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Huertas R, Torres-Jerez I, Curtin SJ, Scheible W, Udvardi M. Medicago truncatula PHO2 genes have distinct roles in phosphorus homeostasis and symbiotic nitrogen fixation. FRONTIERS IN PLANT SCIENCE 2023; 14:1211107. [PMID: 37409286 PMCID: PMC10319397 DOI: 10.3389/fpls.2023.1211107] [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: 04/24/2023] [Accepted: 05/22/2023] [Indexed: 07/07/2023]
Abstract
Three PHO2-like genes encoding putative ubiquitin-conjugating E2 enzymes of Medicago truncatula were characterized for potential roles in phosphorous (P) homeostasis and symbiotic nitrogen fixation (SNF). All three genes, MtPHO2A, B and C, contain miR399-binding sites characteristic of PHO2 genes in other plant species. Distinct spatiotemporal expression patterns and responsiveness of gene expression to P- and N-deprivation in roots and shoots indicated potential roles, especially for MtPHO2B, in P and N homeostasis. Phenotypic analysis of pho2 mutants revealed that MtPHO2B is integral to Pi homeostasis, affecting Pi allocation during plant growth under nutrient-replete conditions, while MtPHO2C had a limited role in controlling Pi homeostasis. Genetic analysis also revealed a connection between Pi allocation, plant growth and SNF performance. Under N-limited, SNF conditions, Pi allocation to different organs was dependent on MtPHO2B and, to a lesser extent, MtPHO2C and MtPHO2A. MtPHO2A also affected Pi homeostasis associated with nodule formation. Thus, MtPHO2 genes play roles in systemic and localized, i.e., nodule, P homeostasis affecting SNF.
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Affiliation(s)
- Raul Huertas
- Noble Research Institute LLC, Ardmore, OK, United States
| | | | - Shaun J. Curtin
- United States Department of Agriculture, Plant Science Research Unit, St. Paul, MN, United States
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, United States
- Center for Plant Precision Genomics, University of Minnesota, St. Paul, MN, United States
- Center for Genome Engineering, University of Minnesota, St. Paul, MN, United States
| | - Wolf Scheible
- Noble Research Institute LLC, Ardmore, OK, United States
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Leng J, Wei X, Jin X, Wang L, Fan K, Zou K, Zheng Z, Saridis G, Zhao N, Zhou D, Duanmu D, Wang E, Cui H, Bucher M, Xue L. ARBUSCULAR MYCORRHIZA-INDUCED KINASES AMK8 and AMK24 associate with the receptor-like kinase KINASE3 to regulate arbuscular mycorrhizal symbiosis in Lotus japonicus. THE PLANT CELL 2023; 35:2006-2026. [PMID: 36808553 DOI: 10.1093/plcell/koad050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 01/17/2023] [Accepted: 02/01/2023] [Indexed: 05/30/2023]
Abstract
Arbuscular mycorrhizal (AM) symbiosis is a widespread, ancient mutualistic association between plants and fungi, and facilitates nutrient uptake into plants. Cell surface receptor-like kinases (RLKs) and receptor-like cytoplasmic kinases (RLCKs) play pivotal roles in transmembrane signaling, while few RLCKs are known to function in AM symbiosis. Here, we show that 27 out of 40 AM-induced kinases (AMKs) are transcriptionally upregulated by key AM transcription factors in Lotus japonicus. Nine AMKs are only conserved in AM-host lineages, among which the SPARK-RLK-encoding gene KINASE3 (KIN3) and the RLCK paralogues AMK8 and AMK24 are required for AM symbiosis. KIN3 expression is directly regulated by the AP2 transcription factor CTTC MOTIF-BINDING TRANSCRIPTION FACTOR1 (CBX1), which regulates the reciprocal exchange of nutrients in AM symbiosis, via the AW-box motif in the KIN3 promoter. Loss of function mutations in KIN3, AMK8, or AMK24 result in reduced mycorrhizal colonization in L. japonicus. AMK8 and AMK24 physically interact with KIN3. KIN3 and AMK24 are active kinases and AMK24 directly phosphorylates KIN3 in vitro. Moreover, CRISPR-Cas9-mediated mutagenesis of OsRLCK171, the sole homolog of AMK8 and AMK24 in rice (Oryza sativa), leads to diminished mycorrhization with stunted arbuscules. Overall, our results reveal a crucial role of the CBX1-driven RLK/RLCK complex in the evolutionarily conserved signaling pathway enabling arbuscule formation.
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Affiliation(s)
- Junchen Leng
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiaotong Wei
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Xinyi Jin
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Longxiang Wang
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Kai Fan
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ke Zou
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zichao Zheng
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Georgios Saridis
- Institute for Plant Science, Cologne Biocenter, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Zuelpicher Str. 47b, Cologne D-50674, Germany
| | - Ningkang Zhao
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Dan Zhou
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Deqiang Duanmu
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ertao Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, SIBS, Chinese Academy of Sciences, Shanghai 200032, China
| | - Haitao Cui
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Marcel Bucher
- Institute for Plant Science, Cologne Biocenter, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Zuelpicher Str. 47b, Cologne D-50674, Germany
| | - Li Xue
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
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Rodas AL, Roque E, Hamza R, Gómez-Mena C, Beltrán JP, Cañas LA. SUPERMAN strikes again in legumes. FRONTIERS IN PLANT SCIENCE 2023; 14:1120342. [PMID: 36794219 PMCID: PMC9923009 DOI: 10.3389/fpls.2023.1120342] [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: 12/09/2022] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
The SUPERMAN (SUP) gene was described in Arabidopsis thaliana over 30 years ago. SUP was classified as a cadastral gene required to maintain the boundaries between reproductive organs, thus controlling stamen and carpel number in flowers. We summarize the information on the characterization of SUP orthologs in plant species other than Arabidopsis, focusing on the findings for the MtSUP, the ortholog in the legume Medicago truncatula. M. truncatula has been widely used as a model system to study the distinctive developmental traits of this family of plants, such as the existence of compound inflorescence and complex floral development. MtSUP participates in the complex genetic network controlling these developmental processes in legumes, sharing conserved functions with SUP. However, transcriptional divergence between SUP and MtSUP provided context-specific novel functions for a SUPERMAN ortholog in a legume species. MtSUP controls the number of flowers per inflorescence and the number of petals, stamens and carpels regulating the determinacy of ephemeral meristems that are unique in legumes. Results obtained in M. truncatula provided new insights to the knowledge of compound inflorescence and flower development in legumes. Since legumes are valuable crop species worldwide, with high nutritional value and important roles in sustainable agriculture and food security, new information on the genetic control of their compound inflorescence and floral development could be used for plant breeding.
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Rai A, Hirakawa H, Rai M, Shimizu Y, Shirasawa K, Kikuchi S, Seki H, Yamazaki M, Toyoda A, Isobe S, Muranaka T, Saito K. Chromosome-scale genome assembly of Glycyrrhiza uralensis revealed metabolic gene cluster centred specialized metabolites biosynthesis. DNA Res 2022; 29:6916896. [PMID: 36535891 PMCID: PMC9763095 DOI: 10.1093/dnares/dsac043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 11/21/2022] [Indexed: 12/24/2022] Open
Abstract
A high-quality genome assembly is imperative to explore the evolutionary basis of characteristic attributes that define chemotype and provide essential resources for a molecular breeding strategy for enhanced production of medicinal metabolites. Here, using single-molecule high-fidelity (HiFi) sequencing reads, we report chromosome-scale genome assembly for Chinese licorice (Glycyrrhiza uralensis), a widely used herbal and natural medicine. The entire genome assembly was achieved in eight chromosomes, with contig and scaffold N50 as 36.02 and 60.2 Mb, respectively. With only 17 assembly gaps and half of the chromosomes having no or one assembly gap, the presented genome assembly is among the best plant genomes to date. Our results showed an advantage of using highly accurate long-read HiFi sequencing data for assembling a highly heterozygous genome including its complexed repeat content. Additionally, our analysis revealed that G. uralensis experienced a recent whole-genome duplication at approximately 59.02 million years ago post a gamma (γ) whole-genome triplication event, which contributed to its present chemotype features. The metabolic gene cluster analysis identified 355 gene clusters, which included the entire biosynthesis pathway of glycyrrhizin. The genome assembly and its annotations provide an essential resource for licorice improvement through molecular breeding and the discovery of valuable genes for engineering bioactive components and understanding the evolution of specialized metabolites biosynthesis.
