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Zhang Y, Liu J, Yu J, Zhang H, Yang Z. Relationship between the Phenylpropanoid Pathway and Dwarfism of Paspalum seashore Based on RNA-Seq and iTRAQ. Int J Mol Sci 2021; 22:ijms22179568. [PMID: 34502485 PMCID: PMC8431245 DOI: 10.3390/ijms22179568] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/27/2021] [Accepted: 08/31/2021] [Indexed: 11/24/2022] Open
Abstract
Seashore paspalum is a major warm-season turfgrass requiring frequent mowing. The use of dwarf cultivars with slow growth is a promising method to decrease mowing frequency. The present study was conducted to provide an in-depth understanding of the molecular mechanism of T51 dwarfing in the phenylpropane pathway and to screen the key genes related to dwarfing. For this purpose, we obtained transcriptomic information based on RNA-Seq and proteomic information based on iTRAQ for the dwarf mutant T51 of seashore paspalum. The combined results of transcriptomic and proteomic analysis were used to identify the differential expression pattern of genes at the translational and transcriptional levels. A total of 8311 DEGs were detected at the transcription level, of which 2540 were upregulated and 5771 were downregulated. Based on the transcripts, 2910 proteins were identified using iTRAQ, of which 392 (155 upregulated and 237 downregulated) were DEPs. The phenylpropane pathway was found to be significantly enriched at both the transcriptional and translational levels. Combined with the decrease in lignin content and the increase in flavonoid content in T51, we found that the dwarf phenotype of T51 is closely related to the abnormal synthesis of lignin and flavonoids in the phenylpropane pathway. CCR and HCT may be the key genes for T51 dwarf. This study provides the basis for further study on the dwarfing mechanism of seashore paspalum. The screening of key genes lays a foundation for further studies on the molecular mechanism of seashore paspalum dwarfing.
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Alabdullah AK, Borrill P, Martin AC, Ramirez-Gonzalez RH, Hassani-Pak K, Uauy C, Shaw P, Moore G. A Co-Expression Network in Hexaploid Wheat Reveals Mostly Balanced Expression and Lack of Significant Gene Loss of Homeologous Meiotic Genes Upon Polyploidization. Front Plant Sci 2019; 10:1325. [PMID: 31681395 PMCID: PMC6813927 DOI: 10.3389/fpls.2019.01325] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 09/24/2019] [Indexed: 05/05/2023]
Abstract
Polyploidization has played an important role in plant evolution. However, upon polyploidization, the process of meiosis must adapt to ensure the proper segregation of increased numbers of chromosomes to produce balanced gametes. It has been suggested that meiotic gene (MG) duplicates return to a single copy following whole genome duplication to stabilize the polyploid genome. Therefore, upon the polyploidization of wheat, a hexaploid species with three related (homeologous) genomes, the stabilization process may have involved rapid changes in content and expression of MGs on homeologous chromosomes (homeologs). To examine this hypothesis, sets of candidate MGs were identified in wheat using co-expression network analysis and orthology informed approaches. In total, 130 RNA-Seq samples from a range of tissues including wheat meiotic anthers were used to define co-expressed modules of genes. Three modules were significantly correlated with meiotic tissue samples but not with other tissue types. These modules were enriched for GO terms related to cell cycle, DNA replication, and chromatin modification and contained orthologs of known MGs. Overall, 74.4% of genes within these meiosis-related modules had three homeologous copies which was similar to other tissue-related modules. Amongst wheat MGs identified by orthology, rather than co-expression, the majority (93.7%) were either retained in hexaploid wheat at the same number of copies (78.4%) or increased in copy number (15.3%) compared to ancestral wheat species. Furthermore, genes within meiosis-related modules showed more balanced expression levels between homeologs than genes in non-meiosis-related modules. Taken together, our results do not support extensive gene loss nor changes in homeolog expression of MGs upon wheat polyploidization. The construction of the MG co-expression network allowed identification of hub genes and provided key targets for future studies.
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Affiliation(s)
| | - Philippa Borrill
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | | | | | - Keywan Hassani-Pak
- Computational and Analytical Sciences, Rothamsted Research, Harpenden, United Kingdom
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Peter Shaw
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Graham Moore
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
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3
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Marburger S, Alexandrou MA, Taggart JB, Creer S, Carvalho G, Oliveira C, Taylor MI. Whole genome duplication and transposable element proliferation drive genome expansion in Corydoradinae catfishes. Proc Biol Sci 2019; 285:rspb.2017.2732. [PMID: 29445022 PMCID: PMC5829208 DOI: 10.1098/rspb.2017.2732] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 01/25/2018] [Indexed: 01/12/2023] Open
Abstract
Genome size varies significantly across eukaryotic taxa and the largest changes are typically driven by macro-mutations such as whole genome duplications (WGDs) and proliferation of repetitive elements. These two processes may affect the evolutionary potential of lineages by increasing genetic variation and changing gene expression. Here, we elucidate the evolutionary history and mechanisms underpinning genome size variation in a species-rich group of Neotropical catfishes (Corydoradinae) with extreme variation in genome size—0.6 to 4.4 pg per haploid cell. First, genome size was quantified in 65 species and mapped onto a novel fossil-calibrated phylogeny. Two evolutionary shifts in genome size were identified across the tree—the first between 43 and 49 Ma (95% highest posterior density (HPD) 36.2–68.1 Ma) and the second at approximately 19 Ma (95% HPD 15.3–30.14 Ma). Second, restriction-site-associated DNA (RAD) sequencing was used to identify potential WGD events and quantify transposable element (TE) abundance in different lineages. Evidence of two lineage-scale WGDs was identified across the phylogeny, the first event occurring between 54 and 66 Ma (95% HPD 42.56–99.5 Ma) and the second at 20–30 Ma (95% HPD 15.3–45 Ma) based on haplotype numbers per contig and between 35 and 44 Ma (95% HPD 30.29–64.51 Ma) and 20–30 Ma (95% HPD 15.3–45 Ma) based on SNP read ratios. TE abundance increased considerably in parallel with genome size, with a single TE-family (TC1-IS630-Pogo) showing several increases across the Corydoradinae, with the most recent at 20–30 Ma (95% HPD 15.3–45 Ma) and an older event at 35–44 Ma (95% HPD 30.29–64.51 Ma). We identified signals congruent with two WGD duplication events, as well as an increase in TE abundance across different lineages, making the Corydoradinae an excellent model system to study the effects of WGD and TEs on genome and organismal evolution.
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Affiliation(s)
- Sarah Marburger
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Deiniol Road, Bangor, Gwynedd LL57 2UW, UK.,School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - Markos A Alexandrou
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Deiniol Road, Bangor, Gwynedd LL57 2UW, UK.,Wildlands Conservation Science, LLC PO Box 1846, Lompoc, CA 93438, USA
| | - John B Taggart
- Institute of Aquaculture, University of Stirling, Stirling FK9 4LA, UK
| | - Simon Creer
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Deiniol Road, Bangor, Gwynedd LL57 2UW, UK
| | - Gary Carvalho
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Deiniol Road, Bangor, Gwynedd LL57 2UW, UK
| | - Claudio Oliveira
- Departamento de Morfologia, Instituto de Biociências/UNESP, Rua Professor Doutor Antonio Celso Wagner Zanin, s/n°18618-689 Botucatu, São Paulo, Brazil
| | - Martin I Taylor
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
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4
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Zhang JF, Xu YQ, Dong JM, Peng LN, Feng X, Wang X, Li F, Miao Y, Yao SK, Zhao QQ, Feng SS, Hu BZ, Li FL. Genome-wide identification of wheat (Triticum aestivum) expansins and expansin expression analysis in cold-tolerant and cold-sensitive wheat cultivars. PLoS One 2018; 13:e0195138. [PMID: 29596529 PMCID: PMC5875846 DOI: 10.1371/journal.pone.0195138] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 03/16/2018] [Indexed: 12/20/2022] Open
Abstract
Plant expansins are proteins involved in cell wall loosening, plant growth, and development, as well as in response to plant diseases and other stresses. In this study, we identified 128 expansin coding sequences from the wheat (Triticum aestivum) genome. These sequences belong to 45 homoeologous copies of TaEXPs, including 26 TaEXPAs, 15 TaEXPBs and four TaEXLAs. No TaEXLB was identified. Gene expression and sub-expression profiles revealed that most of the TaEXPs were expressed either only in root tissues or in multiple organs. Real-time qPCR analysis showed that many TaEXPs were differentially expressed in four different tissues of the two wheat cultivars—the cold-sensitive ‘Chinese Spring (CS)’ and the cold-tolerant ‘Dongnongdongmai 1 (D1)’ cultivars. Our results suggest that the differential expression of TaEXPs could be related to low-temperature tolerance or sensitivity of different wheat cultivars. Our study expands our knowledge on wheat expansins and sheds new light on the functions of expansins in plant development and stress response.
