. glumaepatula, O. brachyantha, O. punctata, and O. sativa subsp. japonica, 40 each in O. barthii and O. meridionalis, 41 in O. nivara, and 42 in O. sativa subsp. indica. Gene duplication analysis as well as non-synonymous and synonymous substitutions in the duplicated gene pairs indicated that this family is shaped majorly by the negative or purifying selection pressure through the long-term evolution process. We identified the presence of two additional hetero-domains, namely TerCH and CoatomerE (specifically in O. sativa subsp. indica), which were not reported previously in plant CDCPs. The in silico expression analysis revealed some of the members to be responsive to various abiotic stresses. Furthermore, the qRT-PCR based analysis identified some members to be highly inducive specifically in salt-tolerant genotype in response to salinity. The cis-regulatory element analysis predicted the presence of numerous stress as well as a few phytohormone-responsive elements in their promoter region. The data presented in this study would be helpful in the characterization of these CDCPs from rice, particularly in relation to abiotic stress tolerance.
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Affiliation(s)
- Surabhi Tomar
- Plant Stress Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India; (S.T.); (A.S.)
| | - Ashish Subba
- Plant Stress Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India; (S.T.); (A.S.)
| | - Meenu Bala
- School of Genetic Engineering, ICAR-Indian Institute of Agricultural Biotechnology, Ranchi 834010, India; (M.B.); (A.K.S.)
| | - Anil Kumar Singh
- School of Genetic Engineering, ICAR-Indian Institute of Agricultural Biotechnology, Ranchi 834010, India; (M.B.); (A.K.S.)
- ICAR-National Institute for Plant Biotechnology, LBS Centre, Pusa Campus, New Delhi 110012, India
| | - Ashwani Pareek
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India;
- National Agri-Food Biotechnology Institute, Mohali 140306, India
| | - Sneh Lata Singla-Pareek
- Plant Stress Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India; (S.T.); (A.S.)
- Correspondence:
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15
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Dai SF, Zhu XG, Hutang GR, Li JY, Tian JQ, Jiang XH, Zhang D, Gao LZ. Genome Size Variation and Evolution Driven by Transposable Elements in the Genus Oryza. FRONTIERS IN PLANT SCIENCE 2022; 13:921937. [PMID: 35874017 PMCID: PMC9301470 DOI: 10.3389/fpls.2022.921937] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 05/16/2022] [Indexed: 05/08/2023]
Abstract
Genome size variation and evolutionary forces behind have been long pursued in flowering plants. The genus Oryza, consisting of approximately 25 wild species and two cultivated rice, harbors eleven extant genome types, six of which are diploid (AA, BB, CC, EE, FF, and GG) and five of which are tetraploid (BBCC, CCDD, HHJJ, HHKK, and KKLL). To obtain the most comprehensive knowledge of genome size variation in the genus Oryza, we performed flow cytometry experiments and estimated genome sizes of 166 accessions belonging to 16 non-AA genome Oryza species. k-mer analyses were followed to verify the experimental results of the two accessions for each species. Our results showed that genome sizes largely varied fourfold in the genus Oryza, ranging from 279 Mb in Oryza brachyantha (FF) to 1,203 Mb in Oryza ridleyi (HHJJ). There was a 2-fold variation (ranging from 570 to 1,203 Mb) in genome size among the tetraploid species, while the diploid species had 3-fold variation, ranging from 279 Mb in Oryza brachyantha (FF) to 905 Mb in Oryza australiensis (EE). The genome sizes of the tetraploid species were not always two times larger than those of the diploid species, and some diploid species even had larger genome sizes than those of tetraploids. Nevertheless, we found that genome sizes of newly formed allotetraploids (BBCC-) were almost equal to totaling genome sizes of their parental progenitors. Our results showed that the species belonging to the same genome types had similar genome sizes, while genome sizes exhibited a gradually decreased trend during the evolutionary process in the clade with AA, BB, CC, and EE genome types. Comparative genomic analyses further showed that the species with different rice genome types may had experienced dissimilar amplification histories of retrotransposons, resulting in remarkably different genome sizes. On the other hand, the closely related rice species may have experienced similar amplification history. We observed that the contents of transposable elements, long terminal repeats (LTR) retrotransposons, and particularly LTR/Gypsy retrotransposons varied largely but were significantly correlated with genome sizes. Therefore, this study demonstrated that LTR retrotransposons act as an active driver of genome size variation in the genus Oryza.
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Affiliation(s)
- Shuang-feng Dai
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou, China
| | - Xun-ge Zhu
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Ge-rang Hutang
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Jia-yue Li
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou, China
| | - Jia-qi Tian
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou, China
| | - Xian-hui Jiang
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou, China
| | - Dan Zhang
- College of Tropical Crops, Hainan University, Haikou, China
| | - Li-zhi Gao
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou, China
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- College of Tropical Crops, Hainan University, Haikou, China
- *Correspondence: Li-zhi Gao,
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Ren G, Jiang Y, Li A, Yin M, Li M, Mu W, Wu Y, Liu J. The genome sequence provides insights into salt tolerance of Achnatherum splendens (Gramineae), a constructive species of alkaline grassland. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:116-128. [PMID: 34487631 PMCID: PMC8710827 DOI: 10.1111/pbi.13699] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 08/18/2021] [Accepted: 09/01/2021] [Indexed: 05/02/2023]
Abstract
Achnatherum splendens Trin. (Gramineae) is a constructive species of the arid grassland ecosystem in Northwest China and is a major forage grass. It has good tolerance of salt and drought stress in alkaline habitats. Here, we report its chromosome-level genome, determined through a combination of Illumina HiSeq sequencing, PacBio sequencing and Hi-C technology. The final assembly of the ~1.17 Gb genome sequence had a super-scaffold N50 of 40.3 Mb. A total of 57 374 protein-coding genes were annotated, of which 54 426 (94.5%) genes have functional protein annotations. Approximately 735 Mb (62.37%) of the assembly were identified as repetitive elements, and among these, LTRs (40.53%) constitute the highest proportion, having made a major contribution to the expansion of genome size in A. splendens. Phylogenetic analysis revealed that A. splendens diverged from the Brachypodium distachyon-Hordeum vulgare-Aegilops tauschii subclade around 37 million years ago (Ma) and that a clade comprising these four species diverged from the Phyllostachys edulis clade ~47 Ma. Genomic synteny indicates that A. splendens underwent an additional species-specific whole-genome duplication (WGD) 18-20 Ma, which further promoted an increase in copies of numerous saline-alkali-related gene families in the A. splendens genome. By transcriptomic analysis, we further found that many of these duplicated genes from this extra WGD exhibited distinct functional divergence in response to salt stress. This WGD, therefore, contributed to the strong resistance to salt stress and widespread arid adaptation of A. splendens.
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Affiliation(s)
- Guangpeng Ren
- State Key Laboratory of Grassland Agro‐EcosystemsInstitute of Innovation Ecology & School of Life SciencesLanzhou UniversityLanzhouChina
| | - Yanyou Jiang
- State Key Laboratory of Grassland Agro‐EcosystemsInstitute of Innovation Ecology & School of Life SciencesLanzhou UniversityLanzhouChina
| | - Ao Li
- State Key Laboratory of Grassland Agro‐EcosystemsInstitute of Innovation Ecology & School of Life SciencesLanzhou UniversityLanzhouChina
| | - Mou Yin
- State Key Laboratory of Grassland Agro‐EcosystemsInstitute of Innovation Ecology & School of Life SciencesLanzhou UniversityLanzhouChina
| | - Minjie Li
- State Key Laboratory of Grassland Agro‐EcosystemsInstitute of Innovation Ecology & School of Life SciencesLanzhou UniversityLanzhouChina
| | - Wenjie Mu
- State Key Laboratory of Grassland Agro‐EcosystemsInstitute of Innovation Ecology & School of Life SciencesLanzhou UniversityLanzhouChina
| | - Ying Wu
- State Key Laboratory of Grassland Agro‐EcosystemsInstitute of Innovation Ecology & School of Life SciencesLanzhou UniversityLanzhouChina
| | - Jianquan Liu
- State Key Laboratory of Grassland Agro‐EcosystemsInstitute of Innovation Ecology & School of Life SciencesLanzhou UniversityLanzhouChina
- Key Laboratory of Bio‐Resources and Eco‐Environment of the Ministry of Education & State Key Lab of Hydraulics & Mountain River EngineeringCollege of Life SciencesSichuan UniversityChengduChina
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Yuan G, Liu J, An G, Li W, Si W, Sun D, Zhu Y. Genome-Wide Identification and Characterization of the Trehalose-6-phosphate Synthetase (TPS) Gene Family in Watermelon ( Citrullus lanatus) and Their Transcriptional Responses to Salt Stress. Int J Mol Sci 2021; 23:276. [PMID: 35008702 PMCID: PMC8745194 DOI: 10.3390/ijms23010276] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/24/2021] [Accepted: 12/25/2021] [Indexed: 12/27/2022] Open
Abstract
With the increase in watermelon cultivation area, there is an urgent need to explore enzymatic and genetic resources for the sustainable development of watermelon, especially under salt stress. Among the various compounds known, trehalose plays an important role in regulating abiotic stress tolerances in diverse organisms, including plants. Therefore, the present study comprehensively analyzed the trehalose-6-phosphate synthase (TPS) gene family in watermelon. The study analyzed the functional classification, evolutionary characteristics, and expression patterns of the watermelon TPS genes family. Seven ClTPSs were identified and classified into two distinct classes according to gene structure and phylogeny. Evolutionary analysis suggested the role of purifying selection in the evolution of the TPS family members. Further, cis-acting elements related to plant hormones and abiotic stress were identified in the promoter region of the TPS genes. The tissue-specific expression analysis showed that ClTPS genes were widely expressed in roots, stems, leaves, flowers, and fruits, while ClTPS3 was significantly induced under salt stress. The overexpression of ClTPS3 in Arabidopsis thaliana significantly improved salt tolerance. Finally, the STRING functional protein association networks suggested that the transcription factor ClMYB and ClbHLH regulate ClTPS3. Thus, the study indicates the critical role of ClTPS3 in watermelon response to salt stress.
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Affiliation(s)
| | | | | | | | | | - Dexi Sun
- Zhengzhou Fruit Research Institute of the Chinese Academy of Agricultural Sciences, Zhengzhou 450000, China; (G.Y.); (J.L.); (G.A.); (W.L.); (W.S.)
| | - Yingchun Zhu
- Zhengzhou Fruit Research Institute of the Chinese Academy of Agricultural Sciences, Zhengzhou 450000, China; (G.Y.); (J.L.); (G.A.); (W.L.); (W.S.)
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Shen S, Li Y, Wang J, Wei C, Wang Z, Ge W, Yuan M, Zhang L, Wang L, Sun S, Teng J, Xiao Q, Bao S, Feng Y, Zhang Y, Wang J, Hao Y, Lei T, Wang J. Illegitimate Recombination between Duplicated Genes Generated from Recursive Polyploidizations Accelerated the Divergence of the Genus Arachis. Genes (Basel) 2021; 12:genes12121944. [PMID: 34946893 PMCID: PMC8701993 DOI: 10.3390/genes12121944] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 11/29/2021] [Accepted: 11/30/2021] [Indexed: 01/11/2023] Open
Abstract
The peanut (Arachis hypogaea L.) is the leading oil and food crop among the legume family. Extensive duplicate gene pairs generated from recursive polyploidizations with high sequence similarity could result from gene conversion, caused by illegitimate DNA recombination. Here, through synteny-based comparisons of two diploid and three tetraploid peanut genomes, we identified the duplicated genes generated from legume common tetraploidy (LCT) and peanut recent allo-tetraploidy (PRT) within genomes. In each peanut genome (or subgenomes), we inferred that 6.8–13.1% of LCT-related and 11.3–16.5% of PRT-related duplicates were affected by gene conversion, in which the LCT-related duplicates were the most affected by partial gene conversion, whereas the PRT-related duplicates were the most affected by whole gene conversion. Notably, we observed the conversion between duplicates as the long-lasting contribution of polyploidizations accelerated the divergence of different Arachis genomes. Moreover, we found that the converted duplicates are unevenly distributed across the chromosomes and are more often near the ends of the chromosomes in each genome. We also confirmed that well-preserved homoeologous chromosome regions may facilitate duplicates’ conversion. In addition, we found that these biological functions contain a higher number of preferentially converted genes, such as catalytic activity-related genes. We identified specific domains that are involved in converted genes, implying that conversions are associated with important traits of peanut growth and development.