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Affiliation(s)
- Amit Rai
- To whom correspondence should be addressed. Tel. +81 045 503 9489; Fax: +81-(0)45-503-9489. ;
| | | | - Megha Rai
- Plant Molecular Science Center, Chiba University, Chiba, Japan,Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan,Institute of Advance Academic Research, Chiba University, Chiba, Japan
| | - Yohei Shimizu
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | | | - Shinji Kikuchi
- Plant Molecular Science Center, Chiba University, Chiba, Japan,Graduate School of Horticulture, Chiba University, Chiba, Japan
| | - Hikaru Seki
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan,Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Japan
| | - Mami Yamazaki
- Plant Molecular Science Center, Chiba University, Chiba, Japan,Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Atsushi Toyoda
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Sachiko Isobe
- Kazusa DNA Research Institute, Kisarazu, Chiba, Japan
| | - Toshiya Muranaka
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan,Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Japan
| | - Kazuki Saito
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan,Plant Molecular Science Center, Chiba University, Chiba, Japan
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5
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Sussmilch FC, Ross JJ, Reid JB. Mendel: From genes to genome. PLANT PHYSIOLOGY 2022; 190:2103-2114. [PMID: 36094356 PMCID: PMC9706470 DOI: 10.1093/plphys/kiac424] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 08/22/2022] [Indexed: 06/15/2023]
Abstract
Two hundred years after the birth of Gregor Mendel, it is an appropriate time to reflect on recent developments in the discipline of genetics, particularly advances relating to the prescient friar's model species, the garden pea (Pisum sativum L.). Mendel's study of seven characteristics established the laws of segregation and independent assortment. The genes underlying four of Mendel's loci (A, LE, I, and R) have been characterized at the molecular level for over a decade. However, the three remaining genes, influencing pod color (GP), pod form (V/P), and the position of flowers (FA/FAS), have remained elusive for a variety of reasons, including a lack of detail regarding the loci with which Mendel worked. Here, we discuss potential candidate genes for these characteristics, in light of recent advances in the genetic resources for pea. These advances, including the pea genome sequence and reverse-genetics techniques, have revitalized pea as an excellent model species for physiological-genetic studies. We also discuss the issues that have been raised with Mendel's results, such as the recent controversy regarding the discrete nature of the characters that Mendel chose and the perceived overly-good fit of his segregations to his hypotheses. We also consider the relevance of these controversies to his lasting contribution. Finally, we discuss the use of Mendel's classical results to teach and enthuse future generations of geneticists, not only regarding the core principles of the discipline, but also its history and the role of hypothesis testing.
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Affiliation(s)
- Frances C Sussmilch
- Discipline of Biological Sciences, School of Natural Sciences, University of Tasmania, Sandy Bay, Tasmania 7005, Australia
| | - John J Ross
- Discipline of Biological Sciences, School of Natural Sciences, University of Tasmania, Sandy Bay, Tasmania 7005, Australia
| | - James B Reid
- Discipline of Biological Sciences, School of Natural Sciences, University of Tasmania, Sandy Bay, Tasmania 7005, Australia
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Wang D, Gong Y, Li Y, Nie S. Genome-wide analysis of the homeodomain-leucine zipper family in Lotus japonicus and the overexpression of LjHDZ7 in Arabidopsis for salt tolerance. FRONTIERS IN PLANT SCIENCE 2022; 13:955199. [PMID: 36186025 PMCID: PMC9515785 DOI: 10.3389/fpls.2022.955199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 08/12/2022] [Indexed: 06/16/2023]
Abstract
The homeodomain-leucine zipper (HD-Zip) family participates in plant growth, development, and stress responses. Here, 40 HD-Zip transcription factors of Lotus japonicus were identified and gave an overview of the phylogeny and gene structures. The expression pattern of these candidate genes was determined in different organs and their response to abiotic stresses, including cold, heat, polyethylene glycol and salinity. The expression of the LjHDZ7 was strongly induced by abiotic stress, especially salt stress. Subsequently, LjHDZ7 gene was overexpressed in Arabidopsis. The transgenic plants grew obviously better than Col-0 plants under salt stress. Furthermore, LjHDZ7 transgenic lines accumulated higher proline contents and showed lower electrolyte leakage and MDA contents than Col-0 plants under salt stress. Antioxidant activities of the LjHDZ7 overexpression lines leaf were significantly higher than those of the Col-0 plants under salt stress. The concentration of Na+ ion in LjHDZ7 overexpression lines was significantly lower than that of Col-0 in leaf and root parts. The concentration of K+ ion in LjHDZ7 overexpression lines was significantly higher than that of Col-0 in the leaf parts. Therefore, these results showed that overexpression of LjHDZ7 increased resistance to salt stress in transgenic Arabidopsis plants, and certain genes of this family can be used as valuable tools for improving abiotic stresses.
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Sudalaimuthuasari N, Ali R, Kottackal M, Rafi M, Al Nuaimi M, Kundu B, Al-Maskari RS, Wang X, Mishra AK, Balan J, Chaluvadi SR, Al Ansari F, Bennetzen JL, Purugganan MD, Hazzouri KM, Amiri KMA. The Genome of the Mimosoid Legume Prosopis cineraria, a Desert Tree. Int J Mol Sci 2022; 23:ijms23158503. [PMID: 35955640 PMCID: PMC9369113 DOI: 10.3390/ijms23158503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/26/2022] [Accepted: 07/28/2022] [Indexed: 11/16/2022] Open
Abstract
The mimosoid legumes are a clade of ~40 genera in the Caesalpinioideae subfamily of the Fabaceae that grow in tropical and subtropical regions. Unlike the better studied Papilionoideae, there are few genomic resources within this legume group. The tree Prosopis cineraria is native to the Near East and Indian subcontinent, where it thrives in very hot desert environments. To develop a tool to better understand desert plant adaptation mechanisms, we sequenced the P. cineraria genome to near-chromosomal assembly, with a total sequence length of ~691 Mb. We predicted 77,579 gene models (76,554 CDS, 361 rRNAs and 664 tRNAs) from the assembled genome, among them 55,325 (~72%) protein-coding genes that were functionally annotated. This genome was found to consist of over 58% repeat sequences, primarily long terminal repeats (LTR-)-retrotransposons. We find an expansion of terpenoid metabolism genes in P. cineraria and its relative Prosopis alba, but not in other legumes. We also observed an amplification of NBS-LRR disease-resistance genes correlated with LTR-associated retrotransposition, and identified 410 retrogenes with an active burst of chimeric retrogene creation that approximately occurred at the same time of divergence of P. cineraria from a common lineage with P. alba~23 Mya. These retrogenes include many biotic defense responses and abiotic stress stimulus responses, as well as the early Nodulin 93 gene. Nodulin 93 gene amplification is consistent with an adaptive response of the species to the low nitrogen in arid desert soil. Consistent with these results, our differentially expressed genes show a tissue specific expression of isoprenoid pathways in shoots, but not in roots, as well as important genes involved in abiotic salt stress in both tissues. Overall, the genome sequence of P. cineraria enriches our understanding of the genomic mechanisms of its disease resistance and abiotic stress tolerance. Thus, it is a very important step in crop and legume improvement.
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Affiliation(s)
- Naganeeswaran Sudalaimuthuasari
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box. 15551, United Arab Emirates; (N.S.); (R.A.); (M.K.); (M.R.); (M.A.N.); (A.K.M.); (J.B.)
| | - Rashid Ali
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box. 15551, United Arab Emirates; (N.S.); (R.A.); (M.K.); (M.R.); (M.A.N.); (A.K.M.); (J.B.)
- Mitrix Bio., 400 Farmington Ave., Farmington, CT 06032, USA
| | - Martin Kottackal
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box. 15551, United Arab Emirates; (N.S.); (R.A.); (M.K.); (M.R.); (M.A.N.); (A.K.M.); (J.B.)
| | - Mohammed Rafi
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box. 15551, United Arab Emirates; (N.S.); (R.A.); (M.K.); (M.R.); (M.A.N.); (A.K.M.); (J.B.)
| | - Mariam Al Nuaimi
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box. 15551, United Arab Emirates; (N.S.); (R.A.); (M.K.); (M.R.); (M.A.N.); (A.K.M.); (J.B.)
| | - Biduth Kundu
- Department of Biology, College of Science, United Arab Emirates University, Al Ain P.O. Box. 15551, United Arab Emirates; (B.K.); (R.S.A.-M.); (F.A.A.)
| | - Raja Saeed Al-Maskari
- Department of Biology, College of Science, United Arab Emirates University, Al Ain P.O. Box. 15551, United Arab Emirates; (B.K.); (R.S.A.-M.); (F.A.A.)
| | - Xuewen Wang
- Department of Genetics, University of Georgia, Athens, GA 30602, USA; (X.W.); (S.R.C.); (J.L.B.)
| | - Ajay Kumar Mishra
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box. 15551, United Arab Emirates; (N.S.); (R.A.); (M.K.); (M.R.); (M.A.N.); (A.K.M.); (J.B.)
| | - Jithin Balan
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box. 15551, United Arab Emirates; (N.S.); (R.A.); (M.K.); (M.R.); (M.A.N.); (A.K.M.); (J.B.)
| | - Srinivasa R. Chaluvadi
- Department of Genetics, University of Georgia, Athens, GA 30602, USA; (X.W.); (S.R.C.); (J.L.B.)
| | - Fatima Al Ansari
- Department of Biology, College of Science, United Arab Emirates University, Al Ain P.O. Box. 15551, United Arab Emirates; (B.K.); (R.S.A.-M.); (F.A.A.)
| | - Jeffrey L. Bennetzen
- Department of Genetics, University of Georgia, Athens, GA 30602, USA; (X.W.); (S.R.C.); (J.L.B.)
| | - Michael D. Purugganan
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi P.O. Box. 129188, United Arab Emirates;
- Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Khaled M. Hazzouri
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box. 15551, United Arab Emirates; (N.S.); (R.A.); (M.K.); (M.R.); (M.A.N.); (A.K.M.); (J.B.)
- Correspondence: (K.M.H.); (K.M.A.A.); Tel.: +971-37135624 (K.M.A.A.)
| | - Khaled M. A. Amiri
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box. 15551, United Arab Emirates; (N.S.); (R.A.); (M.K.); (M.R.); (M.A.N.); (A.K.M.); (J.B.)