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Affiliation(s)
- Jun-Feng Zhang
- College of Life Science, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Yong-Qing Xu
- College of Life Science, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Jia-Min Dong
- College of Life Science, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Li-Na Peng
- College of Life Science, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Xu Feng
- College of Life Science, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Xu Wang
- College of Life Science, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Fei Li
- College of Life Science, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Yu Miao
- College of Life Science, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Shu-Kuan Yao
- College of Life Science, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Qiao-Qin Zhao
- College of Life Science, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Shan-Shan Feng
- College of Life Science, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Bao-Zhong Hu
- Harbin University, Harbin, Heilongjiang, China
- * E-mail: (BZH); (FLL)
| | - Feng-Lan Li
- College of Life Science, Northeast Agricultural University, Harbin, Heilongjiang, China
- * E-mail: (BZH); (FLL)
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Uauy C, Wulff BB, Dubcovsky J. Combining Traditional Mutagenesis with New High-Throughput Sequencing and Genome Editing to Reveal Hidden Variation in Polyploid Wheat. Annu Rev Genet 2017; 51:435-454. [DOI: 10.1146/annurev-genet-120116-024533] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Brande B.H. Wulff
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Jorge Dubcovsky
- Howard Hughes Medical Institute and Department of Plant Sciences, University of California, Davis, California 95616, USA
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Wang Y, Wang X, Wang C, Peng F, Wang R, Xiao X, Zeng J, Kang H, Fan X, Sha L, Zhang H, Zhou Y. Transcriptomic Profiles Reveal the Interactions of Cd/Zn in Dwarf Polish Wheat ( Triticum polonicum L.) Roots. Front Physiol 2017; 8:168. [PMID: 28386232 PMCID: PMC5362637 DOI: 10.3389/fphys.2017.00168] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 03/07/2017] [Indexed: 11/13/2022] Open
Abstract
Different intra- or interspecific wheat show different interactions of Cd/Zn. Normally, Zn has been/being widely utilized to reduce the Cd toxicity. In the present study, the DPW seedlings exhibited strong Cd tolerance. Zn and Cd mutually inhibited their uptake in the roots, showed antagonistic Cd/Zn interactions. However, Zn promoted the Cd transport from the roots to shoots, showed synergistic. In order to discover the interactive molecular responses, a transcriptome, including 123,300 unigenes, was constructed using RNA-Sequencing (RNA-Seq). Compared with CK, the expression of 1,269, 820, and 1,254 unigenes was significantly affected by Cd, Zn, and Cd+Zn, respectively. Only 381 unigenes were co-induced by these three treatments. Several metal transporters, such as cadmium-transporting ATPase and plant cadmium resistance 4, were specifically regulated by Cd+Zn. Other metal-related unigenes, such as ABC transporters, metal chelator, nicotianamine synthase (NAS), vacuolar iron transporters (VIT), metal-nicotianamine transporter YSL (YSL), and nitrate transporter (NRT), were regulated by Cd, but were not regulated by Cd+Zn. These results indicated that these transporters participated in the mutual inhibition of the Cd/Zn uptake in the roots, and also participated in the Cd transport, accumulation and detoxification. Meanwhile, some unigenes involved in other processes, such as oxidation-reduction, auxin metabolism, glutathione (GSH) metabolism nitrate transport, played different and important roles in the detoxification of these heavy metals.
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Affiliation(s)
- Yi Wang
- Triticeae Research Institute, Sichuan Agricultural UniversityWenjiang, China; Key Laboratory of Crop Genetic Resources and Improvement, Ministry of Education, Sichuan Agricultural UniversityWenjiang, China
| | - Xiaolu Wang
- Triticeae Research Institute, Sichuan Agricultural UniversityWenjiang, China; Key Laboratory of Crop Genetic Resources and Improvement, Ministry of Education, Sichuan Agricultural UniversityWenjiang, China
| | - Chao Wang
- Triticeae Research Institute, Sichuan Agricultural UniversityWenjiang, China; Key Laboratory of Crop Genetic Resources and Improvement, Ministry of Education, Sichuan Agricultural UniversityWenjiang, China
| | - Fan Peng
- Triticeae Research Institute, Sichuan Agricultural UniversityWenjiang, China; Key Laboratory of Crop Genetic Resources and Improvement, Ministry of Education, Sichuan Agricultural UniversityWenjiang, China
| | - Ruijiao Wang
- Triticeae Research Institute, Sichuan Agricultural UniversityWenjiang, China; Key Laboratory of Crop Genetic Resources and Improvement, Ministry of Education, Sichuan Agricultural UniversityWenjiang, China
| | - Xue Xiao
- Triticeae Research Institute, Sichuan Agricultural UniversityWenjiang, China; Key Laboratory of Crop Genetic Resources and Improvement, Ministry of Education, Sichuan Agricultural UniversityWenjiang, China
| | - Jian Zeng
- College of Resources, Sichuan Agricultural University Wenjiang, China
| | - Houyang Kang
- Triticeae Research Institute, Sichuan Agricultural UniversityWenjiang, China; Key Laboratory of Crop Genetic Resources and Improvement, Ministry of Education, Sichuan Agricultural UniversityWenjiang, China
| | - Xing Fan
- Triticeae Research Institute, Sichuan Agricultural UniversityWenjiang, China; Key Laboratory of Crop Genetic Resources and Improvement, Ministry of Education, Sichuan Agricultural UniversityWenjiang, China
| | - Lina Sha
- Triticeae Research Institute, Sichuan Agricultural UniversityWenjiang, China; Key Laboratory of Crop Genetic Resources and Improvement, Ministry of Education, Sichuan Agricultural UniversityWenjiang, China
| | - Haiqin Zhang
- Triticeae Research Institute, Sichuan Agricultural UniversityWenjiang, China; Key Laboratory of Crop Genetic Resources and Improvement, Ministry of Education, Sichuan Agricultural UniversityWenjiang, China
| | - Yonghong Zhou
- Triticeae Research Institute, Sichuan Agricultural UniversityWenjiang, China; Key Laboratory of Crop Genetic Resources and Improvement, Ministry of Education, Sichuan Agricultural UniversityWenjiang, China
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7
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Lou H, Dong L, Zhang K, Wang DW, Zhao M, Li Y, Rong C, Qin H, Zhang A, Dong Z, Wang D. High-throughput mining of E-genome-specific SNPs for characterizingThinopyrum elongatumintrogressions in common wheat. Mol Ecol Resour 2017; 17:1318-1329. [DOI: 10.1111/1755-0998.12659] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2015] [Revised: 12/25/2016] [Accepted: 01/30/2017] [Indexed: 01/01/2023]
Affiliation(s)
- Haijuan Lou
- The State Key Laboratory of Plant Cell and Chromosome Engineering; Institute of Genetics and Developmental Biology; Chinese Academy of Sciences; Beijing 100101 China
- University of Chinese Academy of Sciences; Beijing 100049 China
| | - Lingli Dong
- The State Key Laboratory of Plant Cell and Chromosome Engineering; Institute of Genetics and Developmental Biology; Chinese Academy of Sciences; Beijing 100101 China
| | - Kunpu Zhang
- The State Key Laboratory of Plant Cell and Chromosome Engineering; Institute of Genetics and Developmental Biology; Chinese Academy of Sciences; Beijing 100101 China
| | - Da-Wei Wang
- The State Key Laboratory of Plant Cell and Chromosome Engineering; Institute of Genetics and Developmental Biology; Chinese Academy of Sciences; Beijing 100101 China
- University of Chinese Academy of Sciences; Beijing 100049 China
| | - Maolin Zhao
- The State Key Laboratory of Plant Cell and Chromosome Engineering; Institute of Genetics and Developmental Biology; Chinese Academy of Sciences; Beijing 100101 China
| | - Yiwen Li
- The State Key Laboratory of Plant Cell and Chromosome Engineering; Institute of Genetics and Developmental Biology; Chinese Academy of Sciences; Beijing 100101 China
| | - Chaowu Rong
- The State Key Laboratory of Plant Cell and Chromosome Engineering; Institute of Genetics and Developmental Biology; Chinese Academy of Sciences; Beijing 100101 China
| | - Huanju Qin
- The State Key Laboratory of Plant Cell and Chromosome Engineering; Institute of Genetics and Developmental Biology; Chinese Academy of Sciences; Beijing 100101 China
| | - Aimin Zhang
- The State Key Laboratory of Plant Cell and Chromosome Engineering; Institute of Genetics and Developmental Biology; Chinese Academy of Sciences; Beijing 100101 China
| | - Zhenying Dong
- The State Key Laboratory of Plant Cell and Chromosome Engineering; Institute of Genetics and Developmental Biology; Chinese Academy of Sciences; Beijing 100101 China
| | - Daowen Wang
- The State Key Laboratory of Plant Cell and Chromosome Engineering; Institute of Genetics and Developmental Biology; Chinese Academy of Sciences; Beijing 100101 China
- The Collaborative Innovation Center for Grain Crops; Henan Agricultural University; Zhengzhou 450002 China
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Krasileva KV, Vasquez-Gross HA, Howell T, Bailey P, Paraiso F, Clissold L, Simmonds J, Ramirez-Gonzalez RH, Wang X, Borrill P, Fosker C, Ayling S, Phillips AL, Uauy C, Dubcovsky J. Uncovering hidden variation in polyploid wheat. Proc Natl Acad Sci U S A 2017; 114:E913-E921. [PMID: 28096351 PMCID: PMC5307431 DOI: 10.1073/pnas.1619268114] [Citation(s) in RCA: 313] [Impact Index Per Article: 44.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Comprehensive reverse genetic resources, which have been key to understanding gene function in diploid model organisms, are missing in many polyploid crops. Young polyploid species such as wheat, which was domesticated less than 10,000 y ago, have high levels of sequence identity among subgenomes that mask the effects of recessive alleles. Such redundancy reduces the probability of selection of favorable mutations during natural or human selection, but also allows wheat to tolerate high densities of induced mutations. Here we exploited this property to sequence and catalog more than 10 million mutations in the protein-coding regions of 2,735 mutant lines of tetraploid and hexaploid wheat. We detected, on average, 2,705 and 5,351 mutations per tetraploid and hexaploid line, respectively, which resulted in 35-40 mutations per kb in each population. With these mutation densities, we identified an average of 23-24 missense and truncation alleles per gene, with at least one truncation or deleterious missense mutation in more than 90% of the captured wheat genes per population. This public collection of mutant seed stocks and sequence data enables rapid identification of mutations in the different copies of the wheat genes, which can be combined to uncover previously hidden variation. Polyploidy is a central phenomenon in plant evolution, and many crop species have undergone recent genome duplication events. Therefore, the general strategy and methods developed herein can benefit other polyploid crops.