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Affiliation(s)
- Shaoqi Shen
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan 063000, China; (S.S.); (Y.L.); (J.W.); (C.W.); (Z.W.); (W.G.); (M.Y.); (L.Z.); (L.W.); (S.S.); (J.T.); (Q.X.); (S.B.); (Y.F.); (Y.Z.); (J.W.); (Y.H.)
| | - Yuxian Li
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan 063000, China; (S.S.); (Y.L.); (J.W.); (C.W.); (Z.W.); (W.G.); (M.Y.); (L.Z.); (L.W.); (S.S.); (J.T.); (Q.X.); (S.B.); (Y.F.); (Y.Z.); (J.W.); (Y.H.)
| | - Jianyu Wang
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan 063000, China; (S.S.); (Y.L.); (J.W.); (C.W.); (Z.W.); (W.G.); (M.Y.); (L.Z.); (L.W.); (S.S.); (J.T.); (Q.X.); (S.B.); (Y.F.); (Y.Z.); (J.W.); (Y.H.)
| | - Chendan Wei
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan 063000, China; (S.S.); (Y.L.); (J.W.); (C.W.); (Z.W.); (W.G.); (M.Y.); (L.Z.); (L.W.); (S.S.); (J.T.); (Q.X.); (S.B.); (Y.F.); (Y.Z.); (J.W.); (Y.H.)
| | - Zhenyi Wang
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan 063000, China; (S.S.); (Y.L.); (J.W.); (C.W.); (Z.W.); (W.G.); (M.Y.); (L.Z.); (L.W.); (S.S.); (J.T.); (Q.X.); (S.B.); (Y.F.); (Y.Z.); (J.W.); (Y.H.)
| | - Weina Ge
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan 063000, China; (S.S.); (Y.L.); (J.W.); (C.W.); (Z.W.); (W.G.); (M.Y.); (L.Z.); (L.W.); (S.S.); (J.T.); (Q.X.); (S.B.); (Y.F.); (Y.Z.); (J.W.); (Y.H.)
| | - Min Yuan
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan 063000, China; (S.S.); (Y.L.); (J.W.); (C.W.); (Z.W.); (W.G.); (M.Y.); (L.Z.); (L.W.); (S.S.); (J.T.); (Q.X.); (S.B.); (Y.F.); (Y.Z.); (J.W.); (Y.H.)
| | - Lan Zhang
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan 063000, China; (S.S.); (Y.L.); (J.W.); (C.W.); (Z.W.); (W.G.); (M.Y.); (L.Z.); (L.W.); (S.S.); (J.T.); (Q.X.); (S.B.); (Y.F.); (Y.Z.); (J.W.); (Y.H.)
| | - Li Wang
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan 063000, China; (S.S.); (Y.L.); (J.W.); (C.W.); (Z.W.); (W.G.); (M.Y.); (L.Z.); (L.W.); (S.S.); (J.T.); (Q.X.); (S.B.); (Y.F.); (Y.Z.); (J.W.); (Y.H.)
| | - Sangrong Sun
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan 063000, China; (S.S.); (Y.L.); (J.W.); (C.W.); (Z.W.); (W.G.); (M.Y.); (L.Z.); (L.W.); (S.S.); (J.T.); (Q.X.); (S.B.); (Y.F.); (Y.Z.); (J.W.); (Y.H.)
| | - Jia Teng
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan 063000, China; (S.S.); (Y.L.); (J.W.); (C.W.); (Z.W.); (W.G.); (M.Y.); (L.Z.); (L.W.); (S.S.); (J.T.); (Q.X.); (S.B.); (Y.F.); (Y.Z.); (J.W.); (Y.H.)
| | - Qimeng Xiao
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan 063000, China; (S.S.); (Y.L.); (J.W.); (C.W.); (Z.W.); (W.G.); (M.Y.); (L.Z.); (L.W.); (S.S.); (J.T.); (Q.X.); (S.B.); (Y.F.); (Y.Z.); (J.W.); (Y.H.)
| | - Shoutong Bao
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan 063000, China; (S.S.); (Y.L.); (J.W.); (C.W.); (Z.W.); (W.G.); (M.Y.); (L.Z.); (L.W.); (S.S.); (J.T.); (Q.X.); (S.B.); (Y.F.); (Y.Z.); (J.W.); (Y.H.)
| | - Yishan Feng
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan 063000, China; (S.S.); (Y.L.); (J.W.); (C.W.); (Z.W.); (W.G.); (M.Y.); (L.Z.); (L.W.); (S.S.); (J.T.); (Q.X.); (S.B.); (Y.F.); (Y.Z.); (J.W.); (Y.H.)
| | - Yan Zhang
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan 063000, China; (S.S.); (Y.L.); (J.W.); (C.W.); (Z.W.); (W.G.); (M.Y.); (L.Z.); (L.W.); (S.S.); (J.T.); (Q.X.); (S.B.); (Y.F.); (Y.Z.); (J.W.); (Y.H.)
| | - Jiaqi Wang
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan 063000, China; (S.S.); (Y.L.); (J.W.); (C.W.); (Z.W.); (W.G.); (M.Y.); (L.Z.); (L.W.); (S.S.); (J.T.); (Q.X.); (S.B.); (Y.F.); (Y.Z.); (J.W.); (Y.H.)
| | - Yanan Hao
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan 063000, China; (S.S.); (Y.L.); (J.W.); (C.W.); (Z.W.); (W.G.); (M.Y.); (L.Z.); (L.W.); (S.S.); (J.T.); (Q.X.); (S.B.); (Y.F.); (Y.Z.); (J.W.); (Y.H.)
| | - Tianyu Lei
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan 063000, China; (S.S.); (Y.L.); (J.W.); (C.W.); (Z.W.); (W.G.); (M.Y.); (L.Z.); (L.W.); (S.S.); (J.T.); (Q.X.); (S.B.); (Y.F.); (Y.Z.); (J.W.); (Y.H.)
- Correspondence: (T.L.); (J.W.)
| | - Jinpeng Wang
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan 063000, China; (S.S.); (Y.L.); (J.W.); (C.W.); (Z.W.); (W.G.); (M.Y.); (L.Z.); (L.W.); (S.S.); (J.T.); (Q.X.); (S.B.); (Y.F.); (Y.Z.); (J.W.); (Y.H.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- Correspondence: (T.L.); (J.W.)
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Seetharam AS, Yu Y, Bélanger S, Clark LG, Meyers BC, Kellogg EA, Hufford MB. The Streptochaeta Genome and the Evolution of the Grasses. FRONTIERS IN PLANT SCIENCE 2021; 12:710383. [PMID: 34671369 PMCID: PMC8521107 DOI: 10.3389/fpls.2021.710383] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 09/08/2021] [Indexed: 05/15/2023]
Abstract
In this work, we sequenced and annotated the genome of Streptochaeta angustifolia, one of two genera in the grass subfamily Anomochlooideae, a lineage sister to all other grasses. The final assembly size is over 99% of the estimated genome size. We find good collinearity with the rice genome and have captured most of the gene space. Streptochaeta is similar to other grasses in the structure of its fruit (a caryopsis or grain) but has peculiar flowers and inflorescences that are distinct from those in the outgroups and in other grasses. To provide tools for investigations of floral structure, we analyzed two large families of transcription factors, AP2-like and R2R3 MYBs, that are known to control floral and spikelet development in rice and maize among other grasses. Many of these are also regulated by small RNAs. Structure of the gene trees showed that the well documented whole genome duplication at the origin of the grasses (ρ) occurred before the divergence of the Anomochlooideae lineage from the lineage leading to the rest of the grasses (the spikelet clade) and thus that the common ancestor of all grasses probably had two copies of the developmental genes. However, Streptochaeta (and by inference other members of Anomochlooideae) has lost one copy of many genes. The peculiar floral morphology of Streptochaeta may thus have derived from an ancestral plant that was morphologically similar to the spikelet-bearing grasses. We further identify 114 loci producing microRNAs and 89 loci generating phased, secondary siRNAs, classes of small RNAs known to be influential in transcriptional and post-transcriptional regulation of several plant functions.
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Affiliation(s)
- Arun S. Seetharam
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, United States
| | - Yunqing Yu
- Donald Danforth Plant Science Center, St. Louis, MO, United States
| | | | - Lynn G. Clark
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, United States
| | - Blake C. Meyers
- Donald Danforth Plant Science Center, St. Louis, MO, United States
- Division of Plant Sciences, University of Missouri, Columbia, MO, United States
| | | | - Matthew B. Hufford
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, United States
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Hu W, Ren Q, Chen Y, Xu G, Qian Y. Genome-wide identification and analysis of WRKY gene family in maize provide insights into regulatory network in response to abiotic stresses. BMC PLANT BIOLOGY 2021; 21:427. [PMID: 34544366 PMCID: PMC8451115 DOI: 10.1186/s12870-021-03206-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 09/02/2021] [Indexed: 05/23/2023]
Abstract
BACKGROUND The WRKY transcription factor family plays significant roles in biotic and abiotic stress responses, which has been associated with various biological processes in higher plants. However, very little is known regarding the structure and function of WRKY genes in maize. RESULTS In this study, a total of 140 ZmWRKY proteins encoded by 125 ZmWRKY genes were eventually identified in maize. On the basis of features of molecular structure and a comparison of phylogenetic relationships of WRKY transcription factor families from Arabidopsis, rice and maize, all 140 ZmWRKY proteins in maize were divided into three main groups (Groups I, II and III) and the Group II was further classified into five subgroups. The characteristics of exon-intron structure of these putative ZmWRKY genes and conserved protein motifs of their encoded ZmWRKY proteins were also presented respectively, which was in accordance with the group classification results. Promoter analysis suggested that ZmWRKY genes shared many abiotic stress-related elements and hormone-related elements. Gene duplication analysis revealed that the segmental duplication and purifying selection might play a significant role during the evolution of the WRKY gene family in maize. Using RNA-seq data, transcriptome analysis indicated that most of ZmWRKY genes displayed differential expression patterns at different developmental stages of maize. Further, by quantitative real-time PCR analysis, twenty-one ZmWRKY genes were confirmed to respond to two different abiotic stress treatments, suggesting their potential roles in various abiotic stress responses. In addition, RNA-seq dataset was used to conduct weighted gene co-expression network analysis (WGCNA) in order to recognize gene subsets possessing similar expression patterns and highly correlated with each other within different metabolic networks. Further, subcellular localization prediction, functional annotation and interaction analysis of ZmWRKY proteins were also performed to predict their interactions and associations involved in potential regulatory network. CONCLUSIONS Taken together, the present study will serve to present an important theoretical basis for further exploring function and regulatory mechanism of ZmWRKY genes in the growth, development, and adaptation to abiotic stresses in maize.
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Affiliation(s)
- Wenjing Hu
- Anhui Provincial Key Lab. of the Conservation and Exploitation of Biological Resources, Anhui Normal University, Wuhu, 241000 China
| | - Qiaoyu Ren
- Anhui Provincial Key Lab. of the Conservation and Exploitation of Biological Resources, Anhui Normal University, Wuhu, 241000 China
| | - Yali Chen
- Anhui Provincial Key Lab. of the Conservation and Exploitation of Biological Resources, Anhui Normal University, Wuhu, 241000 China
| | - Guoliang Xu
- Anhui Provincial Key Lab. of the Conservation and Exploitation of Biological Resources, Anhui Normal University, Wuhu, 241000 China
| | - Yexiong Qian
- Anhui Provincial Key Lab. of the Conservation and Exploitation of Biological Resources, Anhui Normal University, Wuhu, 241000 China
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Mahtha SK, Purama RK, Yadav G. StAR-Related Lipid Transfer (START) Domains Across the Rice Pangenome Reveal How Ontogeny Recapitulated Selection Pressures During Rice Domestication. Front Genet 2021; 12:737194. [PMID: 34567086 PMCID: PMC8455945 DOI: 10.3389/fgene.2021.737194] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 08/16/2021] [Indexed: 02/04/2023] Open
Abstract
The StAR-related lipid transfer (START) domain containing proteins or START proteins, encoded by a plant amplified family of evolutionary conserved genes, play important roles in lipid binding, transport, signaling, and modulation of transcriptional activity in the plant kingdom, but there is limited information on their evolution, duplication, and associated sub- or neo-functionalization. Here we perform a comprehensive investigation of this family across the rice pangenome, using 10 wild and cultivated varieties. Conservation of START domains across all 10 rice genomes suggests low dispensability and critical functional roles for this family, further supported by chromosomal mapping, duplication and domain structure patterns. Analysis of synteny highlights a preponderance of segmental and dispersed duplication among STARTs, while transcriptomic investigation of the main cultivated variety Oryza sativa var. japonica reveals sub-functionalization amongst genes family members in terms of preferential expression across various developmental stages and anatomical parts, such as flowering. Ka/Ks ratios confirmed strong negative/purifying selection on START family evolution, implying that ontogeny recapitulated selection pressures during rice domestication. Our findings provide evidence for high conservation of START genes across rice varieties in numbers, as well as in their stringent regulation of Ka/Ks ratio, and showed strong functional dependency of plants on START proteins for their growth and reproductive development. We believe that our findings advance the limited knowledge about plant START domain diversity and evolution, and pave the way for more detailed assessment of individual structural classes of START proteins among plants and their domain specific substrate preferences, to complement existing studies in animals and yeast.