- Department of Biology, College of Science, United Arab Emirates University, Al Ain P.O. Box. 15551, United Arab Emirates; (B.K.); (R.S.A.-M.); (F.A.A.)
- Correspondence: (K.M.H.); (K.M.A.A.); Tel.: +971-37135624 (K.M.A.A.)
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Shimamura M, Kumaki T, Hashimoto S, Saeki K, Ayabe SI, Higashitani A, Akashi T, Sato S, Aoki T. Phenolic Acids Induce Nod Factor Production in <i>Lotus japonicus</i>–<i>Mesorhizobium</i> Symbiosis. Microbes Environ 2022; 37. [PMID: 35283370 PMCID: PMC8958295 DOI: 10.1264/jsme2.me21094] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
In legume–rhizobia symbiosis, partner recognition and the initiation of symbiosis processes require the mutual exchange of chemical signals. Chemicals, generally (iso)flavonoids, in the root exudates of the host plant induce the expression of nod genes in rhizobia, and, thus, are called nod gene inducers. The expression of nod genes leads to the production of lipochitooligosaccharides (LCOs) called Nod factors. Natural nod gene inducer(s) in Lotus japonicus–Mesorhizobium symbiosis remain unknown. Therefore, we developed an LCO detection method based on ultra-high-performance liquid chromatography–tandem-quadrupole mass spectrometry (UPLC-TQMS) to identify these inducers and used it herein to screen 40 phenolic compounds and aldonic acids for their ability to induce LCOs in Mesorhizobium japonicum MAFF303099. We identified five phenolic acids with LCO-inducing activities, including p-coumaric, caffeic, and ferulic acids. The induced LCOs caused root hair deformation, and nodule numbers in L. japonicus inoculated with M. japonicum were increased by these phenolic acids. The three phenolic acids listed above induced the expression of the nodA, nodB, and ttsI genes in a strain harboring a multicopy plasmid encoding NodD1, but not that encoding NodD2. The presence of p-coumaric and ferulic acids in the root exudates of L. japonicus was confirmed by UPLC-TQMS, and the induction of ttsI::lacZ in the strain harboring the nodD1 plasmid was detected in the rhizosphere of L. japonicus. Based on these results, we propose that phenolic acids are a novel type of nod gene inducer in L. japonicus–Mesorhizobium symbiosis.
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Affiliation(s)
| | | | | | - Kazuhiko Saeki
- Department of Biological Sciences and Kyousei Science Center for Life and Nature, Nara Women’s University
| | | | | | | | - Shusei Sato
- Graduate School of Life Sciences, Tohoku University
| | - Toshio Aoki
- Department of Applied Biological Sciences, Nihon University
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9
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Discovery of SNPs in important legumes through comparative genome analysis and conversion of SNPs into PCR-based markers. J Genet 2021. [DOI: 10.1007/s12041-021-01320-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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10
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Eriksson JS, Bacon CD, Bennett DJ, Pfeil BE, Oxelman B, Antonelli A. Gene count from target sequence capture places three whole genome duplication events in Hibiscus L. (Malvaceae). BMC Ecol Evol 2021; 21:107. [PMID: 34078291 PMCID: PMC8170824 DOI: 10.1186/s12862-021-01751-7] [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: 07/22/2020] [Accepted: 01/27/2021] [Indexed: 11/24/2022] Open
Abstract
Background The great diversity in plant genome size and chromosome number is partly due to polyploidization (i.e. genome doubling events). The differences in genome size and chromosome number among diploid plant species can be a window into the intriguing phenomenon of past genome doubling that may be obscured through time by the process of diploidization. The genus Hibiscus L. (Malvaceae) has a wide diversity of chromosome numbers and a complex genomic history. Hibiscus is ideal for exploring past genomic events because although two ancient genome duplication events have been identified, more are likely to be found due to its diversity of chromosome numbers. To reappraise the history of whole-genome duplication events in Hibiscus, we tested three alternative scenarios describing different polyploidization events. Results Using target sequence capture, we designed a new probe set for Hibiscus and generated 87 orthologous genes from four diploid species. We detected paralogues in > 54% putative single-copy genes. 34 of these genes were selected for testing three different genome duplication scenarios using gene counting. All species of Hibiscus sampled shared one genome duplication with H. syriacus, and one whole genome duplication occurred along the branch leading to H. syriacus. Conclusions Here, we corroborated the independent genome doubling previously found in the lineage leading to H. syriacus and a shared genome doubling of this lineage and the remainder of Hibiscus. Additionally, we found a previously undiscovered genome duplication shared by the /Pavonia and /Malvaviscus clades (both nested within Hibiscus) with the occurrences of two copies in what were otherwise single-copy genes. Our results highlight the complexity of genomic diversity in some plant groups, which makes orthology assessment and accurate phylogenomic inference difficult.
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Affiliation(s)
- J S Eriksson
- School of Bioscience, Systems Biology Research Center, 541 45, Skövde, Sweden. .,Gothenburg Global Biodiversity Centre, Box 461, 405 30, Gothenburg, Sweden.
| | - C D Bacon
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30, Gothenburg, Sweden.,Gothenburg Global Biodiversity Centre, Box 461, 405 30, Gothenburg, Sweden
| | - D J Bennett
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30, Gothenburg, Sweden.,Gothenburg Global Biodiversity Centre, Box 461, 405 30, Gothenburg, Sweden
| | - B E Pfeil
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30, Gothenburg, Sweden.,Gothenburg Global Biodiversity Centre, Box 461, 405 30, Gothenburg, Sweden
| | - B Oxelman
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30, Gothenburg, Sweden.,Gothenburg Global Biodiversity Centre, Box 461, 405 30, Gothenburg, Sweden
| | - A Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30, Gothenburg, Sweden.,Gothenburg Global Biodiversity Centre, Box 461, 405 30, Gothenburg, Sweden.,Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK.,Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3 RB, UK
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11
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Zhao Y, Zhang R, Jiang KW, Qi J, Hu Y, Guo J, Zhu R, Zhang T, Egan AN, Yi TS, Huang CH, Ma H. Nuclear phylotranscriptomics and phylogenomics support numerous polyploidization events and hypotheses for the evolution of rhizobial nitrogen-fixing symbiosis in Fabaceae. MOLECULAR PLANT 2021; 14:748-773. [PMID: 33631421 DOI: 10.1016/j.molp.2021.02.006] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 07/31/2020] [Accepted: 02/19/2021] [Indexed: 05/20/2023]
Abstract
Fabaceae are the third largest angiosperm family, with 765 genera and ∼19 500 species. They are important both economically and ecologically, and global Fabaceae crops are intensively studied in part for their nitrogen-fixing ability. However, resolution of the intrasubfamilial Fabaceae phylogeny and divergence times has remained elusive, precluding a reconstruction of the evolutionary history of symbiotic nitrogen fixation in Fabaceae. Here, we report a highly resolved phylogeny using >1500 nuclear genes from newly sequenced transcriptomes and genomes of 391 species, along with other datasets, for a total of 463 legumes spanning all 6 subfamilies and 333 of 765 genera. The subfamilies are maximally supported as monophyletic. The clade comprising subfamilies Cercidoideae and Detarioideae is sister to the remaining legumes, and Duparquetioideae and Dialioideae are successive sisters to the clade of Papilionoideae and Caesalpinioideae. Molecular clock estimation revealed an early radiation of subfamilies near the K/Pg boundary, marked by mass extinction, and subsequent divergence of most tribe-level clades within ∼15 million years. Phylogenomic analyses of thousands of gene families support 28 proposed putative whole-genome duplication/whole-genome triplication events across Fabaceae, including those at the ancestors of Fabaceae and five of the subfamilies, and further analyses supported the Fabaceae ancestral polyploidy. The evolution of rhizobial nitrogen-fixing nodulation in Fabaceae was probed by ancestral character reconstruction and phylogenetic analyses of related gene families and the results support the hypotheses of one or two switch(es) to rhizobial nodulation followed by multiple losses. Collectively, these results provide a foundation for further morphological and functional evolutionary analyses across Fabaceae.
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Affiliation(s)
- Yiyong Zhao
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200433, China; Department of Biology, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Rong Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Lanhei Road, Kunming 650201, China
| | - Kai-Wen Jiang
- Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming 650224, PR China; Ningbo Botanical Garden Herbarium, Ningbo 315201, PR China
| | - Ji Qi
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200433, China
| | - Yi Hu
- Department of Biology, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Jing Guo
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200433, China
| | - Renbin Zhu
- Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, PR China
| | - Taikui Zhang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200433, China
| | - Ashley N Egan
- Department of Biology, Utah Valley University, Orem, UT 84058, USA
| | - Ting-Shuang Yi
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Lanhei Road, Kunming 650201, China.
| | - Chien-Hsun Huang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200433, China.
| | - Hong Ma
- Department of Biology, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA.