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Affiliation(s)
- Ksenia V Krasileva
- Department of Plant Sciences, University of California, Davis, CA 95616
- The Sainsbury Laboratory, Norwich NR4 7UH, United Kingdom
- The Earlham Institute, Norwich NR4 7UG, United Kingdom
| | | | - Tyson Howell
- Department of Plant Sciences, University of California, Davis, CA 95616
| | - Paul Bailey
- The Earlham Institute, Norwich NR4 7UG, United Kingdom
| | - Francine Paraiso
- Department of Plant Sciences, University of California, Davis, CA 95616
| | - Leah Clissold
- The Earlham Institute, Norwich NR4 7UG, United Kingdom
| | | | - Ricardo H Ramirez-Gonzalez
- The Earlham Institute, Norwich NR4 7UG, United Kingdom
- John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Xiaodong Wang
- Department of Plant Sciences, University of California, Davis, CA 95616
| | | | | | - Sarah Ayling
- The Earlham Institute, Norwich NR4 7UG, United Kingdom
| | | | | | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, CA 95616;
- Howard Hughes Medical Institute, Chevy Chase, MD 20815
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Chopra R, Burow G, Simpson CE, Chagoya J, Mudge J, Burow MD. Transcriptome Sequencing of Diverse Peanut (Arachis) Wild Species and the Cultivated Species Reveals a Wealth of Untapped Genetic Variability. G3 (Bethesda) 2016; 6:3825-36. [PMID: 27729436 DOI: 10.1534/g3.115.026898] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
To test the hypothesis that the cultivated peanut species possesses almost no molecular variability, we sequenced a diverse panel of 22 Arachis accessions representing Arachis hypogaea botanical classes, A-, B-, and K- genome diploids, a synthetic amphidiploid, and a tetraploid wild species. RNASeq was performed on pools of three tissues, and de novo assembly was performed. Realignment of individual accession reads to transcripts of the cultivar OLin identified 306,820 biallelic SNPs. Among 10 naturally occurring tetraploid accessions, 40,382 unique homozygous SNPs were identified in 14,719 contigs. In eight diploid accessions, 291,115 unique SNPs were identified in 26,320 contigs. The average SNP rate among the 10 cultivated tetraploids was 0.5, and among eight diploids was 9.2 per 1000 bp. Diversity analysis indicated grouping of diploids according to genome classification, and cultivated tetraploids by subspecies. Cluster analysis of variants indicated that sequences of B genome species were the most similar to the tetraploids, and the next closest diploid accession belonged to the A genome species. A subset of 66 SNPs selected from the dataset was validated; of 782 SNP calls, 636 (81.32%) were confirmed using an allele-specific discrimination assay. We conclude that substantial genetic variability exists among wild species. Additionally, significant but lesser variability at the molecular level occurs among accessions of the cultivated species. This survey is the first to report significant SNP level diversity among transcripts, and may explain some of the phenotypic differences observed in germplasm surveys. Understanding SNP variants in the Arachis accessions will benefit in developing markers for selection.
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Gruber MY, Xia J, Yu M, Steppuhn H, Wall K, Messer D, Sharpe AG, Acharya SN, Wishart DS, Johnson D, Miller DR, Taheri A. Transcript analysis in two alfalfa salt tolerance selected breeding populations relative to a non-tolerant population. Genome 2016; 60:104-127. [PMID: 28045337 DOI: 10.1139/gen-2016-0111] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
With the growing limitations on arable land, alfalfa (a widely cultivated, low-input forage) is now being selected to extend cultivation into saline lands for low-cost biofeedstock purposes. Here, minerals and transcriptome profiles were compared between two new salinity-tolerant North American alfalfa breeding populations and a more salinity-sensitive western Canadian alfalfa population grown under hydroponic saline conditions. All three populations accumulated two-fold higher sodium in roots than shoots as a function of increased electrical conductivity. At least 50% of differentially expressed genes (p < 0.05) were down-regulated in the salt-sensitive population growing under high salinity, while expression remained unchanged in the saline-tolerant populations. In particular, most reduction in transcript levels in the salt-sensitive population was observed in genes specifying cell wall structural components, lipids, secondary metabolism, auxin and ethylene hormones, development, transport, signalling, heat shock, proteolysis, pathogenesis-response, abiotic stress, RNA processing, and protein metabolism. Transcript diversity for transcription factors, protein modification, and protein degradation genes was also more strongly affected in salt-tolerant CW064027 than in salt-tolerant Bridgeview and salt-sensitive Rangelander, while both saline-tolerant populations showed more substantial up-regulation in redox-related genes and B-ZIP transcripts. The report highlights the first use of bulked genotypes as replicated samples to compare the transcriptomes of obligate out-cross breeding populations in alfalfa.