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Affiliation(s)
- Sanjeet Kumar Mahtha
- Computational Biology Laboratory, National Institute of Plant Genome Research, New Delhi, India
| | - Ravi Kiran Purama
- Computational Biology Laboratory, National Institute of Plant Genome Research, New Delhi, India
| | - Gitanjali Yadav
- Computational Biology Laboratory, National Institute of Plant Genome Research, New Delhi, India
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
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Wang Y, Chen F, Ma Y, Zhang T, Sun P, Lan M, Li F, Fang W. An ancient whole-genome duplication event and its contribution to flavor compounds in the tea plant (Camellia sinensis). HORTICULTURE RESEARCH 2021; 8:176. [PMID: 34333548 PMCID: PMC8325681 DOI: 10.1038/s41438-021-00613-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 05/12/2021] [Accepted: 05/20/2021] [Indexed: 05/14/2023]
Abstract
Tea, coffee, and cocoa are the three most popular nonalcoholic beverages in the world and have extremely high economic and cultural value. The genomes of four tea plant varieties have recently been sequenced, but there is some debate regarding the characterization of a whole-genome duplication (WGD) event in tea plants. Whether the WGD in the tea plant is shared with other plants in order Ericales and how it contributed to tea plant evolution remained unanswered. Here we re-analyzed the tea plant genome and provided evidence that tea experienced only WGD event after the core-eudicot whole-genome triplication (WGT) event. This WGD was shared by the Polemonioids-Primuloids-Core Ericales (PPC) sections, encompassing at least 17 families in the order Ericales. In addition, our study identified eight pairs of duplicated genes in the catechins biosynthesis pathway, four pairs of duplicated genes in the theanine biosynthesis pathway, and one pair of genes in the caffeine biosynthesis pathway, which were expanded and retained following this WGD. Nearly all these gene pairs were expressed in tea plants, implying the contribution of the WGD. This study shows that in addition to the role of the recent tandem gene duplication in the accumulation of tea flavor-related genes, the WGD may have been another main factor driving the evolution of tea flavor.
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Affiliation(s)
- Ya Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Fei Chen
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Yuanchun Ma
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Taikui Zhang
- College of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Pengchuan Sun
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Meifang Lan
- College of Life Sciences, North China University of Science and Technology, Tangshan, 063099, China
| | - Fang Li
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wanping Fang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
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23
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Cacho NI, McIntyre PJ, Kliebenstein DJ, Strauss SY. Genome size evolution is associated with climate seasonality and glucosinolates, but not life history, soil nutrients or range size, across a clade of mustards. ANNALS OF BOTANY 2021; 127:887-902. [PMID: 33675229 PMCID: PMC8225284 DOI: 10.1093/aob/mcab028] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 02/21/2021] [Indexed: 05/02/2023]
Abstract
BACKGROUND AND AIMS We investigate patterns of evolution of genome size across a morphologically and ecologically diverse clade of Brassicaceae, in relation to ecological and life history traits. While numerous hypotheses have been put forward regarding autecological and environmental factors that could favour small vs. large genomes, a challenge in understanding genome size evolution in plants is that many hypothesized selective agents are intercorrelated. METHODS We contribute genome size estimates for 47 species of Streptanthus Nutt. and close relatives, and take advantage of many data collections for this group to assemble data on climate, life history, soil affinity and composition, geographic range and plant secondary chemistry to identify simultaneous correlates of variation in genome size in an evolutionary framework. We assess models of evolution across clades and use phylogenetically informed analyses as well as model selection and information criteria approaches to identify variables that can best explain genome size variation in this clade. KEY RESULTS We find differences in genome size and heterogeneity in its rate of evolution across subclades of Streptanthus and close relatives. We show that clade-wide genome size is positively associated with climate seasonality and glucosinolate compounds. Model selection and information criteria approaches identify a best model that includes temperature seasonality and fraction of aliphatic glucosinolates, suggesting a possible role for genome size in climatic adaptation or a role for biotic interactions in shaping the evolution of genome size. We find no evidence supporting hypotheses of life history, range size or soil nutrients as forces shaping genome size in this system. CONCLUSIONS Our findings suggest climate seasonality and biotic interactions as potential forces shaping the evolution of genome size and highlight the importance of evaluating multiple factors in the context of phylogeny to understand the effect of possible selective agents on genome size.
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Affiliation(s)
- N Ivalú Cacho
- Instituto de Biología, Universidad Nacional Autónoma de México. Circuito Exterior, Ciudad Universitaria, Mexico City, Mexico
- Center for Population Biology, University of California, One Shields Avenue, Davis, CA, USA
- Department of Evolution of Ecology, University of California, One Shields Avenue, Davis, CA, USA
| | - Patrick J McIntyre
- Center for Population Biology, University of California, One Shields Avenue, Davis, CA, USA
- NatureServe, Boulder, CO, USA
| | - Daniel J Kliebenstein
- Department of Plant Sciences, University of California, One Shields Avenue, Davis, CA, USA
- DynaMo Centre of Excellence, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, Denmark
| | - Sharon Y Strauss
- Center for Population Biology, University of California, One Shields Avenue, Davis, CA, USA
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24
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Wei C, Wang Z, Wang J, Teng J, Shen S, Xiao Q, Bao S, Feng Y, Zhang Y, Li Y, Sun S, Yue Y, Wu C, Wang Y, Zhou T, Xu W, Yu J, Wang L, Wang J. Conversion between 100-million-year-old duplicated genes contributes to rice subspecies divergence. BMC Genomics 2021; 22:460. [PMID: 34147070 PMCID: PMC8214281 DOI: 10.1186/s12864-021-07776-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 06/03/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Duplicated gene pairs produced by ancient polyploidy maintain high sequence similarity over a long period of time and may result from illegitimate recombination between homeologous chromosomes. The genomes of Asian cultivated rice Oryza sativa ssp. indica (XI) and Oryza sativa ssp. japonica (GJ) have recently been updated, providing new opportunities for investigating ongoing gene conversion events and their impact on genome evolution. RESULTS Using comparative genomics and phylogenetic analyses, we evaluated gene conversion rates between duplicated genes produced by polyploidization 100 million years ago (mya) in GJ and XI. At least 5.19-5.77% of genes duplicated across the three rice genomes were affected by whole-gene conversion after the divergence of GJ and XI at ~ 0.4 mya, with more (7.77-9.53%) showing conversion of only portions of genes. Independently converted duplicates surviving in the genomes of different subspecies often use the same donor genes. The ongoing gene conversion frequency was higher near chromosome termini, with a single pair of homoeologous chromosomes, 11 and 12, in each rice genome being most affected. Notably, ongoing gene conversion has maintained similarity between very ancient duplicates, provided opportunities for further gene conversion, and accelerated rice divergence. Chromosome rearrangements after polyploidization are associated with ongoing gene conversion events, and they directly restrict recombination and inhibit duplicated gene conversion between homeologous regions. Furthermore, we found that the converted genes tended to have more similar expression patterns than nonconverted duplicates. Gene conversion affects biological functions associated with multiple genes, such as catalytic activity, implying opportunities for interaction among members of large gene families, such as NBS-LRR disease-resistance genes, contributing to the occurrence of the gene conversion. CONCLUSION Duplicated genes in rice subspecies generated by grass polyploidization ~ 100 mya remain affected by gene conversion at high frequency, with important implications for the divergence of rice subspecies.
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Affiliation(s)
- Chendan Wei
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Zhenyi Wang
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Jianyu Wang
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Jia Teng
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Shaoqi Shen
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Qimeng Xiao
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Shoutong Bao
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Yishan Feng
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Yan Zhang
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Yuxian Li
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Sangrong Sun
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Yuanshuai Yue
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Chunyang Wu
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Yanli Wang
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Tianning Zhou
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Wenbo Xu
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Jigao Yu
- University of Chinese Academy of Sciences, Beijing, 100049, China.,State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Science, Beijing, 100093, China
| | - Li Wang
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China.
| | - Jinpeng Wang
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China. .,State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Science, Beijing, 100093, China.
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Madani H, Escrich A, Hosseini B, Sanchez-Muñoz R, Khojasteh A, Palazon J. Effect of Polyploidy Induction on Natural Metabolite Production in Medicinal Plants. Biomolecules 2021; 11:biom11060899. [PMID: 34204200 PMCID: PMC8234191 DOI: 10.3390/biom11060899] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 06/13/2021] [Accepted: 06/15/2021] [Indexed: 12/13/2022] Open
Abstract
Polyploidy plays an important role in plant diversification and speciation. The ploidy level of plants is associated with morphological and biochemical characteristics, and its modification has been used as a strategy to alter the quantitative and qualitative patterns of secondary metabolite production in different medicinal plants. Polyploidization can be induced by many anti-mitotic agents, among which colchicine, oryzalin, and trifluralin are the most common. Other variables involved in the induction process include the culture media, explant types, and exposure times. Due to the effects of polyploidization on plant growth and development, chromosome doubling has been applied in plant breeding to increase the levels of target compounds and improve morphological characteristics. Prompted by the importance of herbal medicines and the increasing demand for drugs based on plant secondary metabolites, this review presents an overview of how polyploidy can be used to enhance metabolite production in medicinal plants.
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Affiliation(s)
- Hadi Madani
- Department of Horticulture, Faculty of Agriculture, Urmia University, Urmia 5756151818, Iran; (H.M.); (B.H.)
| | - Ainoa Escrich
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, 08003 Barcelona, Spain;
| | - Bahman Hosseini
- Department of Horticulture, Faculty of Agriculture, Urmia University, Urmia 5756151818, Iran; (H.M.); (B.H.)