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12
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Peng Z, Chen H, Tan L, Shu H, Varshney RK, Zhou Z, Zhao Z, Luo Z, Chitikineni A, Wang L, Maku J, López Y, Gallo M, Zhou H, Wang J. Natural polymorphisms in a pair of NSP2 homoeologs can cause loss of nodulation in peanut. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:1104-1118. [PMID: 33130897 DOI: 10.1093/jxb/eraa505] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 10/27/2020] [Indexed: 06/11/2023]
Abstract
Microbial symbiosis in legumes is achieved through nitrogen-fixing root nodules, and these are important for sustainable agriculture. The molecular mechanisms underlying development of root nodules in polyploid legume crops are largely understudied. Through map-based cloning and QTL-seq approaches, we identified a pair of homoeologous GRAS transcription factor genes, Nodulation Signaling Pathway 2 (AhNSP2-B07 or Nb) and AhNSP2-A08 (Na), controlling nodulation in cultivated peanut (Arachis hypogaea L.), an allotetraploid legume crop, which exhibited non-Mendelian and Mendelian inheritance, respectively. The segregation of nodulation in the progeny of Nananbnb genotypes followed a 3:1 Mendelian ratio, in contrast to the 5:3~1:1 non-Mendelian ratio for nanaNbnb genotypes. Additionally, a much higher frequency of the nb allele (13%) than the na allele (4%) exists in the peanut germplasm collection, suggesting that Nb is less essential than Na in nodule organogenesis. Our findings reveal the genetic basis of naturally occurred non-nodulating peanut plants, which can be potentially used for nitrogen fixation improvement in peanut. Furthermore, the results have implications for and provide insights into the evolution of homoeologous genes in allopolyploid species.
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Affiliation(s)
- Ze Peng
- Agronomy Department, University of Florida, Gainesville, FL, USA
| | - Huiqiong Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Lubin Tan
- Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China
| | - Hongmei Shu
- Agronomy Department, University of Florida, Gainesville, FL, USA
| | - Rajeev K Varshney
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India
| | - Zhekai Zhou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Zifan Zhao
- Agronomy Department, University of Florida, Gainesville, FL, USA
| | - Ziliang Luo
- Agronomy Department, University of Florida, Gainesville, FL, USA
| | - Annapurna Chitikineni
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India
| | - Liping Wang
- Agronomy Department, University of Florida, Gainesville, FL, USA
| | - James Maku
- Sciences and Mathematics Department, Glenville State College, Glenville, WV, USA
| | - Yolanda López
- Agronomy Department, University of Florida, Gainesville, FL, USA
| | - Maria Gallo
- Delaware Valley University, Doylestown, PA, USA
| | - Hai Zhou
- Agronomy Department, University of Florida, Gainesville, FL, USA
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Jianping Wang
- Agronomy Department, University of Florida, Gainesville, FL, USA
- Genetics Institute, Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, USA
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13
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Rodas AL, Roque E, Hamza R, Gómez-Mena C, Minguet EG, Wen J, Mysore KS, Beltrán JP, Cañas LA. MtSUPERMAN plays a key role in compound inflorescence and flower development in Medicago truncatula. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:816-830. [PMID: 33176041 DOI: 10.1111/tpj.15075] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 09/18/2020] [Accepted: 09/23/2020] [Indexed: 06/11/2023]
Abstract
Legumes have unique features, such as compound inflorescences and a complex floral ontogeny. Thus, the study of regulatory genes in these species during inflorescence and floral development is essential to understand their role in the evolutionary origin of developmental novelties. The SUPERMAN (SUP) gene encodes a C2H2 zinc-finger transcriptional repressor that regulates the floral organ number in the third and fourth floral whorls of Arabidopsis thaliana. In this work, we present the functional characterization of the Medicago truncatula SUPERMAN (MtSUP) gene based on gene expression analysis, complementation and overexpression assays, and reverse genetic approaches. Our findings provide evidence that MtSUP is the orthologous gene of SUP in M. truncatula. We have unveiled novel functions for a SUP-like gene in eudicots. MtSUP controls not only the number of floral organs in the inner two whorls, but also in the second whorl of the flower. Furthermore, MtSUP regulates the activity of the secondary inflorescence meristem, thus controlling the number of flowers produced. Our work provides insight into the regulatory network behind the compound inflorescence and flower development in this angiosperm family.
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Affiliation(s)
- Ana L Rodas
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Ciudad Politécnica de la Innovación, Edf. 8E. C/Ingeniero Fausto Elio s/n. E-46022, Valencia, Spain
| | - Edelín Roque
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Ciudad Politécnica de la Innovación, Edf. 8E. C/Ingeniero Fausto Elio s/n. E-46022, Valencia, Spain
| | - Rim Hamza
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Ciudad Politécnica de la Innovación, Edf. 8E. C/Ingeniero Fausto Elio s/n. E-46022, Valencia, Spain
| | - Concepción Gómez-Mena
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Ciudad Politécnica de la Innovación, Edf. 8E. C/Ingeniero Fausto Elio s/n. E-46022, Valencia, Spain
| | - Eugenio G Minguet
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Ciudad Politécnica de la Innovación, Edf. 8E. C/Ingeniero Fausto Elio s/n. E-46022, Valencia, Spain
| | - Jiangqi Wen
- Plant Biology Division, Noble Research Institute, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | - Kirankumar S Mysore
- Plant Biology Division, Noble Research Institute, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | - José P Beltrán
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Ciudad Politécnica de la Innovación, Edf. 8E. C/Ingeniero Fausto Elio s/n. E-46022, Valencia, Spain
| | - Luis A Cañas
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Ciudad Politécnica de la Innovación, Edf. 8E. C/Ingeniero Fausto Elio s/n. E-46022, Valencia, Spain
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14
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Slawinski L, Israel A, Paillot C, Thibault F, Cordaux R, Atanassova R, Dédaldéchamp F, Laloi M. Early Response to Dehydration Six-Like Transporter Family: Early Origin in Streptophytes and Evolution in Land Plants. FRONTIERS IN PLANT SCIENCE 2021; 12:681929. [PMID: 34552602 PMCID: PMC8450595 DOI: 10.3389/fpls.2021.681929] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 07/09/2021] [Indexed: 05/23/2023]
Abstract
Carbon management by plants involves the activity of many sugar transporters, which play roles in sugar subcellular partitioning and reallocation at the whole organism scale. Among these transporters, the early response to dehydration six-like (ESL) monosaccharide transporters (MSTs) are still poorly characterized although they represent one of the largest sugar transporter subfamilies. In this study, we used an evolutionary genomic approach to infer the evolutionary history of this multigenic family. No ESL could be identified in the genomes of rhodophytes, chlorophytes, and the brown algae Ectocarpus siliculosus, whereas one ESL was identified in the genome of Klebsormidium nitens providing evidence for the early emergence of these transporters in Streptophytes. A phylogenetic analysis using the 519 putative ESL proteins identified in the genomes of 47 Embryophyta species and being representative of the plant kingdom has revealed that ESL protein sequences can be divided into three major groups. The first and second groups originated in the common ancestor of all spermaphytes [ζ: 340 million years ago (MYA)] and of angiosperms (ε: 170-235 MYA), respectively, and the third group originated before the divergence of rosids and asterids (γ/1R: 117 MYA). In some eudicots (Vitales, Malpighiales, Myrtales, Sapindales, Brassicales, Malvales, and Solanales), the ESL family presents remarkable expansions of gene copies associated with tandem duplications. The analysis of non-synonymous and synonymous substitutions for the dN/dS ratio of the ESL copies of the genus Arabidopsis has revealed that ESL genes are evolved under a purifying selection even though the progressive increase of dN/dS ratios in the three groups suggests subdiversification phenomena. To further explore the possible acquisition of novel functions by ESL MSTs, we identified the gene structure and promoter cis-acting elements for Arabidopsis thaliana ESL genes. The expression profiling of Arabidopsis ESL unraveled some gene copies that are almost constitutively expressed, whereas other gene copies display organ-preferential expression patterns. This study provides an evolving framework to better understand the roles of ESL transporters in plant development and response to environmental constraints.