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Affiliation(s)
- M Y Gruber
- a Saskatoon Research Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7J 0X2, Canada.,b Department of Computing Science, University of Alberta, 2-21 Athabasca Hall, Edmonton, AB T6G 2R3, Canada
| | - J Xia
- b Department of Computing Science, University of Alberta, 2-21 Athabasca Hall, Edmonton, AB T6G 2R3, Canada
| | - M Yu
- a Saskatoon Research Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7J 0X2, Canada
| | - H Steppuhn
- c Semiarid Prairie Agricultural Research Centre, Agriculture and Agri-Food Canada, P.O. Box 1030, Swift Current, SK S9H 3X2, Canada
| | - K Wall
- c Semiarid Prairie Agricultural Research Centre, Agriculture and Agri-Food Canada, P.O. Box 1030, Swift Current, SK S9H 3X2, Canada
| | - D Messer
- c Semiarid Prairie Agricultural Research Centre, Agriculture and Agri-Food Canada, P.O. Box 1030, Swift Current, SK S9H 3X2, Canada
| | - A G Sharpe
- d National Research Council, 110 Gymnasium Pl., Saskatoon, SK S7N 0W9, Canada
| | - S N Acharya
- e AAFC Lethbridge Research Centre, Agriculture and Agri-Food Canada, 5403 - 1st Avenue S., Lethbridge, AB T1J 4B1, Canada
| | - D S Wishart
- b Department of Computing Science, University of Alberta, 2-21 Athabasca Hall, Edmonton, AB T6G 2R3, Canada.,f Department of Biological Sciences, University of Alberta, 11455 Saskatchewan Drive, Edmonton, AB T6G 2R3, Canada
| | - D Johnson
- g Alforex Seeds, an affiliate of Dow AgroSciences, N4505 CTH M, West Salem, WI 54669, USA
| | - D R Miller
- g Alforex Seeds, an affiliate of Dow AgroSciences, N4505 CTH M, West Salem, WI 54669, USA
| | - A Taheri
- a Saskatoon Research Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7J 0X2, Canada
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Rabiger DS, Taylor JM, Spriggs A, Hand ML, Henderson ST, Johnson SD, Oelkers K, Hrmova M, Saito K, Suzuki G, Mukai Y, Carroll BJ, Koltunow AMG. Generation of an integrated Hieracium genomic and transcriptomic resource enables exploration of small RNA pathways during apomixis initiation. BMC Biol 2016; 14:86. [PMID: 27716180 PMCID: PMC5054587 DOI: 10.1186/s12915-016-0311-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 09/21/2016] [Indexed: 11/23/2022] Open
Abstract
Background Application of apomixis, or asexual seed formation, in crop breeding would allow rapid fixation of complex traits, economizing improved crop delivery. Identification of apomixis genes is confounded by the polyploid nature, high genome complexity and lack of genomic sequence integration with reproductive tissue transcriptomes in most apomicts. Results A genomic and transcriptomic resource was developed for Hieracium subgenus Pilosella (Asteraceae) which incorporates characterized sexual, apomictic and mutant apomict plants exhibiting reversion to sexual reproduction. Apomicts develop additional female gametogenic cells that suppress the sexual pathway in ovules. Disrupting small RNA pathways in sexual Arabidopsis also induces extra female gametogenic cells; therefore, the resource was used to examine if changes in small RNA pathways correlate with apomixis initiation. An initial characterization of small RNA pathway genes within Hieracium was undertaken, and ovary-expressed ARGONAUTE genes were identified and cloned. Comparisons of whole ovary transcriptomes from mutant apomicts, relative to the parental apomict, revealed that differentially expressed genes were enriched for processes involved in small RNA biogenesis and chromatin silencing. Small RNA profiles within mutant ovaries did not reveal large-scale alterations in composition or length distributions; however, a small number of differentially expressed, putative small RNA targets were identified. Conclusions The established Hieracium resource represents a substantial contribution towards the investigation of early sexual and apomictic female gamete development, and the generation of new candidate genes and markers. Observed changes in small RNA targets and biogenesis pathways within sexual and apomictic ovaries will underlie future functional research into apomixis initiation in Hieracium. Electronic supplementary material The online version of this article (doi:10.1186/s12915-016-0311-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- David S Rabiger
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Private Bag 2, Glen Osmond, South Australia, 5064, Australia
| | - Jennifer M Taylor
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Bellenden Street, Crace, Australian Capital Territory, 2911, Australia
| | - Andrew Spriggs
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Bellenden Street, Crace, Australian Capital Territory, 2911, Australia
| | - Melanie L Hand
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Private Bag 2, Glen Osmond, South Australia, 5064, Australia
| | - Steven T Henderson
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Private Bag 2, Glen Osmond, South Australia, 5064, Australia
| | - Susan D Johnson
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Private Bag 2, Glen Osmond, South Australia, 5064, Australia
| | - Karsten Oelkers
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Private Bag 2, Glen Osmond, South Australia, 5064, Australia
| | - Maria Hrmova
- Australian Centre for Plant Functional Genomics, University of Adelaide PMB 1, Glen Osmond, South Australia, 5064, Australia
| | - Keisuke Saito
- Division of Natural Science, Osaka Kyoiku University, Osaka, 582-8582, Japan
| | - Go Suzuki
- Division of Natural Science, Osaka Kyoiku University, Osaka, 582-8582, Japan
| | - Yasuhiko Mukai
- Division of Natural Science, Osaka Kyoiku University, Osaka, 582-8582, Japan
| | - Bernard J Carroll
- School of Chemistry and Molecular Biosciences, University of Queensland, St. Lucia, Queensland, 4072, Australia
| | - Anna M G Koltunow
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Private Bag 2, Glen Osmond, South Australia, 5064, Australia.
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Wang Y, Wang C, Wang X, Peng F, Wang R, Jiang Y, Zeng J, Fan X, Kang H, Sha L, Zhang H, Xiao X, Zhou Y. De Novo Sequencing and Characterization of the Transcriptome of Dwarf Polish Wheat (Triticum polonicum L.). Int J Genomics 2016; 2016:5781412. [PMID: 27429972 DOI: 10.1155/2016/5781412] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 04/12/2016] [Accepted: 05/31/2016] [Indexed: 12/02/2022] Open
Abstract
Construction as well as characterization of a polish wheat transcriptome is a crucial step to study useful traits of polish wheat. In this study, a transcriptome, including 76,014 unigenes, was assembled from dwarf polish wheat (DPW) roots, stems, and leaves using the software of Trinity. Among these unigenes, 61,748 (81.23%) unigenes were functionally annotated in public databases and classified into differentially functional types. Aligning this transcriptome against draft wheat genome released by the International Wheat Genome Sequencing Consortium (IWGSC), 57,331 (75.42%) unigenes, including 26,122 AB-specific and 2,622 D-specific unigenes, were mapped on A, B, and/or D genomes. Compared with the transcriptome of T. turgidum, 56,343 unigenes were matched with 103,327 unigenes of T. turgidum. Compared with the genomes of rice and barley, 14,404 and 7,007 unigenes were matched with 14,608 genes of barley and 7,708 genes of rice, respectively. On the other hand, 2,148, 1,611, and 2,707 unigenes were expressed specifically in roots, stems, and leaves, respectively. Finally, 5,531 SSR sequences were observed from 4,531 unigenes, and 518 primer pairs were designed.
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Glover NM, Redestig H, Dessimoz C. Homoeologs: What Are They and How Do We Infer Them? Trends Plant Sci 2016; 21:609-621. [PMID: 27021699 PMCID: PMC4920642 DOI: 10.1016/j.tplants.2016.02.005] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Revised: 02/09/2016] [Accepted: 02/20/2016] [Indexed: 05/18/2023]
Abstract
The evolutionary history of nearly all flowering plants includes a polyploidization event. Homologous genes resulting from allopolyploidy are commonly referred to as 'homoeologs', although this term has not always been used precisely or consistently in the literature. With several allopolyploid genome sequencing projects under way, there is a pressing need for computational methods for homoeology inference. Here we review the definition of homoeology in historical and modern contexts and propose a precise and testable definition highlighting the connection between homoeologs and orthologs. In the second part, we survey experimental and computational methods of homoeolog inference, considering the strengths and limitations of each approach. Establishing a precise and evolutionarily meaningful definition of homoeology is essential for understanding the evolutionary consequences of polyploidization.
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Affiliation(s)
- Natasha M Glover
- Bayer CropScience NV, Technologiepark 38, 9052 Gent, Belgium; University College London, Gower Street, London WC1E 6BT, UK
| | | | - Christophe Dessimoz
- University College London, Gower Street, London WC1E 6BT, UK; University of Lausanne, Biophore, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, Biophore, 1015 Lausanne, Switzerland.
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14
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Wang Y, Xiao X, Wang X, Zeng J, Kang H, Fan X, Sha L, Zhang H, Zhou Y. RNA-Seq and iTRAQ Reveal the Dwarfing Mechanism of Dwarf Polish Wheat (Triticum polonicum L.). Int J Biol Sci 2016; 12:653-66. [PMID: 27194943 PMCID: PMC4870709 DOI: 10.7150/ijbs.14577] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 02/15/2016] [Indexed: 11/05/2022] Open
Abstract
The dwarfing mechanism of Rht-dp in dwarf Polish wheat (DPW) is unknown. Each internode of DPW was significantly shorter than it in high Polish wheat (HPW), and the dwarfism was insensitive to photoperiod, abscisic acid (ABA), gibberellin (GA), cytokinin (CK), auxin and brassinolide (BR). To understand the mechanism, three sets of transcripts, DPW, HPW, and a chimeric set (a combination of DPW and HPW), were constructed using RNA sequencing (RNA-Seq). Based on the chimeric transcripts, 2,446 proteins were identified using isobaric tags for relative and absolute quantification (iTRAQ). A total of 108 unigenes and 12 proteins were considered as dwarfism-related differentially expressed genes (DEGs) and differentially expressed proteins (DEPs), respectively. Among of these DEGs and DEPs, 6 DEGs and 6 DEPs were found to be involved in flavonoid and S-adenosyl-methionine (SAM) metabolisms; 5 DEGs and 3 DEPs were involved in cellulose metabolism, cell wall plasticity and cell expansion; 2 DEGs were auxin transporters; 2 DEPs were histones; 1 DEP was a peroxidase. These DEGs and DEPs reduced lignin and cellulose contents, increased flavonoid content, possibly decreased S-adenosyl-methionine (SAM) and polyamine contents and increased S-adenosyl-L-homocysteine hydrolase (SAHH) content in DPW stems, which could limit auxin transport and reduce extensibility of the cell wall, finally limited cell expansion (the cell size of DPW was significantly smaller than HPW cells) and caused dwarfism in DPW.