| | - Raul Sanchez-Muñoz
- Laboratory of Functional Plant Biology, Department of Biology, Ghent University, K.L. Ledeganckststraat 35, B-9000 Ghent, Belgium;
| | - Abbas Khojasteh
- Department of Plant Physiology, Faculty of Pharmacy, University of Barcelona, Av. Joan, XXIII, 08028 Barcelona, Spain;
| | - Javier Palazon
- Department of Plant Physiology, Faculty of Pharmacy, University of Barcelona, Av. Joan, XXIII, 08028 Barcelona, Spain;
- Correspondence:
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26
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Zhang L, Hou D, Li C, Li X, Fan J, Dong Y, Zhu J, Huang Z, Xu Z, Li L. Molecular characterization and function analysis of the rice OsDUF1664 family. BIOTECHNOL BIOTEC EQ 2021. [DOI: 10.1080/13102818.2020.1853606] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Affiliation(s)
- Lin Zhang
- Rice Institute of Sichuan Agricultural University, Chengdu, Sichuan, PR China
| | - Dejia Hou
- Department of Physics, College of Science, Huazhong Agricultural University, Wuhan, Hubei, PR China
| | - Chunliu Li
- Rice Institute of Sichuan Agricultural University, Chengdu, Sichuan, PR China
| | - Xiaohong Li
- Rice Institute of Sichuan Agricultural University, Chengdu, Sichuan, PR China
| | - Jiangbo Fan
- Rice Institute of Sichuan Agricultural University, Chengdu, Sichuan, PR China
| | - Yilun Dong
- Rice Institute of Sichuan Agricultural University, Chengdu, Sichuan, PR China
| | - Jianqing Zhu
- Rice Institute of Sichuan Agricultural University, Chengdu, Sichuan, PR China
| | - Zhengjian Huang
- Rice Institute of Sichuan Agricultural University, Chengdu, Sichuan, PR China
| | - Zhengjun Xu
- Rice Institute of Sichuan Agricultural University, Chengdu, Sichuan, PR China
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu, Sichuan, PR China
| | - Lihua Li
- Rice Institute of Sichuan Agricultural University, Chengdu, Sichuan, PR China
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu, Sichuan, PR China
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27
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Lai DL, Yan J, Fan Y, Li Y, Ruan JJ, Wang JZ, Fan Y, Cheng XB, Cheng JP. Genome-wide identification and phylogenetic relationships of the Hsp70 gene family of Aegilops tauschii, wild emmer wheat ( Triticum dicoccoides) and bread wheat ( Triticum aestivum). 3 Biotech 2021; 11:301. [PMID: 34194894 DOI: 10.1007/s13205-021-02639-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 01/03/2021] [Indexed: 12/22/2022] Open
Abstract
Heat shock protein 70 (Hsp70) plays an important role in plant development. It is closely related to the physiological process of cell development and the response to abiotic and biological stress. However, the classification and evolution of Hsp70 genes in bread wheat, wild emmer wheat and Aegilops tauschii are still unclear. Therefore, this study conducted a comprehensive bioinformatics analysis of Hsp70 gene in three species. Among these three species, 113, 79 and 36 Hsp70 genes were identified. They are divided into six subfamilies. Group vi-1 is different from Arabidopsis thaliana. It may be the result of early evolutionary segregation. The number of exons in different subfamilies (from 1 to 13) was different, but the distribution patterns of exons / introns in the same subfamily were similar. The results of Hsp70 promoter region analysis showed that the cis-regulatory elements of A. tauschii and wild emmer wheat were different from those of wheat. In addition, CpG island proportion of wild emmer Hsp70 was higher than that of wheat, which may be the molecular basis of heat resistance of wild wheat relative to cultivated wheat. Further comprehensive analysis of chromosome location and repeat events of Hsp70 gene showed that whole-genome duplication and tandem duplication events contributed to the evolution and expansion of Hsp70 gene in wheat. The results of non-synonymous substitution and synonymous substitution analysis showed that Hsp70 genes of three species had undergone purification selection. The expression profile analysis showed that Hsp70 gene was highly expressed in the roots during the vegetative growth period. In addition, TaHsp70 gene was highly expressed under various stress. The identification, classification and evolution of Hsp70 in wheat and its relatives provided a basis for further research on its evolution and its molecular mechanism in response to stress. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02639-5.
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Affiliation(s)
- Di-Li Lai
- College of Agriculture, Guizhou University, Guiyang, 550025 People's Republic of China
| | - Jun Yan
- School of Pharmacy and Bioengineering, Chengdu University, Chengdu, 610106 People's Republic of China
| | - Yu Fan
- College of Agriculture, Guizhou University, Guiyang, 550025 People's Republic of China
| | - Yao Li
- School of Public Health, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137 People's Republic of China
| | - Jing-Jun Ruan
- College of Agriculture, Guizhou University, Guiyang, 550025 People's Republic of China
| | - Jun-Zhen Wang
- Research Station of Alpine Crops, Xichang Institute of Agricultural Sciences, Liangshan, 616150 People's Republic of China
| | - Yue Fan
- College of Agriculture, Guizhou University, Guiyang, 550025 People's Republic of China
| | - Xiao-Bin Cheng
- Department of Environmental and Life Sciences, Sichuan MinZu College, Kangding, 626001 People's Republic of China
| | - Jian-Ping Cheng
- College of Agriculture, Guizhou University, Guiyang, 550025 People's Republic of China
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28
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Liu H, Shen J, Yuan C, Lu D, Acharya BR, Wang M, Chen D, Zhang W. The Cyclophilin ROC3 Regulates ABA-Induced Stomatal Closure and the Drought Stress Response of Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2021; 12:668792. [PMID: 34113366 PMCID: PMC8186832 DOI: 10.3389/fpls.2021.668792] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 04/28/2021] [Indexed: 05/28/2023]
Abstract
Drought causes a major constraint on plant growth, development, and crop productivity. Drought stress enhances the synthesis and mobilization of the phytohormone abscisic acid (ABA). Enhanced cellular levels of ABA promote the production of reactive oxygen species (ROS), which in turn induce anion channel activity in guard cells that consequently leads to stomatal closure. Although Cyclophilins (CYPs) are known to participate in the biotic stress response, their involvement in guard cell ABA signaling and the drought response remains to be established. The Arabidopsis thaliana gene ROC3 encodes a CYP. Arabidopsis roc3 T-DNA mutants showed a reduced level of ABA-activated S-type anion currents, and stomatal closure than wild type (WT). Also, roc3 mutants exhibited rapid loss of water in leaf than wild type. Two complementation lines of roc3 mutants showed similar stomatal response to ABA as observed for WT. Both complementation lines also showed similar water loss as WT by leaf detached assay. Biochemical assay suggested that ROC3 positively regulates ROS accumulation by inhibiting catalase activity. In response to ABA treatment or drought stress, roc3 mutant show down regulation of a number of stress responsive genes. All findings indicate that ROC3 positively regulates ABA-induced stomatal closure and the drought response by regulating ROS homeostasis and the expression of various stress-activated genes.
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Affiliation(s)
- Huiping Liu
- Key Laboratory of Plant Development and Environmental Adaption Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, China
| | - Jianlin Shen
- Key Laboratory of Plant Development and Environmental Adaption Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, China
| | - Chao Yuan
- Key Laboratory of Plant Development and Environmental Adaption Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, China
| | - Dongxue Lu
- Key Laboratory of Plant Development and Environmental Adaption Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, China
| | - Biswa R. Acharya
- College of Natural and Agricultural Sciences, University of California, Riverside, Riverside, CA, United States
| | - Mei Wang
- Key Laboratory of Plant Development and Environmental Adaption Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, China
| | - Donghua Chen
- Key Laboratory of Plant Development and Environmental Adaption Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, China
| | - Wei Zhang
- Key Laboratory of Plant Development and Environmental Adaption Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, China
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29
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Song X, Sun P, Yuan J, Gong K, Li N, Meng F, Zhang Z, Li X, Hu J, Wang J, Yang Q, Jiao B, Nie F, Liu T, Chen W, Feng S, Pei Q, Yu T, Kang X, Zhao W, Cui C, Yu Y, Wu T, Shan L, Liu M, Qin Z, Lin H, Varshney RK, Li X, Paterson AH, Wang X. The celery genome sequence reveals sequential paleo-polyploidizations, karyotype evolution and resistance gene reduction in apiales. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:731-744. [PMID: 33095976 PMCID: PMC8051603 DOI: 10.1111/pbi.13499] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 10/18/2020] [Indexed: 05/04/2023]
Abstract
Celery (Apium graveolens L. 2n = 2x = 22), a member of the Apiaceae family, is among the most important and globally grown vegetables. Here, we report a high-quality genome sequence assembly, anchored to 11 chromosomes, with total length of 3.33 Gb and N50 scaffold length of 289.78 Mb. Most (92.91%) of the genome is composed of repetitive sequences, with 62.12% of 31 326 annotated genes confined to the terminal 20% of chromosomes. Simultaneous bursts of shared long-terminal repeats (LTRs) in different Apiaceae plants suggest inter-specific exchanges. Two ancestral polyploidizations were inferred, one shared by Apiales taxa and the other confined to Apiaceae. We reconstructed 8 Apiales proto-chromosomes, inferring their evolutionary trajectories from the eudicot common ancestor to extant plants. Transcriptome sequencing in three tissues (roots, leaves and petioles), and varieties with different-coloured petioles, revealed 4 and 2 key genes in pathways regulating anthocyanin and coumarin biosynthesis, respectively. A remarkable paucity of NBS disease-resistant genes in celery (62) and other Apiales was explained by extensive loss and limited production of these genes during the last ~10 million years, raising questions about their biotic defence mechanisms and motivating research into effects of chemicals, for example coumarins, that give off distinctive odours. Celery genome sequencing and annotation facilitates further research into important gene functions and breeding, and comparative genomic analyses in Apiales.
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30
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Molecular evolution and expression analysis of ADP-ribosylation factors (ARFs) from longan embryogenic callus. Gene 2021; 777:145461. [PMID: 33515723 DOI: 10.1016/j.gene.2021.145461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 01/11/2021] [Accepted: 01/20/2021] [Indexed: 11/21/2022]
Abstract
ADP-ribosylation modification considered as a model to study histone post-translational modification in chromatin modification. Despite it was reported in many plants, the study of ARFs gene family in longan was still unclear. In this study, 14 longan ARFs genes were identified using the longan genome (the third-generation genome) and further divided into two major groups, including the DlARF in the I-II group and the ARF-like (DlARL) in the III-V group, according to their structure and evolutionary characteristics. Whole-genome duplication (WGD) and segmental duplication events played a major role in the expansion of the DlARFs gene family, the synteny and phylogenetic analyses provided a deeper insight into the evolutionary characteristics of the DlARFs. Protein-protein interactions suggested that some DlARFs proteins may interact to participate in biological processes. Promoter analysis showed more stress response elements in DlARF5, DlGB1, DlARL1, DlARL2, and DlARL8a, suggesting that they may participate in abiotic stress. Expression profiles of DlARFs by quantitative real-time PCR (qRT-PCR) showed that they were abundant accumulation during early somatic embryogenesis (SE). Expression pattern analysis of RNA-seq and qRT-PCR revealed that some ARFs members regulated early SE, and respond to exogenous hormones and abiotic stress such as abscisic acid (ABA), gibberellin A3 (GA3), salicylic acid (SA), methyl jasmonate (MeJA), cold, and heat. Our study provides new insights for further research on the potential function of DlARFs, which may be useful for the improvement of longan.
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Waseem M, Aslam MM, Shaheen I. The DUF221 domain-containing (DDP) genes identification and expression analysis in tomato under abiotic and phytohormone stress. GM CROPS & FOOD 2021; 12:586-599. [PMID: 34379048 PMCID: PMC8820248 DOI: 10.1080/21645698.2021.1962207] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The domain of unknown function (DUF221 domain-containing) proteins regulates various aspects of plant growth, development, responses to abiotic stresses, and hormone transduction pathways. To understand the role of DDP proteins in tomato, a comprehensive genome-wide analysis was performed in the tomato genome. A total of 12 DDP genes were identified and distributed in 8 chromosomes in the tomato genome. Phylogenetically all SlDDPs were clustered into four clades, subsequently supported by their gene structure and conserved motifs distribution. The SlDDPs contained various cis-acting elements involved in plant responses to abiotic and various phytohormones stresses. The tissue-specific expression profile analysis revealed the constitutive expression of SlDDPs in roots, leaves, and developmental phases of fruit. It was found that SlDDP1, SlDDP3, SlDDP4, SlDDP9, SlDDP10, and SlDDP12 exhibited high expression levels in fruits at different development stages. Of these genes, SlDDP12 contained ethylene (ERE) responsive elements in their promoter regions, suggesting its role in ethylene-dependent fruit ripening. It was found that a single SlDDP induced by two or more abiotic and phytohormone stresses. These include, SlDDP1, SlDDP2, SlDDP3, SlDDP4, SlDDP7, SlDDP8, and SlDDP10 was induced under salt, drought, ABA, and IAA stresses. Moreover, tomato SlDDPs were targeted by multiple miRNA gene families as well. In conclusion, this study predicted that the putative DDP genes might help improve abiotic and phytohormone tolerance in plants, particularly tomato, rice, and other economically important crop plant species.