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15
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Koenen EJM, Ojeda DI, Bakker FT, Wieringa JJ, Kidner C, Hardy OJ, Pennington RT, Herendeen PS, Bruneau A, Hughes CE. The Origin of the Legumes is a Complex Paleopolyploid Phylogenomic Tangle Closely Associated with the Cretaceous-Paleogene (K-Pg) Mass Extinction Event. Syst Biol 2020; 70:508-526. [PMID: 32483631 PMCID: PMC8048389 DOI: 10.1093/sysbio/syaa041] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 05/06/2020] [Accepted: 05/25/2020] [Indexed: 12/17/2022] Open
Abstract
The consequences of the Cretaceous–Paleogene (K–Pg) boundary (KPB) mass extinction for the evolution of plant diversity remain poorly understood, even though evolutionary turnover of plant lineages at the KPB is central to understanding assembly of the Cenozoic biota. The apparent concentration of whole genome duplication (WGD) events around the KPB may have played a role in survival and subsequent diversification of plant lineages. To gain new insights into the origins of Cenozoic biodiversity, we examine the origin and early evolution of the globally diverse legume family (Leguminosae or Fabaceae). Legumes are ecologically (co-)dominant across many vegetation types, and the fossil record suggests that they rose to such prominence after the KPB in parallel with several well-studied animal clades including Placentalia and Neoaves. Furthermore, multiple WGD events are hypothesized to have occurred early in legume evolution. Using a recently inferred phylogenomic framework, we investigate the placement of WGDs during early legume evolution using gene tree reconciliation methods, gene count data and phylogenetic supernetwork reconstruction. Using 20 fossil calibrations we estimate a revised timeline of legume evolution based on 36 nuclear genes selected as informative and evolving in an approximately clock-like fashion. To establish the timing of WGDs we also date duplication nodes in gene trees. Results suggest either a pan-legume WGD event on the stem lineage of the family, or an allopolyploid event involving (some of) the earliest lineages within the crown group, with additional nested WGDs subtending subfamilies Papilionoideae and Detarioideae. Gene tree reconciliation methods that do not account for allopolyploidy may be misleading in inferring an earlier WGD event at the time of divergence of the two parental lineages of the polyploid, suggesting that the allopolyploid scenario is more likely. We show that the crown age of the legumes dates to the Maastrichtian or early Paleocene and that, apart from the Detarioideae WGD, paleopolyploidy occurred close to the KPB. We conclude that the early evolution of the legumes followed a complex history, in which multiple auto- and/or allopolyploidy events coincided with rapid diversification and in association with the mass extinction event at the KPB, ultimately underpinning the evolutionary success of the Leguminosae in the Cenozoic. [Allopolyploidy; Cretaceous–Paleogene (K–Pg) boundary; Fabaceae, Leguminosae; paleopolyploidy; phylogenomics; whole genome duplication events]
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Affiliation(s)
- Erik J M Koenen
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, CH-8008, Zurich, Switzerland
| | - Dario I Ojeda
- Service Évolution Biologique et Écologie, Faculté des Sciences, Université Libre de Bruxelles, Avenue Franklin Roosevelt 50, 1050, Brussels, Belgium.,Norwegian Institute of Bioeconomy Research, Høgskoleveien 8, 1433 Ås, Norway
| | - Freek T Bakker
- Biosystematics Group, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Jan J Wieringa
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR, Leiden, The Netherlands
| | - Catherine Kidner
- Royal Botanic Gardens Edinburgh, 20a Inverleith Row, Edinburgh EH3 5LR, UK.,School of Biological Sciences, University of Edinburgh, King's Buildings, Mayfield Rd, Edinburgh, EH9 3JU, UK
| | - Olivier J Hardy
- Service Évolution Biologique et Écologie, Faculté des Sciences, Université Libre de Bruxelles, Avenue Franklin Roosevelt 50, 1050, Brussels, Belgium
| | - R Toby Pennington
- Royal Botanic Gardens Edinburgh, 20a Inverleith Row, Edinburgh EH3 5LR, UK.,Geography, University of Exeter, Amory Building, Rennes Drive, Exeter, EX4 4RJ, UK
| | | | - Anne Bruneau
- Institut de Recherche en Biologie Végétale and Département de Sciences Biologiques, Université de Montréal, 4101 Sherbrooke St E, Montreal, QC H1X 2B2, Canada
| | - Colin E Hughes
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, CH-8008, Zurich, Switzerland
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16
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Abd El-Wahab MMH, Aljabri M, Sarhan MS, Osman G, Wang S, Mabrouk M, El-Shabrawi HM, Gabr AMM, Abd El-Haliem AM, O’Sullivan DM, El-Soda M. High-Density SNP-Based Association Mapping of Seed Traits in Fenugreek Reveals Homology with Clover. Genes (Basel) 2020; 11:E893. [PMID: 32764325 PMCID: PMC7464718 DOI: 10.3390/genes11080893] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 07/28/2020] [Accepted: 08/02/2020] [Indexed: 12/02/2022] Open
Abstract
Fenugreek as a self-pollinated plant is ideal for genome-wide association mapping where traits can be marked by their association with natural mutations. However, fenugreek is poorly investigated at the genomic level due to the lack of information regarding its genome. To fill this gap, we genotyped a collection of 112 genotypes with 153,881 SNPs using double digest restriction site-associated DNA sequencing. We used 38,142 polymorphic SNPs to prove the suitability of the population for association mapping. One significant SNP was associated with both seed length and seed width, and another SNP was associated with seed color. Due to the lack of a comprehensive genetic map, it is neither possible to align the newly developed markers to chromosomes nor to predict the underlying genes. Therefore, systematic targeting of those markers to homologous genomes of other legumes can overcome those problems. A BLAST search using the genomic fenugreek sequence flanking the identified SNPs showed high homology with several members of the Trifolieae tribe indicating the potential of translational approaches to improving our understanding of the fenugreek genome. Using such a comprehensively-genotyped fenugreek population is the first step towards identifying genes underlying complex traits and to underpin fenugreek marker-assisted breeding programs.
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Affiliation(s)
- Mustafa M. H. Abd El-Wahab
- Department of Agronomy, Faculty of Agriculture, Cairo University, Giza 12613, Egypt; (M.M.H.A.E.-W.); (M.M.)
| | - Maha Aljabri
- Department of Biology, Faculty of Applied Sciences, Umm Al-Qura University, Makkah 21955, Saudi Arabia; (M.A.); (G.O.)
- Research Laboratories Centre, Faculty of Applied Science, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Mohamed S. Sarhan
- Environmental Studies and Research Unit, Cairo University, Giza 12613, Egypt;
| | - Gamal Osman
- Department of Biology, Faculty of Applied Sciences, Umm Al-Qura University, Makkah 21955, Saudi Arabia; (M.A.); (G.O.)
- Research Laboratories Centre, Faculty of Applied Science, Umm Al-Qura University, Makkah 21955, Saudi Arabia
- Agricultural Genetic Engineering Research Institute (AGERI), ARC, Giza 12915, Egypt
| | - Shichen Wang
- Genomics and Bioinformatics Service Texas A&M AgriLife Research, Amarillo College Station, Amarillo, TX 77845, USA;
| | - Mahmoud Mabrouk
- Department of Agronomy, Faculty of Agriculture, Cairo University, Giza 12613, Egypt; (M.M.H.A.E.-W.); (M.M.)
| | - Hattem M. El-Shabrawi
- Plant Biotechnology Department, National Research Center, Giza 12622, Egypt; (H.M.E.-S.); (A.M.M.G.)
| | - Ahmed M. M. Gabr
- Plant Biotechnology Department, National Research Center, Giza 12622, Egypt; (H.M.E.-S.); (A.M.M.G.)
| | - Ahmed M. Abd El-Haliem
- Plant Physiology, University of Amsterdam, Swammerdam Institute for Life Sciences Amsterdam, 1098 XH Amsterdam, The Netherlands;
| | - Donal M. O’Sullivan
- School of Agriculture, Policy and Development, University of Reading, Whiteknights, Reading RG6 6AR, UK;
| | - Mohamed El-Soda
- Department of Genetics, Faculty of Agriculture, Cairo University, Giza 12613, Egypt
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17
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Forrester NJ, Rebolleda-Gómez M, Sachs JL, Ashman TL. Polyploid plants obtain greater fitness benefits from a nutrient acquisition mutualism. THE NEW PHYTOLOGIST 2020; 227:944-954. [PMID: 32248526 DOI: 10.1111/nph.16574] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 03/20/2020] [Indexed: 06/11/2023]
Abstract
Polyploidy is a key driver of ecological and evolutionary processes in plants, yet little is known about its effects on biotic interactions. This gap in knowledge is especially profound for nutrient acquisition mutualisms, despite the fact that they regulate global nutrient cycles and structure ecosystems. Generalism in mutualistic interactions depends on the range of potential partners (niche breadth), the benefits obtained and ability to maintain benefits across a variety of partners (fitness plasticity). Here, we determine how each of these is influenced by polyploidy in the legume-rhizobium mutualism. We inoculated a broad geographic sample of natural diploid and autotetraploid alfalfa (Medicago sativa) lineages with a diverse panel of Sinorhizobium bacterial symbionts. To analyze the extent and mechanism of generalism, we measured host growth benefits and functional traits. Autotetraploid plants obtained greater fitness enhancement from mutualistic interactions and were better able to maintain this across diverse rhizobial partners (i.e. low plasticity in fitness) relative to diploids. These benefits were not attributed to increases in niche breadth, but instead reflect increased rewards from investment in the mutualism. Polyploid plants displayed greater generalization in bacterial mutualisms relative to diploids, illustrating another axis of advantage for polyploids over diploids.
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Affiliation(s)
- Nicole J Forrester
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Ave., Pittsburgh, PA, 15260, USA
| | - Maria Rebolleda-Gómez
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Ave., Pittsburgh, PA, 15260, USA
| | - Joel L Sachs
- Department of Evolution, Ecology, and Organismal Biology, University of California, 3401 Watkins Drive, Riverside, CA, 92521, USA
| | - Tia-Lynn Ashman
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Ave., Pittsburgh, PA, 15260, USA
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18
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Moharana KC, Venancio TM. Polyploidization events shaped the transcription factor repertoires in legumes (Fabaceae). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:726-741. [PMID: 32270526 DOI: 10.1111/tpj.14765] [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: 11/21/2019] [Revised: 03/13/2020] [Accepted: 03/25/2020] [Indexed: 06/11/2023]
Abstract
Transcription factors (TFs) are essential for plant growth and development. Several legumes (e.g. soybean) are rich sources of protein and oil and have great economic importance. Here we report a phylogenomic analysis of TF families in legumes and their potential association with important traits (e.g. nitrogen fixation). We used TF DNA-binding domains to systematically screen the genomes of 15 leguminous and five non-leguminous species. Transcription factor orthologous groups (OGs) were used to estimate OG sizes in ancestral nodes using a gene birth-death model, which allowed the identification of lineage-specific expansions. The OG analysis and rate of synonymous substitutions show that major TF expansions are strongly associated with whole-genome duplication (WGD) events in the legume (approximately 58 million years ago) and Glycine (approximately 13 million years ago) lineages, which account for a large fraction of the Phaseolus vulgaris and Glycine max TF repertoires. Of the 3407 G. max TFs, 1808 and 676 have homeologs within single syntenic regions in Phaseolus vulgaris and Vitis vinifera, respectively. We found a trend for TFs expanded in legumes to be preferentially transcribed in roots and nodules, supporting their recruitment early in the evolution of nodulation in the legume clade. Some families also showed count differences between G. max and the wild soybean Glycine soja, including genes located within important quantitative trait loci. Our findings strongly support the roles of two WGDs in shaping the TF repertoires in the legume and Glycine lineages, and these are probably related to important aspects of legume and soybean biology.