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Affiliation(s)
- Yi Wang
- 1. Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China
| | - Xue Xiao
- 1. Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China
| | - Xiaolu Wang
- 1. Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China
| | - Jian Zeng
- 2. College of Resources, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China
| | - Houyang Kang
- 1. Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China
| | - Xing Fan
- 1. Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China
| | - Lina Sha
- 1. Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China
| | - Haiqin Zhang
- 1. Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China
| | - Yonghong Zhou
- 1. Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China
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Chandra S, Singh D, Pathak J, Kumari S, Kumar M, Poddar R, Balyan HS, Gupta PK, Prabhu KV, Mukhopadhyay K. De Novo Assembled Wheat Transcriptomes Delineate Differentially Expressed Host Genes in Response to Leaf Rust Infection. PLoS One 2016; 11:e0148453. [PMID: 26840746 PMCID: PMC4739524 DOI: 10.1371/journal.pone.0148453] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 01/17/2016] [Indexed: 11/20/2022] Open
Abstract
Pathogens like Puccinia triticina, the causal organism for leaf rust, extensively damages wheat production. The interaction at molecular level between wheat and the pathogen is complex and less explored. The pathogen induced response was characterized using mock- or pathogen inoculated near-isogenic wheat lines (with or without seedling leaf rust resistance gene Lr28). Four Serial Analysis of Gene Expression libraries were prepared from mock- and pathogen inoculated plants and were subjected to Sequencing by Oligonucleotide Ligation and Detection, which generated a total of 165,767,777 reads, each 35 bases long. The reads were processed and multiple k-mers were attempted for de novo transcript assembly; 22 k-mers showed the best results. Altogether 21,345 contigs were generated and functionally characterized by gene ontology annotation, mining for transcription factors and resistance genes. Expression analysis among the four libraries showed extensive alterations in the transcriptome in response to pathogen infection, reflecting reorganizations in major biological processes and metabolic pathways. Role of auxin in determining pathogenesis in susceptible and resistant lines were imperative. The qPCR expression study of four LRR-RLK (Leucine-rich repeat receptor-like protein kinases) genes showed higher expression at 24 hrs after inoculation with pathogen. In summary, the conceptual model of induced resistance in wheat contributes insights on defense responses and imparts knowledge of Puccinia triticina-induced defense transcripts in wheat plants.
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Affiliation(s)
- Saket Chandra
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi 835215 Jharkhand, India
| | - Dharmendra Singh
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi 835215 Jharkhand, India
| | - Jyoti Pathak
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi 835215 Jharkhand, India
| | - Supriya Kumari
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut 200005, Uttar Pradesh, India
| | - Manish Kumar
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi 835215 Jharkhand, India
| | - Raju Poddar
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi 835215 Jharkhand, India
| | - Harindra Singh Balyan
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut 200005, Uttar Pradesh, India
| | - Puspendra Kumar Gupta
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut 200005, Uttar Pradesh, India
| | - Kumble Vinod Prabhu
- Division of Genetics, Indian Agricultural Research Institute, New Delhi 110012, India
| | - Kunal Mukhopadhyay
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi 835215 Jharkhand, India
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16
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Zhang N, Wang S, Zhang X, Dong Z, Chen F, Cui D. Transcriptome analysis of the Chinese bread wheat cultivar Yunong 201 and its ethyl methanesulfonate mutant line. Gene 2016; 575:285-93. [PMID: 26342963 DOI: 10.1016/j.gene.2015.09.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2015] [Revised: 08/26/2015] [Accepted: 09/01/2015] [Indexed: 12/20/2022]
Abstract
Roche 454 next-generation sequencing was applied to obtain extensive information about the transcriptomes of the bread wheat cultivar Yunong 201 and its EMS mutant line Yunong 3114. Totals of 1.43 million and 1.44 million raw reads were generated, 14,432, 17,845 and 27,867 isotigs were constructed using the reads in Yunong 201, Yunong 3114 and their combination, respectively. Moreover, 29,042, 34,722, and 48,486 unigenes were generated in Yunong 201, Yunong 3114, and combined cultivars, respectively. A total of 50,382 and 59,891 unigenes from the Yunong 201 and Yunong 3114 were mapped on different chromosomes. Of all unigenes, 1363 DEGs were identified in Yunong 201 and Yunong 3114. qRT-PCR analysis confirmed the expression profiles of 40 candidate unigenes possibly related to abiotic stresses. The expression patterns of four annotated DEGs were also verified in the two wheat cultivars under abiotic stresses. This study provided useful information for further analysis of wheat functional genomics.
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Affiliation(s)
- Ning Zhang
- Agronomy College, Collaborative Innovation Center of Henan Grain Crops, National Key Laboratory of Wheat and Corn Crop, Henan Agricultural University, Zhengzhou 450002, China.
| | - Shasha Wang
- Agronomy College, Collaborative Innovation Center of Henan Grain Crops, National Key Laboratory of Wheat and Corn Crop, Henan Agricultural University, Zhengzhou 450002, China.
| | - Xiangfen Zhang
- Agronomy College, Collaborative Innovation Center of Henan Grain Crops, National Key Laboratory of Wheat and Corn Crop, Henan Agricultural University, Zhengzhou 450002, China.
| | - Zhongdong Dong
- Agronomy College, Collaborative Innovation Center of Henan Grain Crops, National Key Laboratory of Wheat and Corn Crop, Henan Agricultural University, Zhengzhou 450002, China.
| | - Feng Chen
- Agronomy College, Collaborative Innovation Center of Henan Grain Crops, National Key Laboratory of Wheat and Corn Crop, Henan Agricultural University, Zhengzhou 450002, China.
| | - Dangqun Cui
- Agronomy College, Collaborative Innovation Center of Henan Grain Crops, National Key Laboratory of Wheat and Corn Crop, Henan Agricultural University, Zhengzhou 450002, China.
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17
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Chen F, Zhu Z, Zhou X, Yan Y, Dong Z, Cui D. High-Throughput Sequencing Reveals Single Nucleotide Variants in Longer-Kernel Bread Wheat. Front Plant Sci 2016; 7:1193. [PMID: 27551288 PMCID: PMC4976665 DOI: 10.3389/fpls.2016.01193] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 07/25/2016] [Indexed: 05/09/2023]
Abstract
The transcriptomes of bread wheat Yunong 201 and its ethyl methanesulfonate derivative Yunong 3114 were obtained by next-sequencing technology. Single nucleotide variants (SNVs) in the wheat strains were explored and compared. A total of 5907 and 6287 non-synonymous SNVs were acquired for Yunong 201 and 3114, respectively. A total of 4021 genes with SNVs were obtained. The genes that underwent non-synonymous SNVs were significantly involved in ATP binding, protein phosphorylation, and cellular protein metabolic process. The heat map analysis also indicated that most of these mutant genes were significantly differentially expressed at different developmental stages. The SNVs in these genes possibly contribute to the longer kernel length of Yunong 3114. Our data provide useful information on wheat transcriptome for future studies on wheat functional genomics. This study could also help in illustrating the gene functions of the non-synonymous SNVs of Yunong 201 and 3114.
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18
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Li X, Gao S, Tang Y, Li L, Zhang F, Feng B, Fang Z, Ma L, Zhao C. Genome-wide identification and evolutionary analyses of bZIP transcription factors in wheat and its relatives and expression profiles of anther development related TabZIP genes. BMC Genomics 2015; 16:976. [PMID: 26581444 PMCID: PMC4652339 DOI: 10.1186/s12864-015-2196-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 11/05/2015] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Among the largest and most diverse transcription factor families in plants, basic leucine zipper (bZIP) family participate in regulating various processes, including floral induction and development, stress and hormone signaling, photomorphogenesis, seed maturation and germination, and pathogen defense. Although common wheat (Triticum aestivum L.) is one of the most widely cultivated and consumed food crops in the world, there is no comprehensive analysis of bZIPs in wheat, especially those involved in anther development. Previous studies have demonstrated wheat, T. urartu, Ae. tauschii, barley and Brachypodium are evolutionarily close in Gramineae family, however, the real evolutionary relationship still remains mysterious. RESULTS In this study, 187 bZIP family genes were comprehensively identified from current wheat genome. 98, 96 and 107 members of bZIP family were also identified from the genomes of T.urartu, Ae.tauschii and barley, respectively. Orthology analyses suggested 69.4 % of TubZIPs were orthologous to 68.8 % of AetbZIPs and wheat had many more in-paralogs in the bZIP family than its relatives. It was deduced wheat had a closer phylogenetic relationship with barley and Brachypodium than T.urartu and Ae.tauschii. bZIP proteins in wheat, T.urartu and Ae.tauschii were divided into 14 subgroups based on phylogenetic analyses. Using Affymetrix microarray data, 48 differentially expressed TabZIP genes were identified to be related to anther development from comparison between the male sterility line and the restorer line. Genes with close evolutionary relationship tended to share similar gene structures. 15 of 23 selected TabZIP genes contained LTR elements in their promoter regions. Expression of 21 among these 23 TabZIP genes were obviously responsive to low temperature. These 23 TabZIP genes all exhibited distinct tissue-specific expression pattern. Among them, 11 TabZIP genes were predominantly expressed in anther and most of them showed over-dominance expression mode in the cross combination TY806 × BS366. CONCLUSIONS The genome-wide identification provided an overall insight of bZIP gene family in wheat and its relatives. The evolutionary relationship of wheat and its relatives was proposed based on orthology analyses. Microarray and expression analyses suggested the potential involvement of bZIP genes in anther development and facilitated selection of anther development related gene for further functional characterization.