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Affiliation(s)
- Muhammad Waseem
- College of Horticulture, South China Agricultural University, Guangzhou, China
| | | | - Iffat Shaheen
- Faculty of Agriculture Science and Technology, Bahauddin Zakariya University, Multan, Pakistan
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32
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Li C, Hou D, Zhang L, Li X, Fan J, Dong Y, Zhu J, Huang Z, Xu Z, Li L. Molecular characterization and function analysis of the rice OsDUF617 family. BIOTECHNOL BIOTEC EQ 2021. [DOI: 10.1080/13102818.2021.1934541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Affiliation(s)
- Chunliu Li
- Rice Institute of Sichuan Agricultural University, Chengdu, Sichuan, PR China
| | - Dejia Hou
- Department of Physics, College of Science, Huazhong Agricultural University, Wuhan, Hubei, PR China
| | - Lin Zhang
- Rice Institute of Sichuan Agricultural University, Chengdu, Sichuan, PR China
| | - Xiaohong Li
- Rice Institute of Sichuan Agricultural University, Chengdu, Sichuan, PR China
| | - Jiangbo Fan
- Rice Institute of Sichuan Agricultural University, Chengdu, Sichuan, PR China
| | - Yilun Dong
- Rice Institute of Sichuan Agricultural University, Chengdu, Sichuan, PR China
| | - Jianqing Zhu
- Rice Institute of Sichuan Agricultural University, Chengdu, Sichuan, PR China
| | - Zhengjian Huang
- Rice Institute of Sichuan Agricultural University, Chengdu, Sichuan, PR China
| | - Zhengjun Xu
- Rice Institute of Sichuan Agricultural University, Chengdu, Sichuan, PR China
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu, Sichuan, PR China
| | - Lihua Li
- Rice Institute of Sichuan Agricultural University, Chengdu, Sichuan, PR China
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu, Sichuan, PR China
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Jiang M, He Y, Chen X, Zhang X, Guo Y, Yang S, Huang J, Traw MB. CRISPR-based assessment of genomic structure in the conserved SQUAMOSA promoter-binding-like gene clusters in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:1301-1314. [PMID: 32996244 DOI: 10.1111/tpj.15001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/14/2020] [Accepted: 09/03/2020] [Indexed: 05/07/2023]
Abstract
Although SQUAMOSA promoter-binding-like (SPL) transcription factors are important regulators of development in rice (Oryza sativa), prior assessments of the SPL family have been limited to single genes. A functional comparison across the full gene family in standardized genetic backgrounds has not been reported previously. Here, we demonstrate that the SPL gene family in rice is enriched due to the most recent whole genome duplication (WGD). Notably, 10 of 19 rice SPL genes (52%) cluster in four units that have persisted for at least 50 million years. We show that SPL gene grouping and retention following WGD is widespread in angiosperms, suggesting the conservatism and importance of this gene arrangement. We used Cas9 editing to generate transformation lines for all 19 SPL genes in a common set of backgrounds, and found that knockouts of 14 SPL genes exhibited defects in plant height, 10 exhibited defects in panicle size, and nine had altered grain lengths. We observed subfunctionalization of genes in the paleoduplicated pairs, but little evidence of neofunctionalization. Expression of OsSPL3 was negatively correlated with that of its closest neighbor in its synteny group, OsSPL4, and its sister paired gene, OsSPL12, in the opposing group. Nucleotide diversity was lower in eight of the nine singleton genes in domesticated rice, relative to wild rice, whereas the reverse was true for the paired genes. Together, these results provide functional information on eight previously unexamined OsSPL family members and suggest that paleoduplicate pair redundancy benefits plant survival and innovation.
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Affiliation(s)
- Mengmeng Jiang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Ying He
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Xiaonan Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Xiaohui Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Yanru Guo
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Sihai Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Ju Huang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - M Brian Traw
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
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Wang J, Yu J, Sun P, Li C, Song X, Lei T, Li Y, Yuan J, Sun S, Ding H, Duan X, Shen S, Shen Y, Li J, Meng F, Xie Y, Wang J, Hou Y, Zhang J, Zhang X, Li XQ, Paterson AH, Wang X. Paleo-polyploidization in Lycophytes. GENOMICS, PROTEOMICS & BIOINFORMATICS 2020; 18:333-340. [PMID: 33157303 PMCID: PMC7801247 DOI: 10.1016/j.gpb.2020.10.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 01/13/2019] [Accepted: 04/17/2019] [Indexed: 11/26/2022]
Abstract
Lycophytes and seed plants constitute the typical vascular plants. Lycophytes have been thought to have no paleo-polyploidization although the event is known to be critical for the fast expansion of seed plants. Here, genomic analyses including the homologous gene dot plot analysis detected multiple paleo-polyploidization events, with one occurring approximately 13-15 million years ago (MYA) and another about 125-142 MYA, during the evolution of the genome of Selaginella moellendorffii, a model lycophyte. In addition, comparative analysis of reconstructed ancestral genomes of lycophytes and angiosperms suggested that lycophytes were affected by more paleo-polyploidization events than seed plants. Results from the present genomic analyses indicate that paleo-polyploidization has contributed to the successful establishment of both lineages-lycophytes and seed plants-of vascular plants.
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Affiliation(s)
- Jinpeng Wang
- Center for Computational Biology and Genomics, and School of Life Sciences, North China University of Science and Technology, Tangshan 063200, China; National Key Laboratory for North China Crop Improvement and Regulation, Agriculture University of Hebei, Baoding 071001, China; State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Science, Beijing 100093, China
| | - Jigao Yu
- Center for Computational Biology and Genomics, and School of Life Sciences, North China University of Science and Technology, Tangshan 063200, China; State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Science, Beijing 100093, China
| | - Pengchuan Sun
- Center for Computational Biology and Genomics, and School of Life Sciences, North China University of Science and Technology, Tangshan 063200, China
| | - Chao Li
- Center for Computational Biology and Genomics, and School of Life Sciences, North China University of Science and Technology, Tangshan 063200, China
| | - Xiaoming Song
- Center for Computational Biology and Genomics, and School of Life Sciences, North China University of Science and Technology, Tangshan 063200, China; National Key Laboratory for North China Crop Improvement and Regulation, Agriculture University of Hebei, Baoding 071001, China
| | - Tianyu Lei
- Center for Computational Biology and Genomics, and School of Life Sciences, North China University of Science and Technology, Tangshan 063200, China
| | - Yuxian Li
- Center for Computational Biology and Genomics, and School of Life Sciences, North China University of Science and Technology, Tangshan 063200, China
| | - Jiaqing Yuan
- Center for Computational Biology and Genomics, and School of Life Sciences, North China University of Science and Technology, Tangshan 063200, China
| | - Sangrong Sun
- Center for Computational Biology and Genomics, and School of Life Sciences, North China University of Science and Technology, Tangshan 063200, China
| | - Hongling Ding
- Center for Computational Biology and Genomics, and School of Life Sciences, North China University of Science and Technology, Tangshan 063200, China
| | - Xueqian Duan
- Center for Computational Biology and Genomics, and School of Life Sciences, North China University of Science and Technology, Tangshan 063200, China
| | - Shaoqi Shen
- Center for Computational Biology and Genomics, and School of Life Sciences, North China University of Science and Technology, Tangshan 063200, China
| | - Yanshuang Shen
- Center for Computational Biology and Genomics, and School of Life Sciences, North China University of Science and Technology, Tangshan 063200, China
| | - Jing Li
- Center for Computational Biology and Genomics, and School of Life Sciences, North China University of Science and Technology, Tangshan 063200, China
| | - Fanbo Meng
- Center for Computational Biology and Genomics, and School of Life Sciences, North China University of Science and Technology, Tangshan 063200, China
| | - Yangqin Xie
- Center for Computational Biology and Genomics, and School of Life Sciences, North China University of Science and Technology, Tangshan 063200, China
| | - Jianyu Wang
- Center for Computational Biology and Genomics, and School of Life Sciences, North China University of Science and Technology, Tangshan 063200, China
| | - Yue Hou
- Center for Computational Biology and Genomics, and School of Life Sciences, North China University of Science and Technology, Tangshan 063200, China
| | - Jin Zhang
- Center for Computational Biology and Genomics, and School of Life Sciences, North China University of Science and Technology, Tangshan 063200, China
| | - Xianchun Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Science, Beijing 100093, China
| | - Xiu-Qing Li
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, New Brunswick, E3B 4Z7, Canada
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Athens, Athens, GA 30602, USA; Department of Plant Biology, University of Georgia, Athens, GA 30602, USA; Department of Crop and Soil Science, University of Georgia, Athens, GA 30602, USA; Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Xiyin Wang
- Center for Computational Biology and Genomics, and School of Life Sciences, North China University of Science and Technology, Tangshan 063200, China; National Key Laboratory for North China Crop Improvement and Regulation, Agriculture University of Hebei, Baoding 071001, China.
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Song X, Wang J, Li N, Yu J, Meng F, Wei C, Liu C, Chen W, Nie F, Zhang Z, Gong K, Li X, Hu J, Yang Q, Li Y, Li C, Feng S, Guo H, Yuan J, Pei Q, Yu T, Kang X, Zhao W, Lei T, Sun P, Wang L, Ge W, Guo D, Duan X, Shen S, Cui C, Yu Y, Xie Y, Zhang J, Hou Y, Wang J, Wang J, Li X, Paterson AH, Wang X. Deciphering the high-quality genome sequence of coriander that causes controversial feelings. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:1444-1456. [PMID: 31799788 PMCID: PMC7206992 DOI: 10.1111/pbi.13310] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 11/03/2019] [Accepted: 11/17/2019] [Indexed: 05/11/2023]
Abstract
Coriander (Coriandrum sativum L. 2n = 2x = 22), a plant from the Apiaceae family, also called cilantro or Chinese parsley, is a globally important crop used as vegetable, spice, fragrance and traditional medicine. Here, we report a high-quality assembly and analysis of its genome sequence, anchored to 11 chromosomes, with total length of 2118.68 Mb and N50 scaffold length of 160.99 Mb. We found that two whole-genome duplication events, respectively, dated to ~45-52 and ~54-61 million years ago, were shared by the Apiaceae family after their split from lettuce. Unbalanced gene loss and expression are observed between duplicated copies produced by these two events. Gene retention, expression, metabolomics and comparative genomic analyses of terpene synthase (TPS) gene family, involved in terpenoid biosynthesis pathway contributing to coriander's special flavour, revealed that tandem duplication contributed to coriander TPS gene family expansion, especially compared to their carrot counterparts. Notably, a TPS gene highly expressed in all 4 tissues and 3 development stages studied is likely a major-effect gene encoding linalool synthase and myrcene synthase. The present genome sequencing, transcriptome, metabolome and comparative genomic efforts provide valuable insights into the genome evolution and spice trait biology of Apiaceae and other related plants, and facilitated further research into important gene functions and crop improvement.
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Yang X, Xia X, Zeng Y, Nong B, Zhang Z, Wu Y, Tian Q, Zeng W, Gao J, Zhou W, Liang H, Li D, Deng G. Genome-wide identification of the peptide transporter family in rice and analysis of the PTR expression modulation in two near-isogenic lines with different nitrogen use efficiency. BMC PLANT BIOLOGY 2020; 20:193. [PMID: 32375632 PMCID: PMC7203820 DOI: 10.1186/s12870-020-02419-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 04/29/2020] [Indexed: 05/18/2023]
Abstract
BACKGROUND Nitrogen (N) is a major nutrient element for crop growth. In plants, the members of the peptide transporter (PTR) gene family may involve in nitrate uptake and transport. Here, we identified PTR gene family in rice and analyzed their expression profile in near-isogenic lines. RESULTS We identified 96, 85 and 78 PTR genes in Nipponbare, R498 and Oryza glaberrima, and the phylogenetic trees were similar in Asian cultivated rice and African cultivated rice. The number of PTR genes was higher in peanut (125) and soybean (127). The 521 PTR genes in rice, maize, sorghum, peanut, soybean and Arabidopsis could be classified into 4 groups, and their distribution was different between monocots and dicots. In Nipponbare genome, the 25 PTR genes were distributed in 5 segmental duplication regions on chromosome 1, 2, 3, 4, 5, 7, 8, 9, and 10. The PTR genes in rice have 0-11 introns and 1-12 exons, and 16 of them have the NPF (NRT1/PTR family) domain. The results of RNA-seq showed that the number of differentially expressed genes (DEGs) between NIL15 and NIL19 at three stages were 928, 1467, and 1586, respectively. Under low N conditions, the number of differentially expressed PTR genes increased significantly. The RNA-seq data was analyzed using WGCNA to predict the potential interaction between genes. We classified the genes with similar expression pattern into one module, and obtained 25 target modules. Among these modules, three modules may be involved in rice N uptake and utilization, especially the brown module, in which hub genes were annotated as protein kinase that may regulate rice N metabolism. CONCLUSIONS In this study, we comprehensively analyzed the PTR gene family in rice. 96 PTR genes were identified in Nippobare genome and 25 of them were located on five large segmental duplication regions. The Ka/Ks ratio indicated that many PTR genes had undergone positive selection. The RNA-seq results showed that many PTR genes were involved in rice nitrogen use efficiency (NUE), and protein kinases might play an important role in this process. These results provide a fundamental basis to improve the rice NUE via molecular breeding.