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Affiliation(s)
- Kanhu C Moharana
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Thiago M Venancio
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
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19
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A Tale of Two Families: Whole Genome and Segmental Duplications Underlie Glutamine Synthetase and Phosphoenolpyruvate Carboxylase Diversity in Narrow-Leafed Lupin ( Lupinus angustifolius L.). Int J Mol Sci 2020; 21:ijms21072580. [PMID: 32276381 PMCID: PMC7177731 DOI: 10.3390/ijms21072580] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 04/04/2020] [Accepted: 04/06/2020] [Indexed: 01/04/2023] Open
Abstract
Narrow-leafed lupin (Lupinus angustifolius L.) has recently been supplied with advanced genomic resources and, as such, has become a well-known model for molecular evolutionary studies within the legume family—a group of plants able to fix nitrogen from the atmosphere. The phylogenetic position of lupins in Papilionoideae and their evolutionary distance to other higher plants facilitates the use of this model species to improve our knowledge on genes involved in nitrogen assimilation and primary metabolism, providing novel contributions to our understanding of the evolutionary history of legumes. In this study, we present a complex characterization of two narrow-leafed lupin gene families—glutamine synthetase (GS) and phosphoenolpyruvate carboxylase (PEPC). We combine a comparative analysis of gene structures and a synteny-based approach with phylogenetic reconstruction and reconciliation of the gene family and species history in order to examine events underlying the extant diversity of both families. Employing the available evidence, we show the impact of duplications on the initial complement of the analyzed gene families within the genistoid clade and posit that the function of duplicates has been largely retained. In terms of a broader perspective, our results concerning GS and PEPC gene families corroborate earlier findings pointing to key whole genome duplication/triplication event(s) affecting the genistoid lineage.
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Bu F, Rutten L, Roswanjaya YP, Kulikova O, Rodriguez‐Franco M, Ott T, Bisseling T, van Zeijl A, Geurts R. Mutant analysis in the nonlegume Parasponia andersonii identifies NIN and NF-YA1 transcription factors as a core genetic network in nitrogen-fixing nodule symbioses. THE NEW PHYTOLOGIST 2020; 226:541-554. [PMID: 31863481 PMCID: PMC7154530 DOI: 10.1111/nph.16386] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 12/04/2019] [Indexed: 05/13/2023]
Abstract
●Nitrogen-fixing nodulation occurs in 10 taxonomic lineages, with either rhizobia or Frankia bacteria. To establish such an endosymbiosis, two processes are essential: nodule organogenesis and intracellular bacterial infection. In the legume-rhizobium endosymbiosis, both processes are guarded by the transcription factor NODULE INCEPTION (NIN) and its downstream target genes of the NUCLEAR FACTOR Y (NF-Y) complex. ●It is hypothesized that nodulation has a single evolutionary origin c. 110 Ma, followed by many independent losses. Despite a significant body of knowledge of the legume-rhizobium symbiosis, it remains elusive which signalling modules are shared between nodulating species in different taxonomic clades. We used Parasponia andersonii to investigate the role of NIN and NF-YA genes in rhizobium nodulation in a nonlegume system. ●Consistent with legumes, P. andersonii PanNIN and PanNF-YA1 are coexpressed in nodules. By analyzing single, double and higher-order CRISPR-Cas9 knockout mutants, we show that nodule organogenesis and early symbiotic expression of PanNF-YA1 are PanNIN-dependent and that PanNF-YA1 is specifically required for intracellular rhizobium infection. ●This demonstrates that NIN and NF-YA1 have conserved symbiotic functions. As Parasponia and legumes diverged soon after the birth of the nodulation trait, we argue that NIN and NF-YA1 represent core transcriptional regulators in this symbiosis.
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Affiliation(s)
- Fengjiao Bu
- Laboratory of Molecular BiologyDepartment of Plant ScienceWageningen UniversityDroevendaalsesteeg 16708PBWageningenthe Netherlands
| | - Luuk Rutten
- Laboratory of Molecular BiologyDepartment of Plant ScienceWageningen UniversityDroevendaalsesteeg 16708PBWageningenthe Netherlands
| | - Yuda Purwana Roswanjaya
- Laboratory of Molecular BiologyDepartment of Plant ScienceWageningen UniversityDroevendaalsesteeg 16708PBWageningenthe Netherlands
- Center of Technology for Agricultural ProductionAgency for the Assessment and Application of Technology (BPPT)10340JakartaIndonesia
| | - Olga Kulikova
- Laboratory of Molecular BiologyDepartment of Plant ScienceWageningen UniversityDroevendaalsesteeg 16708PBWageningenthe Netherlands
| | | | - Thomas Ott
- Cell BiologyFaculty of BiologyUniversity of Freiburg79104FreiburgGermany
| | - Ton Bisseling
- Laboratory of Molecular BiologyDepartment of Plant ScienceWageningen UniversityDroevendaalsesteeg 16708PBWageningenthe Netherlands
| | - Arjan van Zeijl
- Laboratory of Molecular BiologyDepartment of Plant ScienceWageningen UniversityDroevendaalsesteeg 16708PBWageningenthe Netherlands
| | - Rene Geurts
- Laboratory of Molecular BiologyDepartment of Plant ScienceWageningen UniversityDroevendaalsesteeg 16708PBWageningenthe Netherlands
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21
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Ren L, Huang W, Cannon SB. Reconstruction of ancestral genome reveals chromosome evolution history for selected legume species. THE NEW PHYTOLOGIST 2019; 223:2090-2103. [PMID: 30834536 DOI: 10.1111/nph.15770] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 02/24/2019] [Indexed: 05/18/2023]
Abstract
Reconstruction of an ancestral genome for a set of plant species has been a challenging task because of complex histories that may include whole-genome duplications, segmental duplications, independent gene duplications or losses, diploidization and rearrangement events. Here, we describe the reconstruction a hypothetical ancestral genome for the papilionoid legumes (the largest subfamily within the third largest family in flowering plants), and evaluate the results relative to phylogenetic and chromosomal count data for this group of legumes, spanning 294 diverse papilionoid genera. To reconstruct the ancestral genomes for nine legume species with sequenced genomes, we used a maximum likelihood approach combined with a novel method for identifying informative markers for this purpose. Analyzing genomes from four species within the Phaseoleae, two in Dalbergieae, two in the 'inverted repeat loss' clade, and one in the Robinieae, we infer a common ancestral genome with nine chromosomes. The reconstructed genome structural histories are consistent with chromosomal and phylogenetic histories, but we also infer that a common ancestor with nine chromosomes was probably intermediate to an earlier state of 14 chromosomes following a whole-genome duplication that pre-dated the radiation of the papilionoid legumes, evidence for which is found in early-diverging papilionoid lineages.
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Affiliation(s)
- Longhui Ren
- Interdepartmental Genetics Graduate Program, 2014 Molecular Biology, Iowa State University, 2437 Pammel Drive, Ames, IA, 50011, USA
| | - Wei Huang
- Department of Agronomy, Iowa State University, 716 Farm House Ln, Ames, IA, 50011, USA
| | - Steven B Cannon
- Corn Insects and Crop Genetics Research Unit, US Department of Agriculture-Agricultural Research Service, 819 Wallace Rd, Ames, IA, 50011, USA
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Bi R, Chandappa LH, Siddalingaiah L, Raju SKK, Balakrishna SH, Kumar J, Kuruba V, Hittalmani S. Leveraging barrel medic genome sequence for the development and use of genomic resources for genetic analysis and breeding in legumes. ELECTRON J BIOTECHN 2019. [DOI: 10.1016/j.ejbt.2019.02.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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Genome-wide identification and expression analysis of the AAAP family in Medicago truncatula. Genetica 2019; 147:185-196. [PMID: 30905050 DOI: 10.1007/s10709-019-00062-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 03/20/2019] [Indexed: 10/27/2022]
Abstract
The amino acid/auxin permease (AAAP) gene family plays an important role in the long-distance amino acid transport pathway and takes part in various stages of plant growth and development. However, little is known about the AAAP gene family in Medicago truncatula. Here, we identified 86 putative MtAAAP family members using genome sequence information. Based on phylogenetic analysis, these MtAAAP genes were categorized into eight distinct subfamilies. The MtAAAP genes were mapped on 8 chromosomes and duplication events appeared widely, with 19 and 21 pairs of MtAAAP genes showing segment and tandem duplication events, respectively. Ratio of Ka/Ks indicated that duplicated genes underwent purifying selection. Analysis of RNA-seq data showed that MtAAAP genes exhibited specific expression patterns among different tissues and abiotic stress, indicating that MtAAAP members were involved in plant developmental regulation and stress responses. Expression patterns of 16 MtAAAP genes under abiotic stress were verified by qRT-PCR. The present study provides a foundation for the functional analysis of MtAAAPs in developmental regulation and stress responses.