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Affiliation(s)
- Xueyin Li
- Beijing Engineering Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
- College of Agronomy, Northwest A & F University, Yangling, 712100, China.
| | - Shiqing Gao
- Beijing Engineering Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
| | - Yimiao Tang
- Beijing Engineering Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
| | - Lei Li
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, College of Life Sciences, Peking University, Beijing, 100871, China.
| | - Fengjie Zhang
- Beijing Engineering Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
- College of Agriculture, Shanxi Agricultural University, Taigu, 030800, China.
| | - Biane Feng
- Beijing Engineering Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
- College of Agriculture, Shanxi Agricultural University, Taigu, 030800, China.
| | - Zhaofeng Fang
- Beijing Engineering Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
| | - Lingjian Ma
- College of Agronomy, Northwest A & F University, Yangling, 712100, China.
| | - Changping Zhao
- Beijing Engineering Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
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Aramrak A, Kidwell KK, Steber CM, Burke IC. Molecular and phylogenetic characterization of the homoeologous EPSP Synthase genes of allohexaploid wheat, Triticum aestivum (L.). BMC Genomics 2015; 16:844. [PMID: 26492960 PMCID: PMC4619226 DOI: 10.1186/s12864-015-2084-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 10/14/2015] [Indexed: 01/08/2023] Open
Abstract
Background 5-Enolpyruvylshikimate-3-phosphate synthase (EPSPS) is the sixth and penultimate enzyme in the shikimate biosynthesis pathway, and is the target of the herbicide glyphosate. The EPSPS genes of allohexaploid wheat (Triticum aestivum, AABBDD) have not been well characterized. Herein, the three homoeologous copies of the allohexaploid wheat EPSPS gene were cloned and characterized. Methods Genomic and coding DNA sequences of EPSPS from the three related genomes of allohexaploid wheat were isolated using PCR and inverse PCR approaches from soft white spring “Louise’. Development of genome-specific primers allowed the mapping and expression analysis of TaEPSPS-7A1, TaEPSPS-7D1, and TaEPSPS-4A1 on chromosomes 7A, 7D, and 4A, respectively. Sequence alignments of cDNA sequences from wheat and wheat relatives served as a basis for phylogenetic analysis. Results The three genomic copies of wheat EPSPS differed by insertion/deletion and single nucleotide polymorphisms (SNPs), largely in intron sequences. RT-PCR analysis and cDNA cloning revealed that EPSPS is expressed from all three genomic copies. However, TaEPSPS-4A1 is expressed at much lower levels than TaEPSPS-7A1 and TaEPSPS-7D1 in wheat seedlings. Phylogenetic analysis of 1190-bp cDNA clones from wheat and wheat relatives revealed that: 1) TaEPSPS-7A1 is most similar to EPSPS from the tetraploid AB genome donor, T. turgidum (99.7 % identity); 2) TaEPSPS-7D1 most resembles EPSPS from the diploid D genome donor, Aegilops tauschii (100 % identity); and 3) TaEPSPS-4A1 resembles EPSPS from the diploid B genome relative, Ae. speltoides (97.7 % identity). Thus, EPSPS sequences in allohexaploid wheat are preserved from the most two recent ancestors. The wheat EPSPS genes are more closely related to Lolium multiflorum and Brachypodium distachyon than to Oryza sativa (rice). Conclusions The three related EPSPS homoeologues of wheat exhibited conservation of the exon/intron structure and of coding region sequence, but contained significant sequence variation within intron regions. The genome-specific primers developed will enable future characterization of natural and induced variation in EPSPS sequence and expression. This can be useful in investigating new causes of glyphosate herbicide resistance. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2084-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Attawan Aramrak
- Department of Crop and Soil Science, Washington State University, Pullman, WA, USA.
| | - Kimberlee K Kidwell
- Department of Crop and Soil Science, Washington State University, Pullman, WA, USA.
| | - Camille M Steber
- Department of Crop and Soil Science, Washington State University, Pullman, WA, USA. .,Wheat Genetics, Quality, Physiology and Disease Research, USDA-ARS, Pullman, WA, USA.
| | - Ian C Burke
- Department of Crop and Soil Science, Washington State University, Pullman, WA, USA.
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20
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He B, Zhao S, Chen Y, Cao Q, Wei C, Cheng X, Zhang Y. Optimal assembly strategies of transcriptome related to ploidies of eukaryotic organisms. BMC Genomics 2015; 16:65. [PMID: 25759274 PMCID: PMC4343054 DOI: 10.1186/s12864-014-1192-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 12/22/2014] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Several de novo transcriptome assemblers have been developed recently to assemble the short reads generated from the next-generation sequencing platforms and different strategies were employed for assembling transcriptomes of various eukaryotes without genome sequences. Though there are some comparisons among these de novo assembly tools for assembling transcriptomes of different eukaryotic organisms, there is no report about the relationship between assembly strategies and ploidies of the organisms. RESULTS When we de novo assembled transcriptomes of sweet potato (hexaploid), Trametes gallica (a diploid fungus), Oryza meyeriana (a diploid wild rice), five assemblers, including Edena, Oases, Soaptrans, IDBA-tran and Trinity, were used in different strategies (Single-Assembler Single-Parameter, SASP; Single-Assembler Multiple-Parameters, SAMP; Combined De novo Transcriptome Assembly, CDTA, that is multiple assembler multiple parameter). It was found that CDTA strategy has the best performance compared with other two strategies for assembling transcriptome of the hexaploid sweet potato, whereas SAMP strategy with assembler Oases is better than other strategies for assembling transcriptomes of diploid fungus and the wild rice transcriptomes. CONCLUSION Based on the results from ours and others, it is suggested that CDTA strategy is better used for transcriptome assembly of polyploidy organisms and SAMP strategy of Oases is outperformed for those diploid organisms without genome sequences.
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Affiliation(s)
- Bin He
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, 610064, Chengdu, China.
| | - Shirong Zhao
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, 610064, Chengdu, China.
| | - Yuehong Chen
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, 610064, Chengdu, China.
| | - Qinghua Cao
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, 610064, Chengdu, China.
| | - Changhe Wei
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, 610064, Chengdu, China.
| | - Xiaojie Cheng
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, 610064, Chengdu, China.
| | - Yizheng Zhang
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, 610064, Chengdu, China.
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Lucas SJ, Akpınar BA, Šimková H, Kubaláková M, Doležel J, Budak H. Next-generation sequencing of flow-sorted wheat chromosome 5D reveals lineage-specific translocations and widespread gene duplications. BMC Genomics 2014; 15:1080. [PMID: 25487001 PMCID: PMC4298962 DOI: 10.1186/1471-2164-15-1080] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 11/26/2014] [Indexed: 11/14/2022] Open
Abstract
Background The ~17 Gb hexaploid bread wheat genome is a high priority and a major technical challenge for genomic studies. In particular, the D sub-genome is relatively lacking in genetic diversity, making it both difficult to map genetically, and a target for introgression of agriculturally useful traits. Elucidating its sequence and structure will therefore facilitate wheat breeding and crop improvement. Results We generated shotgun sequences from each arm of flow-sorted Triticum aestivum chromosome 5D using 454 FLX Titanium technology, giving 1.34× and 1.61× coverage of the short (5DS) and long (5DL) arms of the chromosome respectively. By a combination of sequence similarity and assembly-based methods, ~74% of the sequence reads were classified as repetitive elements, and coding sequence models of 1314 (5DS) and 2975 (5DL) genes were generated. The order of conserved genes in syntenic regions of previously sequenced grass genomes were integrated with physical and genetic map positions of 518 wheat markers to establish a virtual gene order for chromosome 5D. Conclusions The virtual gene order revealed a large-scale chromosomal rearrangement in the peri-centromeric region of 5DL, and a concentration of non-syntenic genes in the telomeric region of 5DS. Although our data support the large-scale conservation of Triticeae chromosome structure, they also suggest that some regions are evolving rapidly through frequent gene duplications and translocations. Sequence accessions EBI European Nucleotide Archive, Study no. ERP002330 Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1080) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | - Hikmet Budak
- Faculty of Engineering and Natural Sciences, Sabanci University, Orhanlı, 34956 Tuzla, Istanbul, Turkey.