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Affiliation(s)
- Xinghai Yang
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, 174 East Daxue Road, Nanning, 530007, Guangxi, China.
| | - Xiuzhong Xia
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, 174 East Daxue Road, Nanning, 530007, Guangxi, China
| | - Yu Zeng
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, 174 East Daxue Road, Nanning, 530007, Guangxi, China
| | - Baoxuan Nong
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, 174 East Daxue Road, Nanning, 530007, Guangxi, China
| | - Zongqiong Zhang
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, 174 East Daxue Road, Nanning, 530007, Guangxi, China
| | - Yanyan Wu
- Biotechnology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China
| | - Qinglan Tian
- Biotechnology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China
| | - Weiying Zeng
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China
| | - Ju Gao
- Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China
| | - Weiyong Zhou
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, 174 East Daxue Road, Nanning, 530007, Guangxi, China
| | - Haifu Liang
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, 174 East Daxue Road, Nanning, 530007, Guangxi, China
| | - Danting Li
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, 174 East Daxue Road, Nanning, 530007, Guangxi, China.
| | - Guofu Deng
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, 174 East Daxue Road, Nanning, 530007, Guangxi, China.
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Li H, Jiang S, Li C, Liu L, Lin Z, He H, Deng XW, Zhang Z, Wang X. The hybrid protein interactome contributes to rice heterosis as epistatic effects. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 102:116-128. [PMID: 31736145 DOI: 10.1111/tpj.14616] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Revised: 10/27/2019] [Accepted: 11/01/2019] [Indexed: 05/15/2023]
Abstract
Heterosis is the phenomenon in which hybrid progeny exhibits superior traits in comparison with those of their parents. Genomic variations between the two parental genomes may generate epistasis interactions, which is one of the genetic hypotheses explaining heterosis. We postulate that protein-protein interactions specific to F1 hybrids (F1 -specific PPIs) may occur when two parental genomes combine, as the proteome of each parent may supply novel interacting partners. To test our assumption, an inter-subspecies hybrid interactome was simulated by in silico PPI prediction between rice japonica (cultivar Nipponbare) and indica (cultivar 9311). Four-thousand, six-hundred and twelve F1 -specific PPIs accounting for 20.5% of total PPIs in the hybrid interactome were found. Genes participating in F1 -specific PPIs tend to encode metabolic enzymes and are generally localized in genomic regions harboring metabolic gene clusters. To test the genetic effect of F1 -specific PPIs in heterosis, genomic selection analysis was performed for trait prediction with additive, dominant and epistatic effects separately considered in the model. We found that the removal of single nucleotide polymorphisms associated with F1 -specific PPIs reduced prediction accuracy when epistatic effects were considered in the model, but no significant changes were observed when additive or dominant effects were considered. In summary, genomic divergence widely dispersed between japonica and indica rice may generate F1 -specific PPIs, part of which may accumulatively contribute to heterosis according to our computational analysis. These candidate F1 -specific PPIs, especially for those involved in metabolic biosynthesis pathways, are worthy of experimental validation when large-scale protein interactome datasets are generated in hybrid rice in the future.
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Affiliation(s)
- Hong Li
- National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, Haikou, 570228, China
| | - Shuqin Jiang
- National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Chen Li
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Lei Liu
- Beijing Key Laboratory of Plant Resources Research and Development, School of Sciences, Beijing Technology and Business University, Beijing, 100048, China
| | - Zechuan Lin
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing, China
| | - Hang He
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing, China
| | - Xing-Wang Deng
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing, China
| | - Ziding Zhang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Xiangfeng Wang
- National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
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Wang J, Yu J, Li Y, Wei C, Guo H, Liu Y, Zhang J, Li X, Wang X. Sequential Paleotetraploidization shaped the carrot genome. BMC PLANT BIOLOGY 2020; 20:52. [PMID: 32005164 PMCID: PMC6995200 DOI: 10.1186/s12870-020-2235-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 12/31/2019] [Indexed: 06/02/2023]
Abstract
BACKGROUND Carrot (Daucus carota subsp. carota L.) is an important root crop with an available high-quality genome. The carrot genome is thought to have undergone recursive paleo-polyploidization, but the extent, occurrences, and nature of these events are not clearly defined. RESULTS Using a previously published comparative genomics pipeline, we reanalysed the carrot genome and characterized genomic fractionation, as well as gene loss and retention, after each of the two tetraploidization events and inferred a dominant and sensitive subgenome for each event. In particular, we found strong evidence of two sequential tetraploidization events, with one (Dc-α) approximately 46-52 million years ago (Mya) and the other (Dc-β) approximately 77-87 Mya, both likely allotetraploidization in nature. The Dc-β event was likely common to all Apiales plants, occurring around the divergence of Apiales-Bruniales and after the divergence of Apiales-Asterales, likely playing an important role in the derivation and divergence of Apiales species. Furthermore, we found that rounds of polyploidy events contributed to the expansion of gene families responsible for plastidial methylerythritol phosphate (MEP), the precursor of carotenoid accumulation, and shaped underlying regulatory pathways. The alignment of orthologous and paralogous genes related to different events of polyploidization and speciation constitutes a comparative genomics platform for studying Apiales, Asterales, and many other related species. CONCLUSIONS Hierarchical inference of homology revealed two tetraploidization events that shaped the carrot genome, which likely contributed to the successful establishment of Apiales plants and the expansion of MEP, upstream of the carotenoid accumulation pathway.
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Affiliation(s)
- Jinpeng Wang
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan, 063200 Hebei China
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
- College of Mathematics and Science, Handan University, Handan, 056005 Hebei China
| | - Jigao Yu
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan, 063200 Hebei China
| | - Yuxian Li
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan, 063200 Hebei China
| | - Chendan Wei
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan, 063200 Hebei China
| | - He Guo
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan, 063200 Hebei China
| | - Ying Liu
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan, 063200 Hebei China
| | - Jin Zhang
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan, 063200 Hebei China
| | - Xiuqing Li
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, Frederiction, New Brunswick E3B 4Z7 Canada
| | - Xiyin Wang
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan, 063200 Hebei China
- School of Genomics and Bio-Big-Data, Chengdu University of Traditional Chinese Medicine, Chengdu, 610075 China
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Zou L, Liu W, Zhang Z, Edwards EJ, Gathunga EK, Fan P, Duan W, Li S, Liang Z. Gene body demethylation increases expression and is associated with self-pruning during grape genome duplication. HORTICULTURE RESEARCH 2020; 7:84. [PMID: 32528696 PMCID: PMC7261773 DOI: 10.1038/s41438-020-0303-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 02/11/2020] [Accepted: 03/19/2020] [Indexed: 05/15/2023]
Abstract
A colchicine-induced autotetraploid grapevine exhibiting potentially valuable agronomic traits for grape production and breeding, including self-pruning, was identified. This study investigated DNA methylation variation and its role in gene expression during self-pruning in the autotetraploid grapevine. We used RNA-Seq to estimate differentially expressed genes between diploid and autotetraploid grapevine shoot tips. The genes showing increases in the autotetraploid were mainly related to stress response pathways, whereas those showing decreases in the autotetraploid were related to biological metabolism and biosynthesis. Whole-genome bisulfite sequencing was performed to produce single-base methylomes for the diploid and autotetraploid grapevines. Comparison between the methylomes revealed that they were conserved in CG and CHG contexts. In the autotetraploid grapevine, hypodifferentially methylated regions (DMRs) and hyper-DMRs in the gene body increased or decreased gene expression, respectively. Our results indicated that a hypo-DMR in the ACO1 gene body increased its expression and might promote self-pruning. This study reports that hypo-DMRs in the gene body increase gene expression in plants and reveals the mechanism underlying the changes in the modifications affecting gene expression during genome duplication. Overall, our results provide valuable information for understanding the relationships between DNA methylation, gene expression, and autotetraploid breeding in grape.
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Affiliation(s)
- Luming Zou
- Beijing Key Laboratory of Grape Science and Enology and CAS Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 PR China
- University of the Chinese Academy of Sciences, Beijing, 100049 PR China
| | - Wenwen Liu
- Beijing Key Laboratory of Grape Science and Enology and CAS Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 PR China
- University of the Chinese Academy of Sciences, Beijing, 100049 PR China
| | - Zhan Zhang
- Beijing Key Laboratory of Grape Science and Enology and CAS Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 PR China
- University of the Chinese Academy of Sciences, Beijing, 100049 PR China
- College of Life Science, Shanxi Normal University, Shanxi, 041004 PR China
| | | | - Elias Kirabi Gathunga
- Beijing Key Laboratory of Grape Science and Enology and CAS Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 PR China
- University of the Chinese Academy of Sciences, Beijing, 100049 PR China
| | - Peige Fan
- Beijing Key Laboratory of Grape Science and Enology and CAS Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 PR China
| | - Wei Duan
- Beijing Key Laboratory of Grape Science and Enology and CAS Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 PR China
| | - Shaohua Li
- Beijing Key Laboratory of Grape Science and Enology and CAS Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 PR China
- University of the Chinese Academy of Sciences, Beijing, 100049 PR China
| | - Zhenchang Liang
- Beijing Key Laboratory of Grape Science and Enology and CAS Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 PR China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074 PR China
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40
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Zhou Y, Zhang C. Evolutionary patterns of chimeric retrogenes in Oryza species. Sci Rep 2019; 9:17733. [PMID: 31776387 PMCID: PMC6881317 DOI: 10.1038/s41598-019-54085-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 10/30/2019] [Indexed: 11/23/2022] Open
Abstract
Chimeric retroposition is a process by which RNA is reverse transcribed and the resulting cDNA is integrated into the genome along with flanking sequences. This process plays essential roles and drives genome evolution. Although the origination rates of chimeric retrogenes are high in plant genomes, the evolutionary patterns of the retrogenes and their parental genes are relatively uncharacterised in the rice genome. In this study, we evaluated the substitution ratio of 24 retrogenes and their parental genes to clarify their evolutionary patterns. The results indicated that seven gene pairs were under positive selection. Additionally, soon after new chimeric retrogenes were formed, they rapidly evolved. However, an unexpected pattern was also revealed. Specifically, after an undefined period following the formation of new chimeric retrogenes, the parental genes, rather than the new chimeric retrogenes, rapidly evolved under positive selection. We also observed that one retro chimeric gene (RCG3) was highly expressed in infected calli, whereas its parental gene was not. Finally, a comparison of our Ka/Ks analysis with that of other species indicated that the proportion of genes under positive selection is greater for chimeric retrogenes than for non-chimeric retrogenes in the rice genome.
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Affiliation(s)
- Yanli Zhou
- The Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, No. 132 Lanhei Road, Kunming, 650201, Yunnan, China
| | - Chengjun Zhang
- The Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, No. 132 Lanhei Road, Kunming, 650201, Yunnan, China. .,Haiyan Engineering & Technology Center, Kunming Institute of Botany, Chinese Academy of Science, Jiaxing, 314300, Zhejiang, China.
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Wu X, Gong D, Xia F, Dai C, Zhang X, Gao X, Wang S, Qu X, Sun Y, Liu G. A two-step mutation process in the double WS1 homologs drives the evolution of burley tobacco, a special chlorophyll-deficient mutant with abnormal chloroplast development. PLANTA 2019; 251:10. [PMID: 31776784 DOI: 10.1007/s00425-019-03312-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 11/06/2019] [Indexed: 06/10/2023]
Abstract
MAIN CONCLUSION The functional homologs WS1A and WS1B, identified by map-based cloning, control the burley character by affecting chloroplast development in tobacco, contributing to gene isolation and genetic improvement in polyploid crops. Burley represents a special type of tobacco (Nicotiana tabacum L.) cultivar that is characterized by a white stem with a high degree of chlorophyll deficiency. Although important progress in the research of burley tobacco has been made, the molecular mechanisms underlying this character remain unclear. Here, on the basis of our previous genetic analyses and preliminary mapping results, we isolated the White Stem 1A (WS1A) and WS1B genes using a map-based cloning approach. WS1A and WS1B are functional homologs with completely identical biological functions and highly similar expression patterns that control the burley character in tobacco. WS1A and WS1B are derived from Nicotiana sylvestris and Nicotiana tomentosiformis, the diploid ancestors of Nicotiana tabacum, respectively. The two genes encode zinc metalloproteases of the M50 family that are highly homologous to the Ethylene-dependent Gravitropism-deficient and Yellow-green 1 (EGY1) protein of Arabidopsis and the Lutescent 2 (L2) protein of tomato. Transmission electron microscopic examinations indicated that WS1A and WS1B are involved in the development of chloroplasts by controlling the formation of thylakoid membranes, very similar to that observed for EGY1 and L2. The genotyping of historical tobacco varieties revealed that a two-step mutation process occurred in WS1A and WS1B during the evolution of burley tobacco. We also discussed the strategy for gene map-based cloning in polyploid plants with complex genomes. This study will facilitate the identification of agronomically important genes in tobacco and other polyploid crops and provide insights into crop improvement via molecular approaches.