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ÇAKIR Ö, UÇARLI C, TARHAN Ç, PEKMEZ M, TURGUT-KARA N. Nutritional and health benefits of legumes and their distinctive genomic properties. FOOD SCIENCE AND TECHNOLOGY 2019. [DOI: 10.1590/fst.42117] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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de Bruijn S, Zhao T, Muiño JM, Schranz EM, Angenent GC, Kaufmann K. PISTILLATA paralogs in Tarenaya hassleriana have diverged in interaction specificity. BMC PLANT BIOLOGY 2018; 18:368. [PMID: 30577806 PMCID: PMC6303913 DOI: 10.1186/s12870-018-1574-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 11/26/2018] [Indexed: 06/09/2023]
Abstract
BACKGROUND Floral organs are specified by MADS-domain transcription factors that act in a combinatorial manner, as summarized in the (A)BCE model. However, this evolutionarily conserved model is in contrast to a remarkable amount of morphological diversity in flowers. One of the mechanisms suggested to contribute to this diversity is duplication of floral MADS-domain transcription factors. Although gene duplication is often followed by loss of one of the copies, sometimes both copies are retained. If both copies are retained they will initially be redundant, providing freedom for one of the paralogs to change function. Here, we examine the evolutionary fate and functional consequences of a transposition event at the base of the Brassicales that resulted in the duplication of the floral regulator PISTILLATA (PI), using Tarenaya hassleriana (Cleomaceae) as a model system. RESULTS The transposition of a genomic region containing a PI gene led to two paralogs which are located at different positions in the genome. The original PI copy is syntenic in position with most angiosperms, whereas the transposed copy is syntenic with the PI genes in Brassicaceae. The two PI paralogs of T. hassleriana have very similar expression patterns. However, they may have diverged in function, as only one of these PI proteins was able to act heterologously in the first whorl of A. thaliana flowers. We also observed differences in protein complex formation between the two paralogs, and the two paralogs exhibit subtle differences in DNA-binding specificity. Sequence analysis indicates that most of the protein sequence divergence between the two T. hassleriana paralogs emerged in a common ancestor of the Cleomaceae and the Brassicaceae. CONCLUSIONS We found that the PI paralogs in T. hassleriana have similar expression patterns, but may have diverged at the level of protein function. Data suggest that most protein sequence divergence occurred rapidly, prior to the origin of the Brassicaceae and Cleomaceae. It is tempting to speculate that the interaction specificities of the Brassicaceae-specific PI proteins are different compared to the PI found in other angiosperms. This could lead to PI regulating partly different genes in the Brassicaceae, and ultimately might result in change floral in morphology.
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Affiliation(s)
- Suzanne de Bruijn
- Laboratory of Molecular Biology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Bioscience, Wageningen Plant Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Tao Zhao
- Biosystematics Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Jose M. Muiño
- Institute for Biology, Systems Biology of Gene Regulation, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Eric M. Schranz
- Biosystematics Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Gerco C. Angenent
- Laboratory of Molecular Biology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Bioscience, Wageningen Plant Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Kerstin Kaufmann
- Institute for Biology, Plant Cell and Molecular Biology, Humboldt-Universität zu Berlin, Philippstraße 13, 10115 Berlin, Germany
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Szczepaniak A, Książkiewicz M, Podkowiński J, Czyż KB, Figlerowicz M, Naganowska B. Legume Cytosolic and Plastid Acetyl-Coenzyme-A Carboxylase Genes Differ by Evolutionary Patterns and Selection Pressure Schemes Acting before and after Whole-Genome Duplications. Genes (Basel) 2018; 9:genes9110563. [PMID: 30469317 PMCID: PMC6265850 DOI: 10.3390/genes9110563] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 11/09/2018] [Accepted: 11/15/2018] [Indexed: 01/01/2023] Open
Abstract
Acetyl-coenzyme A carboxylase (ACCase, E.C.6.4.1.2) catalyzes acetyl-coenzyme A carboxylation to malonyl coenzyme A. Plants possess two distinct ACCases differing by cellular compartment and function. Plastid ACCase contributes to de novo fatty acid synthesis, whereas cytosolic enzyme to the synthesis of very long chain fatty acids, phytoalexins, flavonoids, and anthocyanins. The narrow leafed lupin (Lupinus angustifolius L.) represents legumes, a plant family which evolved by whole-genome duplications (WGDs). The study aimed on the contribution of these WGDs to the multiplication of ACCase genes and their further evolutionary patterns. The molecular approach involved bacterial artificial chromosome (BAC) library screening, fluorescent in situ hybridization, linkage mapping, and BAC sequencing. In silico analysis encompassed sequence annotation, comparative mapping, selection pressure calculation, phylogenetic inference, and gene expression profiling. Among sequenced legumes, the highest number of ACCase genes was identified in lupin and soybean. The most abundant plastid ACCase subunit genes were accB. ACCase genes in legumes evolved by WGDs, evidenced by shared synteny and Bayesian phylogenetic inference. Transcriptional activity of almost all copies was confirmed. Gene duplicates were conserved by strong purifying selection, however, positive selection occurred in Arachis (accB2) and Lupinus (accC) lineages, putatively predating the WGD event(s). Early duplicated accA and accB genes underwent transcriptional sub-functionalization.
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Affiliation(s)
- Anna Szczepaniak
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, 60-479 Poznań, Poland.
| | - Michał Książkiewicz
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, 60-479 Poznań, Poland.
| | - Jan Podkowiński
- Department of Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznań, Poland.
| | - Katarzyna B Czyż
- Department of Biometry and Bioinformatics, Institute of Plant Genetics, Polish Academy of Sciences, 60-479 Poznań, Poland.
| | - Marek Figlerowicz
- Department of Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznań, Poland.
| | - Barbara Naganowska
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, 60-479 Poznań, Poland.
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27
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Singh J, Kalberer SR, Belamkar V, Assefa T, Nelson MN, Farmer AD, Blackmon WJ, Cannon SB. A transcriptome-SNP-derived linkage map of Apios americana (potato bean) provides insights about genome re-organization and synteny conservation in the phaseoloid legumes. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:333-351. [PMID: 29071392 PMCID: PMC5787225 DOI: 10.1007/s00122-017-3004-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Accepted: 10/10/2017] [Indexed: 06/07/2023]
Abstract
KEY MESSAGE We report a linkage map for Apios americana and describe synteny with selected warm-season legumes. A translocation event in common bean and soybean is confirmed against Apios and Vigna species. Apios (Apios americana; "apios"), a tuberous perennial legume in the Phaseoleae tribe, was widely used as a food by Native Americans. Work in the last 40 years has led to several improved breeding lines. Aspects of the pollination biology (complex floral structure and tripping mechanism) have made controlled crosses difficult, and the previous reports indicated that the plant is likely primarily an outcrosser. We used a pseudo-testcross strategy to construct a genetic map specific to the maternal parent. The map was built using single-nucleotide polymorphism markers identified by comparing the expressed sequences of individuals in the mapping population against a de novo maternal reference transcriptome assembly. The apios map consists of 11 linkage groups and 1121 recombinationally distinct loci, covering ~ 938.6 cM. By sequencing the transcriptomes of all potential pollen parents, we were able to identify the probable pollen donors and to discover new aspects of the pollination biology in apios. No selfing was observed, but multiple pollen parents were seen within individual pods. Comparisons with genome sequences in other species in the Phaseoleae showed extended synteny for most apios linkage groups. This synteny supports the robustness of the map, and also sheds light on the history of the Phaseoleae, as apios is relatively early diverging in this tribe. We detected a translocation event that separates apios and two Vigna species from Phaseolus vulgaris and Glycine max. This apios mapping work provides a general protocol for sequencing-based construction of high-density linkage maps in outcrossing species with heterogeneous pollen parents.
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Affiliation(s)
- Jugpreet Singh
- ORISE Fellow, Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA 50011 USA
| | - Scott R. Kalberer
- Crop Genome Informatics Laboratory, Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA 50011 USA
| | - Vikas Belamkar
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583 USA
| | - Teshale Assefa
- ORISE Fellow, Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA 50011 USA
| | - Matthew N. Nelson
- Royal Botanic Gardens, Kew, Wakehurst Place, Ardingly, West Sussex RH17 6TN UK
| | | | | | - Steven B. Cannon
- Crop Genome Informatics Laboratory, Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA 50011 USA
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Lu Q, Li H, Hong Y, Zhang G, Wen S, Li X, Zhou G, Li S, Liu H, Liu H, Liu Z, Varshney RK, Chen X, Liang X. Genome Sequencing and Analysis of the Peanut B-Genome Progenitor ( Arachis ipaensis). FRONTIERS IN PLANT SCIENCE 2018; 9:604. [PMID: 29774047 PMCID: PMC5943715 DOI: 10.3389/fpls.2018.00604] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 04/16/2018] [Indexed: 05/21/2023]
Abstract
Peanut (Arachis hypogaea L.), an important leguminous crop, is widely cultivated in tropical and subtropical regions. Peanut is an allotetraploid, having A and B subgenomes that maybe have originated in its diploid progenitors Arachis duranensis (A-genome) and Arachis ipaensis (B-genome), respectively. We previously sequenced the former and here present the draft genome of the latter, expanding our knowledge of the unique biology of Arachis. The assembled genome of A. ipaensis is ~1.39 Gb with 39,704 predicted protein-encoding genes. A gene family analysis revealed that the FAR1 family may be involved in regulating peanut special fruit development. Genomic evolutionary analyses estimated that the two progenitors diverged ~3.3 million years ago and suggested that A. ipaensis experienced a whole-genome duplication event after the divergence of Glycine max. We identified a set of disease resistance-related genes and candidate genes for biological nitrogen fixation. In particular, two and four homologous genes that may be involved in the regulation of nodule development were obtained from A. ipaensis and A. duranensis, respectively. We outline a comprehensive network involved in drought adaptation. Additionally, we analyzed the metabolic pathways involved in oil biosynthesis and found genes related to fatty acid and triacylglycerol synthesis. Importantly, three new FAD2 homologous genes were identified from A. ipaensis and one was completely homologous at the amino acid level with FAD2 from A. hypogaea. The availability of the A. ipaensis and A. duranensis genomic assemblies will advance our knowledge of the peanut genome.