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Cannarozzi G, Plaza-Wüthrich S, Esfeld K, Larti S, Wilson YS, Girma D, de Castro E, Chanyalew S, Blösch R, Farinelli L, Lyons E, Schneider M, Falquet L, Kuhlemeier C, Assefa K, Tadele Z. Genome and transcriptome sequencing identifies breeding targets in the orphan crop tef (Eragrostis tef). BMC Genomics 2014; 15:581. [PMID: 25007843 PMCID: PMC4119204 DOI: 10.1186/1471-2164-15-581] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 07/03/2014] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Tef (Eragrostis tef), an indigenous cereal critical to food security in the Horn of Africa, is rich in minerals and protein, resistant to many biotic and abiotic stresses and safe for diabetics as well as sufferers of immune reactions to wheat gluten. We present the genome of tef, the first species in the grass subfamily Chloridoideae and the first allotetraploid assembled de novo. We sequenced the tef genome for marker-assisted breeding, to shed light on the molecular mechanisms conferring tef's desirable nutritional and agronomic properties, and to make its genome publicly available as a community resource. RESULTS The draft genome contains 672 Mbp representing 87% of the genome size estimated from flow cytometry. We also sequenced two transcriptomes, one from a normalized RNA library and another from unnormalized RNASeq data. The normalized RNA library revealed around 38000 transcripts that were then annotated by the SwissProt group. The CoGe comparative genomics platform was used to compare the tef genome to other genomes, notably sorghum. Scaffolds comprising approximately half of the genome size were ordered by syntenic alignment to sorghum producing tef pseudo-chromosomes, which were sorted into A and B genomes as well as compared to the genetic map of tef. The draft genome was used to identify novel SSR markers, investigate target genes for abiotic stress resistance studies, and understand the evolution of the prolamin family of proteins that are responsible for the immune response to gluten. CONCLUSIONS It is highly plausible that breeding targets previously identified in other cereal crops will also be valuable breeding targets in tef. The draft genome and transcriptome will be of great use for identifying these targets for genetic improvement of this orphan crop that is vital for feeding 50 million people in the Horn of Africa.
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Affiliation(s)
- Gina Cannarozzi
- />Institute of Plant Sciences, University of Bern, Altenbergrain 21, Bern, CH-3013 Switzerland
- />Swiss Institute of Bioinformatics, Vital-IT, Quartier Sorge - Batiment Genopode, Lausanne, 1015 Switzerland
| | - Sonia Plaza-Wüthrich
- />Institute of Plant Sciences, University of Bern, Altenbergrain 21, Bern, CH-3013 Switzerland
| | - Korinna Esfeld
- />Institute of Plant Sciences, University of Bern, Altenbergrain 21, Bern, CH-3013 Switzerland
| | - Stéphanie Larti
- />Institute of Plant Sciences, University of Bern, Altenbergrain 21, Bern, CH-3013 Switzerland
- />Clinic for Parodontology, University of Bern, Freiburgstrasse 7, Bern, CH-3010 Switzerland
| | - Yi Song Wilson
- />Institute of Plant Sciences, University of Bern, Altenbergrain 21, Bern, CH-3013 Switzerland
| | - Dejene Girma
- />Institute of Plant Sciences, University of Bern, Altenbergrain 21, Bern, CH-3013 Switzerland
- />Ethiopian Institute of Agricultural Research, National Biotechnology Laboratory (Holetta), P.O. Box 2003, Addis Ababa, Ethiopia
| | - Edouard de Castro
- />Swiss Institute of Bioinformatics, Rue Michel-Servet 1, 1211 Geneva 4, Switzerland
| | - Solomon Chanyalew
- />Ethiopian Institute of Agricultural Research, Debre Zeit Agricultural Research Center, P.O. Box 32, Debre Zeit, Ethiopia
| | - Regula Blösch
- />Institute of Plant Sciences, University of Bern, Altenbergrain 21, Bern, CH-3013 Switzerland
| | - Laurent Farinelli
- />Fasteris SA, Ch. du Pont-du-Centenaire 109, P.O. Box 28, Plan-les-Ouates, CH-1228 Switzerland
| | - Eric Lyons
- />School of Plant Sciences, Univerisity of Arizona, 1140 E. South Campus Drive, 303 Forbes Building, P.O. Box 210036, Tucson, AZ 85721-0036 USA
| | - Michel Schneider
- />Swiss Institute of Bioinformatics, Rue Michel-Servet 1, 1211 Geneva 4, Switzerland
| | - Laurent Falquet
- />Swiss Institute of Bioinformatics, Vital-IT, Quartier Sorge - Batiment Genopode, Lausanne, 1015 Switzerland
- />Faculty of Science, University of Fribourg, Ch. du Musée 10, Fribourg, CH-1700 Switzerland
| | - Cris Kuhlemeier
- />Institute of Plant Sciences, University of Bern, Altenbergrain 21, Bern, CH-3013 Switzerland
| | - Kebebew Assefa
- />Ethiopian Institute of Agricultural Research, Debre Zeit Agricultural Research Center, P.O. Box 32, Debre Zeit, Ethiopia
| | - Zerihun Tadele
- />Institute of Plant Sciences, University of Bern, Altenbergrain 21, Bern, CH-3013 Switzerland
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Camilios-Neto D, Bonato P, Wassem R, Tadra-Sfeir MZ, Brusamarello-Santos LCC, Valdameri G, Donatti L, Faoro H, Weiss VA, Chubatsu LS, Pedrosa FO, Souza EM. Dual RNA-seq transcriptional analysis of wheat roots colonized by Azospirillum brasilense reveals up-regulation of nutrient acquisition and cell cycle genes. BMC Genomics 2014; 15:378. [PMID: 24886190 PMCID: PMC4042000 DOI: 10.1186/1471-2164-15-378] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 05/02/2014] [Indexed: 12/20/2022] Open
Abstract
Background The rapid growth of the world’s population demands an increase in food production that no longer can be reached by increasing amounts of nitrogenous fertilizers. Plant growth promoting bacteria (PGPB) might be an alternative to increase nitrogenous use efficiency (NUE) in important crops such wheat. Azospirillum brasilense is one of the most promising PGPB and wheat roots colonized by A. brasilense is a good model to investigate the molecular basis of plant-PGPB interaction including improvement in plant-NUE promoted by PGPB. Results We performed a dual RNA-Seq transcriptional profiling of wheat roots colonized by A. brasilense strain FP2. cDNA libraries from biological replicates of colonized and non-inoculated wheat roots were sequenced and mapped to wheat and A. brasilense reference sequences. The unmapped reads were assembled de novo. Overall, we identified 23,215 wheat expressed ESTs and 702 A. brasilense expressed transcripts. Bacterial colonization caused changes in the expression of 776 wheat ESTs belonging to various functional categories, ranging from transport activity to biological regulation as well as defense mechanism, production of phytohormones and phytochemicals. In addition, genes encoding proteins related to bacterial chemotaxi, biofilm formation and nitrogen fixation were highly expressed in the sub-set of A. brasilense expressed genes. Conclusions PGPB colonization enhanced the expression of plant genes related to nutrient up-take, nitrogen assimilation, DNA replication and regulation of cell division, which is consistent with a higher proportion of colonized root cells in the S-phase. Our data support the use of PGPB as an alternative to improve nutrient acquisition in important crops such as wheat, enhancing plant productivity and sustainability. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-378) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Emanuel M Souza
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, PR 81531-990, Brazil.
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Leach LJ, Belfield EJ, Jiang C, Brown C, Mithani A, Harberd NP. Patterns of homoeologous gene expression shown by RNA sequencing in hexaploid bread wheat. BMC Genomics 2014; 15:276. [PMID: 24726045 PMCID: PMC4023595 DOI: 10.1186/1471-2164-15-276] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Accepted: 04/02/2014] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Bread wheat (Triticum aestivum) has a large, complex and hexaploid genome consisting of A, B and D homoeologous chromosome sets. Therefore each wheat gene potentially exists as a trio of A, B and D homoeoloci, each of which may contribute differentially to wheat phenotypes. We describe a novel approach combining wheat cytogenetic resources (chromosome substitution 'nullisomic-tetrasomic' lines) with next generation deep sequencing of gene transcripts (RNA-Seq), to directly and accurately identify homoeologue-specific single nucleotide variants and quantify the relative contribution of individual homoeoloci to gene expression. RESULTS We discover, based on a sample comprising ~5-10% of the total wheat gene content, that at least 45% of wheat genes are expressed from all three distinct homoeoloci. Most of these genes show strikingly biased expression patterns in which expression is dominated by a single homoeolocus. The remaining ~55% of wheat genes are expressed from either one or two homoeoloci only, through a combination of extensive transcriptional silencing and homoeolocus loss. CONCLUSIONS We conclude that wheat is tending towards functional diploidy, through a variety of mechanisms causing single homoeoloci to become the predominant source of gene transcripts. This discovery has profound consequences for wheat breeding and our understanding of wheat evolution.