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Affiliation(s)
- Xinru Wu
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China.
- Key Laboratory for Tobacco Gene Resources, State Tobacco Monopoly Administration, Qingdao, 266101, China.
| | - Daping Gong
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
- Key Laboratory for Tobacco Gene Resources, State Tobacco Monopoly Administration, Qingdao, 266101, China
| | - Fei Xia
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
- Key Laboratory for Tobacco Gene Resources, State Tobacco Monopoly Administration, Qingdao, 266101, China
| | - Changbo Dai
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
- Key Laboratory for Tobacco Gene Resources, State Tobacco Monopoly Administration, Qingdao, 266101, China
| | - Xingwei Zhang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
- Key Laboratory for Tobacco Gene Resources, State Tobacco Monopoly Administration, Qingdao, 266101, China
| | - Xiaoming Gao
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
- Key Laboratory for Tobacco Gene Resources, State Tobacco Monopoly Administration, Qingdao, 266101, China
| | - Shaomei Wang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
- Key Laboratory for Tobacco Gene Resources, State Tobacco Monopoly Administration, Qingdao, 266101, China
| | - Xu Qu
- Qingdao Tobacco Seed Co., Ltd, Qingdao, 266101, China
| | - Yuhe Sun
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
- Key Laboratory for Tobacco Gene Resources, State Tobacco Monopoly Administration, Qingdao, 266101, China
| | - Guanshan Liu
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China.
- Key Laboratory for Tobacco Gene Resources, State Tobacco Monopoly Administration, Qingdao, 266101, China.
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Lv M, Hou D, Zhang L, Fan J, Li C, Chen W, Sun Y, Dong Y, Xu J, Cai L, Gao X, Zhu J, Huang Z, Xu Z, Li L. Molecular characterization and function analysis of the rice OsDUF1191 family. BIOTECHNOL BIOTEC EQ 2019. [DOI: 10.1080/13102818.2019.1684843] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Affiliation(s)
- Miaomiao Lv
- Rice Institute of Sichuan Agricultural University, Chengdu, PR China
| | - Dejia Hou
- Department of Physics, College of Science, Huazhong Agricultural University, Wuhan, PR China
| | - Lin Zhang
- Rice Institute of Sichuan Agricultural University, Chengdu, PR China
| | - Jiangbo Fan
- Rice Institute of Sichuan Agricultural University, Chengdu, PR China
| | - Chunliu Li
- Rice Institute of Sichuan Agricultural University, Chengdu, PR China
| | - Wenqian Chen
- Rice Institute of Sichuan Agricultural University, Chengdu, PR China
| | - Yihao Sun
- Rice Institute of Sichuan Agricultural University, Chengdu, PR China
| | - Yilun Dong
- Rice Institute of Sichuan Agricultural University, Chengdu, PR China
| | - Jinghong Xu
- Crop Research Institute, Academy of Agricultural and Forestry Sciences, Chengdu, PR China
| | - Liangjun Cai
- Crop Research Institute, Academy of Agricultural and Forestry Sciences, Chengdu, PR China
| | - Xiaoling Gao
- Rice Institute of Sichuan Agricultural University, Chengdu, PR China
| | - Jianqing Zhu
- Rice Institute of Sichuan Agricultural University, Chengdu, PR China
| | - Zhengjian Huang
- Rice Institute of Sichuan Agricultural University, Chengdu, PR China
| | - Zhengjun Xu
- Rice Institute of Sichuan Agricultural University, Chengdu, PR China
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu, PR China
| | - Lihua Li
- Rice Institute of Sichuan Agricultural University, Chengdu, PR China
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu, PR China
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43
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Liu D, Sun J, Zhu D, Lyu G, Zhang C, Liu J, Wang H, Zhang X, Gao D. Genome-Wide Identification and Expression Profiles of Late Embryogenesis-Abundant (LEA) Genes during Grain Maturation in Wheat ( Triticum aestivum L.). Genes (Basel) 2019; 10:genes10090696. [PMID: 31510067 PMCID: PMC6770980 DOI: 10.3390/genes10090696] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 09/01/2019] [Accepted: 09/06/2019] [Indexed: 12/21/2022] Open
Abstract
Late embryogenesis-abundant (LEA) genes play important roles in plant growth and development, especially the cellular dehydration tolerance during seed maturation. In order to comprehensively understand the roles of LEA family members in wheat, we carried out a series of analyses based on the latest genome sequence of the bread wheat Chinese Spring. 121 Triticum aestivum L. LEA (TaLEA) genes, classified as 8 groups, were identified and characterized. TaLEA genes are distributed in all chromosomes, most of them with a low number of introns (≤3). Expression profiles showed that most TaLEA genes expressed specifically in grains. By qRT-PCR analysis, we confirmed that 12 genes among them showed high expression levels during late stage grain maturation in two spring wheat cultivars, Yangmai16 and Yangmai15. For most genes, the peak of expression appeared earlier in Yangmai16. Statistical analysis indicated that expression level of 8 genes in Yangmai 16 were significantly higher than Yangmai 15 at 25 days after anthesis. Taken together, our results provide more knowledge for future functional analysis and potential utilization of TaLEA genes in wheat breeding.
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Affiliation(s)
- Datong Liu
- Key Laboratory of Wheat Biology and Genetic Improvement for Low & Middle Yangtze Valley, Ministry of Agriculture/Lixiahe Agricultural Institute of Jiangsu Province, Yangzhou 225007, China.
| | - Jing Sun
- Yangzhou University, Yangzhou 225009, China.
| | - Dongmei Zhu
- Key Laboratory of Wheat Biology and Genetic Improvement for Low & Middle Yangtze Valley, Ministry of Agriculture/Lixiahe Agricultural Institute of Jiangsu Province, Yangzhou 225007, China.
| | - Guofeng Lyu
- Key Laboratory of Wheat Biology and Genetic Improvement for Low & Middle Yangtze Valley, Ministry of Agriculture/Lixiahe Agricultural Institute of Jiangsu Province, Yangzhou 225007, China.
| | - Chunmei Zhang
- Key Laboratory of Wheat Biology and Genetic Improvement for Low & Middle Yangtze Valley, Ministry of Agriculture/Lixiahe Agricultural Institute of Jiangsu Province, Yangzhou 225007, China.
| | - Jian Liu
- Key Laboratory of Wheat Biology and Genetic Improvement for Low & Middle Yangtze Valley, Ministry of Agriculture/Lixiahe Agricultural Institute of Jiangsu Province, Yangzhou 225007, China.
| | - Hui Wang
- Key Laboratory of Wheat Biology and Genetic Improvement for Low & Middle Yangtze Valley, Ministry of Agriculture/Lixiahe Agricultural Institute of Jiangsu Province, Yangzhou 225007, China.
| | - Xiao Zhang
- Key Laboratory of Wheat Biology and Genetic Improvement for Low & Middle Yangtze Valley, Ministry of Agriculture/Lixiahe Agricultural Institute of Jiangsu Province, Yangzhou 225007, China.
| | - Derong Gao
- Key Laboratory of Wheat Biology and Genetic Improvement for Low & Middle Yangtze Valley, Ministry of Agriculture/Lixiahe Agricultural Institute of Jiangsu Province, Yangzhou 225007, China.
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Shi Y, Xu H, Shen Q, Lin J, Wang Y, Hua X, Yao W, Yu Q, Ming R, Zhang J. Comparative Analysis of SUS Gene Family between Saccharum officinarum and Saccharum spontaneum. TROPICAL PLANT BIOLOGY 2019; 12:174-185. [PMID: 0 DOI: 10.1007/s12042-019-09230-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 05/09/2019] [Indexed: 05/25/2023]
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45
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Yuan J, Wang J, Yu J, Meng F, Zhao Y, Li J, Sun P, Sun S, Zhang Z, Liu C, Wei C, Guo H, Li X, Duan X, Shen S, Xie Y, Hou Y, Zhang J, Shehzad T, Wang X. Alignment of Rutaceae Genomes Reveals Lower Genome Fractionation Level Than Eudicot Genomes Affected by Extra Polyploidization. FRONTIERS IN PLANT SCIENCE 2019; 10:986. [PMID: 31447866 PMCID: PMC6691040 DOI: 10.3389/fpls.2019.00986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 07/12/2019] [Indexed: 06/10/2023]
Abstract
Owing to their nutritional and commercial values, the genomes of several citrus plants have been sequenced, and the genome of one close relative in the Rutaceae family, atalantia (Atalantia buxifolia), has also been sequenced. Here, we show a family-level comparative analysis of Rutaceae genomes. By using grape as the outgroup and checking cross-genome gene collinearity, we systematically performed a hierarchical and event-related alignment of Rutaceae genomes, and produced a gene list defining homologous regions based on ancestral polyploidization or speciation. We characterized genome fractionation resulting from gene loss or relocation, and found that erosion of gene collinearity could largely be described by a geometric distribution. Moreover, we found that well-assembled Rutaceae genomes retained significantly more genes (65-82%) than other eudicots affected by recursive polyploidization. Additionally, we showed divergent evolutionary rates among Rutaceae plants, with sweet orange evolving faster than others, and by performing evolutionary rate correction, re-dated major evolutionary events during their evolution. We deduced that the divergence between the Rutaceae family and grape occurred about 81.15-91.74 million years ago (mya), while the split between citrus and atalantia plants occurred <10 mya. In addition, we showed that polyploidization led to a copy number expansion of key gene families contributing to the biosynthesis of vitamin C. Overall, the present effort provides an important comparative genomics resource and lays a foundation to understand the evolution and functional innovation of Rutaceae genomes.
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Affiliation(s)
- Jiaqing Yuan
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Jinpeng Wang
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Jigao Yu
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Fanbo Meng
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Yuhao Zhao
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Jing Li
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Pengchuan Sun
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Sangrong Sun
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Zhikang Zhang
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Chao Liu
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Chendan Wei
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - He Guo
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Xinyu Li
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Xueqian Duan
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Shaoqi Shen
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Yangqin Xie
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Yue Hou
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Jin Zhang
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Tariq Shehzad
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, United States
| | - Xiyin Wang
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
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Genome-wide identification and expression analysis of Hsp70, Hsp90, and Hsp100 heat shock protein genes in barley under stress conditions and reproductive development. Funct Integr Genomics 2019; 19:1007-1022. [PMID: 31359217 DOI: 10.1007/s10142-019-00695-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 03/19/2019] [Accepted: 06/10/2019] [Indexed: 10/26/2022]
Abstract
Abiotic stress including extreme temperature disturbs the plant cellular homeostasis consequently limiting the yield potential of crop plants. Heat shock proteins (Hsps) are part of major rescue machinery of plants which aid to combat these stressed conditions by re-establishing protein homeostasis. Hsps with their chaperone and co-chaperone mechanisms regulate the activity of their substrate proteins in an ATP-dependent manner. In the present investigation, a genome-wide identification, evolutionary relationship, and comprehensive expression analysis of Hsp70, Hsp90, and Hsp100 gene families have been done in barley. The barley genome possesses 13 members of the Hsp70 gene family, along with 4 members of the Hsp110 subfamily, and 6 members of Hsp90 and 8 members of the Hsp100 gene family. Hsp genes are distributed on all 7 chromosomes of barley, and their encoded protein members are predicted to be localized to cell organelles such as cytosol, mitochondria, chloroplast, and ER. Despite a larger genome size, there are lesser members of these Hsp genes in barley, owing to less duplication events. The variable expression pattern obtained for genes encoding proteins localized to the same subcellular compartment suggests their diverse roles and involvement in different cellular responses. Expression profiling of these genes was performed by qRT-PCR in an array of 32 tissues, which showed a differential and tissue-specific expression of various members of Hsp gene families. We found the upregulation of HvHspc70-4, HvHsp70Mt70-2, HvHspc70-5a, HvHspc70-5b, HvHspc70-N1, HvHspc70-N2, HvHsp110-3, HvHsp90-1, HvHsp100-1, and HvHsp100-2 upon exposure to heat stress during reproductive development. Furthermore, their higher expression during heat stress, heavy metal stress, drought, and salinity stress was also observed in a tissue-specific manner.