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Nakasugi K, Crowhurst R, Bally J, Waterhouse P. Combining transcriptome assemblies from multiple de novo assemblers in the allo-tetraploid plant Nicotiana benthamiana. PLoS One 2014; 9:e91776. [PMID: 24614631 PMCID: PMC3948916 DOI: 10.1371/journal.pone.0091776] [Citation(s) in RCA: 109] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2013] [Accepted: 02/13/2014] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Nicotiana benthamiana is an allo-tetraploid plant, which can be challenging for de novo transcriptome assemblies due to homeologous and duplicated gene copies. Transcripts generated from such genes can be distinct yet highly similar in sequence, with markedly differing expression levels. This can lead to unassembled, partially assembled or mis-assembled contigs. Due to the different properties of de novo assemblers, no one assembler with any one given parameter space can re-assemble all possible transcripts from a transcriptome. RESULTS In an effort to maximise the diversity and completeness of de novo assembled transcripts, we utilised four de novo transcriptome assemblers, TransAbyss, Trinity, SOAPdenovo-Trans, and Oases, using a range of k-mer sizes and different input RNA-seq read counts. We complemented the parameter space biologically by using RNA from 10 plant tissues. We then combined the output of all assemblies into a large super-set of sequences. Using a method from the EvidentialGene pipeline, the combined assembly was reduced from 9.9 million de novo assembled transcripts to about 235,000 of which about 50,000 were classified as primary. Metrics such as average bit-scores, feature response curves and the ability to distinguish paralogous or homeologous transcripts, indicated that the EvidentialGene processed assembly was of high quality. Of 35 RNA silencing gene transcripts, 34 were identified as assembled to full length, whereas in a previous assembly using only one assembler, 9 of these were partially assembled. CONCLUSIONS To achieve a high quality transcriptome, it is advantageous to implement and combine the output from as many different de novo assemblers as possible. We have in essence taking the 'best' output from each assembler while minimising sequence redundancy. We have also shown that simultaneous assessment of a variety of metrics, not just focused on contig length, is necessary to gauge the quality of assemblies.
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Affiliation(s)
- Kenlee Nakasugi
- School of Biological Sciences, University of Sydney, Sydney, Australia
| | - Ross Crowhurst
- Mount Albert Research Centre, Plant & Food Research, Auckland, New Zealand
| | - Julia Bally
- School of Biological Sciences, University of Sydney, Sydney, Australia
| | - Peter Waterhouse
- School of Biological Sciences, University of Sydney, Sydney, Australia
- The Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, Australia
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Salentijn EM, Esselink DG, Goryunova SV, van der Meer IM, Gilissen LJWJ, Smulders MJM. Quantitative and qualitative differences in celiac disease epitopes among durum wheat varieties identified through deep RNA-amplicon sequencing. BMC Genomics 2013; 14:905. [PMID: 24354426 PMCID: PMC3890609 DOI: 10.1186/1471-2164-14-905] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 12/10/2013] [Indexed: 12/20/2022] Open
Abstract
Background Wheat gluten is important for the industrial quality of bread wheat (Triticum aestivum L.) and durum wheat (T. turgidum L.). Gluten proteins are also the source of immunogenic peptides that can trigger a T cell reaction in celiac disease (CD) patients, leading to inflammatory responses in the small intestine. Various peptides with three major T cell epitopes involved in CD are derived from alpha-gliadin fraction of gluten. Alpha-gliadins are encoded by a large multigene family and amino acid variation in the CD epitopes is known to influence the immunogenicity of individual gene family members. Current commercial methods of gluten detection are unable to distinguish between immunogenic and non-immunogenic CD epitope variants and thus to accurately quantify the overall CD epitope load of a given wheat variety. Such quantification is indispensable for correct selection of wheat varieties with low potential to cause CD. Results A 454 RNA-amplicon sequencing method was developed for alpha-gliadin transcripts encompassing the three major CD epitopes and their variants. The method was used to screen developing grains on plants of 61 different durum wheat cultivars and accessions. A dedicated sequence analysis pipeline returned a total of 304 unique alpha-gliadin transcripts, corresponding to a total of 171 ‘unique deduced protein fragments’ of alpha-gliadins. The numbers of these fragments obtained in each plant were used to calculate quantitative and quantitative differences between the CD epitopes expressed in the endosperm of these wheat plants. A few plants showed a lower fraction of CD epitope-encoding alpha-gliadin transcripts, but none were free of CD epitopes. Conclusions The dedicated 454 RNA-amplicon sequencing method enables 1) the grouping of wheat plants according to the genetic variation in alpha-gliadin transcripts, and 2) the screening for plants which are potentially less CD-immunogenic. The resulting alpha-gliadin sequence database will be useful as a reference in proteomics analysis regarding the immunogenic potential of mature wheat grains.
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Affiliation(s)
- Elma Mj Salentijn
- Plant Research International, Wageningen UR, P,O, Box 16, Wageningen, AA NL-6700, The Netherlands.
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Kugler KG, Siegwart G, Nussbaumer T, Ametz C, Spannagl M, Steiner B, Lemmens M, Mayer KFX, Buerstmayr H, Schweiger W. Quantitative trait loci-dependent analysis of a gene co-expression network associated with Fusarium head blight resistance in bread wheat (Triticum aestivum L.). BMC Genomics 2013; 14:728. [PMID: 24152241 PMCID: PMC4007557 DOI: 10.1186/1471-2164-14-728] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 10/14/2013] [Indexed: 01/04/2023] Open
Abstract
Background Fusarium head blight (FHB) caused by Fusarium graminearum Schwabe is one of the most prevalent diseases of wheat (Triticum aestivum L.) and other small grain cereals. Resistance against the fungus is quantitative and more than 100 quantitative trait loci (QTL) have been described. Two well-validated and highly reproducible QTL, Fhb1 and Qfhs.ifa-5A have been widely investigated, but to date the underlying genes have not been identified. Results We have investigated a gene co-expression network activated in response to F. graminearum using RNA-seq data from near-isogenic lines, harboring either the resistant or the susceptible allele for Fhb1 and Qfhs.ifa-5A. The network identified pathogen-responsive modules, which were enriched for differentially expressed genes between genotypes or different time points after inoculation with the pathogen. Central gene analysis identified transcripts associated with either QTL within the network. Moreover, we present a detailed gene expression analysis of four gene families (glucanases, NBS-LRR, WRKY transcription factors and UDP-glycosyltransferases), which take prominent roles in the pathogen response. Conclusions A combination of a network-driven approach and differential gene expression analysis identified genes and pathways associated with Fhb1 and Qfhs.ifa-5A. We find G-protein coupled receptor kinases and biosynthesis genes for jasmonate and ethylene earlier induced for Fhb1. Similarly, we find genes involved in the biosynthesis and metabolism of riboflavin more abundant for Qfhs.ifa-5A.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Wolfgang Schweiger
- Institute for Biotechnology in Plant Production, IFA-Tulln, University of Natural Resources and Life Sciences, A-3430 Tulln, Austria.
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Krasileva KV, Buffalo V, Bailey P, Pearce S, Ayling S, Tabbita F, Soria M, Wang S, Akhunov E, Uauy C, Dubcovsky J. Separating homeologs by phasing in the tetraploid wheat transcriptome. Genome Biol 2013; 14:R66. [PMID: 23800085 PMCID: PMC4053977 DOI: 10.1186/gb-2013-14-6-r66] [Citation(s) in RCA: 115] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2013] [Accepted: 06/25/2013] [Indexed: 11/10/2022] Open
Abstract
Background The high level of identity among duplicated homoeologous genomes in tetraploid pasta wheat presents substantial challenges for de novo transcriptome assembly. To solve this problem, we develop a specialized bioinformatics workflow that optimizes transcriptome assembly and separation of merged homoeologs. To evaluate our strategy, we sequence and assemble the transcriptome of one of the diploid ancestors of pasta wheat, and compare both assemblies with a benchmark set of 13,472 full-length, non-redundant bread wheat cDNAs. Results A total of 489 million 100 bp paired-end reads from tetraploid wheat assemble in 140,118 contigs, including 96% of the benchmark cDNAs. We used a comparative genomics approach to annotate 66,633 open reading frames. The multiple k-mer assembly strategy increases the proportion of cDNAs assembled full-length in a single contig by 22% relative to the best single k-mer size. Homoeologs are separated using a post-assembly pipeline that includes polymorphism identification, phasing of SNPs, read sorting, and re-assembly of phased reads. Using a reference set of genes, we determine that 98.7% of SNPs analyzed are correctly separated by phasing. Conclusions Our study shows that de novo transcriptome assembly of tetraploid wheat benefit from multiple k-mer assembly strategies more than diploid wheat. Our results also demonstrate that phasing approaches originally designed for heterozygous diploid organisms can be used to separate the close homoeologous genomes of tetraploid wheat. The predicted tetraploid wheat proteome and gene models provide a valuable tool for the wheat research community and for those interested in comparative genomic studies.
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