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Wang Z, Wang J, Pan Y, Lei T, Ge W, Wang L, Zhang L, Li Y, Zhao K, Liu T, Song X, Zhang J, Yu J, Hu J, Wang X. Reconstruction of evolutionary trajectories of chromosomes unraveled independent genomic repatterning between Triticeae and Brachypodium. BMC Genomics 2019; 20:180. [PMID: 30845910 PMCID: PMC6407190 DOI: 10.1186/s12864-019-5566-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Accepted: 02/25/2019] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND After polyploidization, a genome may experience large-scale genome-repatterning, featuring wide-spread DNA rearrangement and loss, and often chromosome number reduction. Grasses share a common tetraploidization, after which the originally doubled chromosome numbers reduced to different chromosome numbers among them. A telomere-centric reduction model was proposed previously to explain chromosome number reduction. With Brachpodium as an intermediate linking different major lineages of grasses and a model plant of the Pooideae plants, we wonder whether it mediated the evolution from ancestral grass karyotype to Triticeae karyotype. RESULTS By inferring the homology among Triticeae, rice, and Brachpodium chromosomes, we reconstructed the evolutionary trajectories of the Triticeae chromosomes. By performing comparative genomics analysis with rice as a reference, we reconstructed the evolutionary trajectories of Pooideae plants, including Ae. Tauschii (2n = 14, DD), barley (2n = 14), Triticum turgidum (2n = 4x = 28, AABB), and Brachypodium (2n = 10). Their extant Pooidea and Brachypodium chromosomes were independently produced after sequential nested chromosome fusions in the last tens of millions of years, respectively, after their split from rice. More frequently than would be expected by chance, in Brachypodium, the 'invading' and 'invaded' chromosomes are homoeologs, originating from duplication of a common ancestral chromosome, that is, with more extensive DNA-level correspondence to one another than random chromosomes, nested chromosome fusion events between homoeologs account for three of seven cases in Brachypodium (P-value≈0.00078). However, this phenomenon was not observed during the formation of other Pooideae chromosomes. CONCLUSIONS Notably, we found that the Brachypodium chromosomes formed through exclusively distinctive trajectories from those of Pooideae plants, and were well explained by the telomere-centric model. Our work will contribute to understanding the structural and functional innovation of chromosomes in different Pooideae lineages and beyond.
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Affiliation(s)
- Zhenyi Wang
- School of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063210, Hebei, China
| | - Jinpeng Wang
- School of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063210, Hebei, China
| | - Yuxin Pan
- School of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063210, Hebei, China
| | - Tianyu Lei
- School of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063210, Hebei, China
| | - Weina Ge
- School of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063210, Hebei, China
| | - Li Wang
- School of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063210, Hebei, China
| | - Lan Zhang
- School of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063210, Hebei, China
| | - Yuxian Li
- School of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063210, Hebei, China
| | - Kanglu Zhao
- School of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China
| | - Tao Liu
- Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063210, Hebei, China.,College of Science, North China University of Science and Technology, Tangshan, 063210, Hebei, China
| | - Xiaoming Song
- School of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063210, Hebei, China
| | - Jiaqi Zhang
- School of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063210, Hebei, China
| | - Jigao Yu
- School of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063210, Hebei, China
| | - Jingjing Hu
- School of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063210, Hebei, China
| | - Xiyin Wang
- School of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China. .,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063210, Hebei, China.
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Li D, Wu D, Li S, Dai Y, Cao Y. Evolutionary and functional analysis of the plant-specific NADPH oxidase gene family in Brassica rapa L. ROYAL SOCIETY OPEN SCIENCE 2019; 6:181727. [PMID: 30891283 PMCID: PMC6408365 DOI: 10.1098/rsos.181727] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 01/31/2019] [Indexed: 05/13/2023]
Abstract
NADPH oxidases (NOXs) have been known as respiratory burst oxidase homologues (RBOHs) in plants. To characterize the evolutionary relationships and functions of RBOHs in Brassica rapa, 134 RBOH homologues were identified from 13 plant species, including 14 members (namely BrRBOH01-14) from B. rapa. There presented 47 gene-pairs among 14 BrRBOHs and other RBOHs, consisting of five pairs within B. rapa, and 15 pairs between B. rapa and Arabidopsis thaliana. Together with phylogenetic analysis, the results suggested that whole-genome duplication might have played an important role in BrRBOH gene expansion, and these duplication events occurred after the divergence of the eudicot and the monocot lineages examined. Furthermore, gene expression of RBOHs in both A. thaliana and B. rapa were assayed via qRT-PCR. An RBOH gene, BrRBOH13 in B. rapa, was transformed into wild-type Arabidopsis plants. The transgenic lines with the overexpressed level of BrRBOH13 conferred to be more tolerant to heavy metal lead (0.05 mM) than wild-type plants. Overall, this integrated analysis at genome-wide level has provided some information on the evolutionary relationships among plant-specific NOXs and the coordinated diversification of gene structure and function in B. rapa.
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Affiliation(s)
- Dahui Li
- Author for correspondence: Dahui Li e-mail:
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Liu C, Zhang TZ. Functional diversifications of GhERF1 duplicate genes after the formation of allotetraploid cotton. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:60-74. [PMID: 30578593 DOI: 10.1111/jipb.12764] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 12/17/2018] [Indexed: 06/09/2023]
Abstract
Whole genome duplication, a prevalent force of evolution in plants, results in massive genome restructuring in different organisms. Roles of the resultant duplicated genes are poorly understood, both functionally and evolutionarily. In the present study, differentially expressed ethylene responsive factors (GhERF1s), anchored on Chr-A07 and Chr-D07, were isolated from a high-yielding cotton hybrid (XZM2) and its parents. The GhERF1 was located in the B3 subgroup of the ethylene responsive factors subfamily involved in conferring tolerance to abiotic stress. Nucleotide sequence analysis of 524 diverse accessions, together with quantitative real-time polymerase chain reaction analysis, elucidated that de-functionalization of GhERF1-7A occurred due to one base insertion following formation of the allotetraploid cotton. Our quantitative trait loci and association mapping analyses highlighted a role for GhERF1-7A in conferring high boll number per plant in modern cotton cultivars. Overexpression of GhERF1-7A in transgenic Arabidopsis resulted in a substantial increase in the number of siliques and total seed yield. Neo-functionalization of GhERF1-7A was also observed in modern cultivars rather than in races and/or landraces, further supporting its role in the development of high-yielding cotton cultivars. Both de- and neo-functionalization occurred in one of the duplicate genes, thus providing new genomic insight into the evolution of allotetraploid cotton species.
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Affiliation(s)
- Chunxiao Liu
- National Key Laboratory of Crop Genetics & Germplasm Enhancement, Cotton Research Institute, Nanjing Agricultural University, Nanjing 210095, China
| | - Tian Zhen Zhang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement, Cotton Research Institute, Nanjing Agricultural University, Nanjing 210095, China
- Crop Science Institute, Agronomy Department, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310029, China
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Zhang H, Ali A, Hou F, Wu T, Guo D, Zeng X, Wang F, Zhao H, Chen X, Xu P, Wu X. Effects of ploidy variation on promoter DNA methylation and gene expression in rice (Oryza sativa L.). BMC PLANT BIOLOGY 2018; 18:314. [PMID: 30497392 PMCID: PMC6267922 DOI: 10.1186/s12870-018-1553-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 11/21/2018] [Indexed: 06/09/2023]
Abstract
BACKGROUND Polyploidy, or whole-genome duplication (WGD) promotes genetic diversification in plants. However, whether WGD is accompanied by epigenetic regulation especially DNA methylation remains yet elusive. Methylation of different region in genomic DNA play discrete role in gene regulation and developmental processes in plants. RESULTS In our study, we used an apomictic rice line (SARII-628) that produces twin seedlings of different ploidy for methylated DNA immunoprecipitation sequencing (MeDIP-seq). We compared the level of methylation and mRNA expression in three different (CG, CHG, and CHH) sequence contexts of promoter region among haploid (1X), diploid (2X), and triploid (3X) seedling. We used MeDIP-Seq analysis of 14 genes to investigate whole genome DNA methylation and found that relative level of DNA methylation across different ploidy was in following order e.g. diploid > triploid > haploid. GO functional classification of differentially methylated genes into 9 comparisons group of promoter, intergenic and intragenic region discovered, these genes were mostly enriched for cellular component, molecular function, and biological process. By the comparison of methylome data, digital gene expression (DGE), mRNA expression profile, and Q-PCR findings LOC_ Os07g31450 and LOC_ Os01g59320 were analyzed for BS-Seq (Bisulphite sequencing). CONCLUSIONS We found that (1) The level of the promoter DNA methylation is negatively correlated with gene expression within each ploidy level. (2) Among all ploidy levels, CG sequence context had highest methylation frequency, and demonstrated that the high CG methylation did reduce gene expression change suggesting that DNA methylation exert repressive function and ensure genome stability during WGD. (3) Alteration in ploidy (from diploid to haploid, or diploid to triploid) reveals supreme changes in methylation frequency of CHH sequence context. Our finding will contribute an understanding towards lower stability of CHH sequence context and educate the effect of promoter region methylation during change in ploidy state in rice.
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Affiliation(s)
- Hongyu Zhang
- 211-Key Laboratory of Crop Genetic Resources and Genetic Improvement, Ministry of Education, Institute of Rice Research, Sichuan Agricultural University, Huimin Road, Chengdu, 611130 China
| | - Asif Ali
- 211-Key Laboratory of Crop Genetic Resources and Genetic Improvement, Ministry of Education, Institute of Rice Research, Sichuan Agricultural University, Huimin Road, Chengdu, 611130 China
| | - Feixue Hou
- 211-Key Laboratory of Crop Genetic Resources and Genetic Improvement, Ministry of Education, Institute of Rice Research, Sichuan Agricultural University, Huimin Road, Chengdu, 611130 China
| | - Tingkai Wu
- 211-Key Laboratory of Crop Genetic Resources and Genetic Improvement, Ministry of Education, Institute of Rice Research, Sichuan Agricultural University, Huimin Road, Chengdu, 611130 China
| | - Daiming Guo
- 211-Key Laboratory of Crop Genetic Resources and Genetic Improvement, Ministry of Education, Institute of Rice Research, Sichuan Agricultural University, Huimin Road, Chengdu, 611130 China
| | - Xiufeng Zeng
- 211-Key Laboratory of Crop Genetic Resources and Genetic Improvement, Ministry of Education, Institute of Rice Research, Sichuan Agricultural University, Huimin Road, Chengdu, 611130 China
| | - Fangfang Wang
- 211-Key Laboratory of Crop Genetic Resources and Genetic Improvement, Ministry of Education, Institute of Rice Research, Sichuan Agricultural University, Huimin Road, Chengdu, 611130 China
| | - Huixia Zhao
- 211-Key Laboratory of Crop Genetic Resources and Genetic Improvement, Ministry of Education, Institute of Rice Research, Sichuan Agricultural University, Huimin Road, Chengdu, 611130 China
| | - Xiaoqiong Chen
- 211-Key Laboratory of Crop Genetic Resources and Genetic Improvement, Ministry of Education, Institute of Rice Research, Sichuan Agricultural University, Huimin Road, Chengdu, 611130 China
| | - Peizhou Xu
- 211-Key Laboratory of Crop Genetic Resources and Genetic Improvement, Ministry of Education, Institute of Rice Research, Sichuan Agricultural University, Huimin Road, Chengdu, 611130 China
| | - Xianjun Wu
- 211-Key Laboratory of Crop Genetic Resources and Genetic Improvement, Ministry of Education, Institute of Rice Research, Sichuan Agricultural University, Huimin Road, Chengdu, 611130 China
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