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Affiliation(s)
- Qing Lu
- South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Haifen Li
- South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Yanbin Hong
- South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Guoqiang Zhang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, National Orchid Conservation Center of China and Orchid Conservation and Research Center of Shenzhen, Shenzhen, China
| | - Shijie Wen
- South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Xingyu Li
- South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Guiyuan Zhou
- South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Shaoxiong Li
- South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Hao Liu
- South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Haiyan Liu
- South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Zhongjian Liu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, National Orchid Conservation Center of China and Orchid Conservation and Research Center of Shenzhen, Shenzhen, China
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
- School of Plant Biology, The Institute of Agriculture, University of Western Australia, University of Western Australia, Crawley, WA, Australia
| | - Xiaoping Chen
- South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- *Correspondence: Xiaoping Chen
| | - Xuanqiang Liang
- South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Xuanqiang Liang
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Roque E, Gómez-Mena C, Ferrándiz C, Beltrán JP, Cañas LA. Functional Genomics and Genetic Control of Flower and Fruit Development in Medicago truncatula: An Overview. Methods Mol Biol 2018; 1822:273-290. [PMID: 30043310 DOI: 10.1007/978-1-4939-8633-0_18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
A-, B-, and C-class genes code for MADS-box transcription factors required for floral organ identity in angiosperms. Other members of the family are also crucial to ensure proper carpel and fruit development. Development of genetic and genomic tools for Medicago truncatula has allowed its use as model system to study the genetic control of flower and fruit development in legumes. M. truncatula contains a single A-class gene, four B-function genes, and three C-class genes in its genome. This has made possible to do extensive functional characterization of these MADS-box transcription factors using gene expression analyses, protein-protein interactions, and forward and reverse genetic approaches. We have demonstrated the functions of these MADS-box transcription factors and the respective contributions of paralogous gene pairs to M. truncatula floral development. We have also defined the evolutionary outcomes of each duplicated pairs thus testing theoretical framework of several models about the evolution by gene duplication. Moreover, we have also studied the function of MADS-box fruit genes and how they may have contributed to the diversification of pod morphology within the Medicago genus. Our findings not only have contributed to increase knowledge in the field of the genetic control of flower and fruit development but also have provided a more complete understanding of the complexity of evolution by gene duplication and protein sequence diversification.
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Affiliation(s)
- Edelín Roque
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Ciudad Politécnica de la Innovación Edf. 8E, C/ Ingeniero Fausto Elio s.n., Valencia, E-46011, Spain
| | - Concepción Gómez-Mena
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Ciudad Politécnica de la Innovación Edf. 8E, C/ Ingeniero Fausto Elio s.n., Valencia, E-46011, Spain
| | - Cristina Ferrándiz
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Ciudad Politécnica de la Innovación Edf. 8E, C/ Ingeniero Fausto Elio s.n., Valencia, E-46011, Spain
| | - José Pío Beltrán
- CSIC-UPV, Institute for Plant Cell and Molecular Biology(IBMCP), Valencia, Spain.
| | - Luis A Cañas
- CSIC-UPV, Institute for Plant Cell and Molecular Biology(IBMCP), Valencia, Spain.
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Kaur G, Guruprasad K, Temple BRS, Shirvanyants DG, Dokholyan NV, Pati PK. Structural complexity and functional diversity of plant NADPH oxidases. Amino Acids 2018; 50:79-94. [PMID: 29071531 PMCID: PMC6492275 DOI: 10.1007/s00726-017-2491-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 09/11/2017] [Indexed: 10/18/2022]
Abstract
Plant NADPH oxidases also known as respiratory burst oxidase homologs (Rbohs) are a family of membrane-bound enzymes that play diverse roles in the defense response and morphogenetic processes via regulated generation of reactive oxygen species. Rbohs are associated with a variety of functions, although the reason for this is not clear. To evaluate using bioinformatics, the possible mechanisms for the observed functional diversity within the plant kingdom, 127 Rboh protein sequences representing 26 plant species were analyzed. Multiple clusters were identified with gene duplications that were both dicot as well as monocot-specific. The N-terminal sequences were observed to be highly variable. The conserved cysteine (equivalent of Cys890) in C-terminal of AtRbohD suggested that the redox-based modification like S-nitrosylation may regulate the activity of other Rbohs. Three-dimensional models corresponding to the N-terminal domain for Rbohs from Arabidopsis thaliana and Oryza sativa were constructed and molecular dynamics studies were carried out to study the role of Ca2+ in the folding of Rboh proteins. Certain mutations indicated possibly affect the structure and function of the plant NADPH oxidases, thereby providing the rationale for further experimental validation.
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Affiliation(s)
- Gurpreet Kaur
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, India
- Bioinformatics, Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
- Max Planck Institute for Developmental Biology, Tuebingen, Germany
| | - Kunchur Guruprasad
- Bioinformatics, Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
| | - Brenda R S Temple
- R. L. Juliano Structural Bioinformatics Core Facility, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - David G Shirvanyants
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Nikolay V Dokholyan
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Pratap Kumar Pati
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, India.
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Jiao K, Li X, Guo W, Su S, Luo D. High-Throughput RNA-Seq Data Analysis of the Single Nucleotide Polymorphisms (SNPs) and Zygomorphic Flower Development in Pea (Pisum sativum L.). Int J Mol Sci 2017; 18:E2710. [PMID: 29261120 PMCID: PMC5751311 DOI: 10.3390/ijms18122710] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 12/10/2017] [Accepted: 12/12/2017] [Indexed: 11/17/2022] Open
Abstract
Pea (Pisum sativum L.) is a model plant that has been used in classical genetics and organ development studies. However, its large and complex genome has hindered research investigations in pea. Here, we generated transcriptomes from different tissues or organs of three pea accessions using next-generation sequencing to assess single nucleotide polymorphisms (SNPs), and further investigated petal differentially expressed genes to elucidate the mechanisms regulating floral zygomorphy. Eighteen samples were sequenced, which yielded a total of 617 million clean reads, and de novo assembly resulted in 87,137 unigenes. A total of 9044 high-quality SNPs were obtained among the three accessions, and a consensus map was constructed. We further discovered several dorsoventral asymmetrically expressed genes that were confirmed by qRT-PCR among different petals, including previously reported three CYC-like proliferating cell factor (TCP) genes. One MADS-box gene was highly expressed in dorsal petals, and several MYB factors were predominantly expressed among dorsal, lateral, and/or ventral petals, together with a ventrally expressed TCP gene. In sum, our comprehensive database complements the existing resources for comparative genetic mapping and facilitates future investigations in legume zygomorphic flower development.
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Affiliation(s)
- Keyuan Jiao
- Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
| | - Xin Li
- College of Life Sciences, Laboratory Center of Life Sciences, Nanjing Agricultural University, Nanjing 210014, China.
| | - Wuxiu Guo
- Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
| | - Shihao Su
- Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
| | - Da Luo
- Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
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Narożna D, Książkiewicz M, Przysiecka Ł, Króliczak J, Wolko B, Naganowska B, Mądrzak CJ. Legume isoflavone synthase genes have evolved by whole-genome and local duplications yielding transcriptionally active paralogs. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 264:149-167. [PMID: 28969795 DOI: 10.1016/j.plantsci.2017.09.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 09/05/2017] [Accepted: 09/11/2017] [Indexed: 05/04/2023]
Abstract
Isoflavone synthase (IFS) is the key enzyme of isoflavonoid biosynthesis. IFS genes were identified in numerous species, although their evolutionary patterns have not yet been reconstructed. To address this issue, we performed structural and functional genomic analysis. Narrow leafed lupin, Lupinus angustifolius L., was used as a reference species for the genus, because it has the most developed molecular tools available. Nuclear genome BAC library clones carrying IFS homologs were localized by linkage mapping and fluorescence in situ hybridization in three chromosome pairs. Annotation of BAC, scaffold and transcriptome sequences confirmed the presence of three full-length IFS genes in the genome. Microsynteny analysis and Bayesian inference provided clear evidence that IFS genes in legumes have evolved by lineage-specific whole-genome and tandem duplications. Gene expression profiling and RNA-seq data mining showed that the vast majority of legume IFS copies have maintained their transcriptional activity. L. angustifolius IFS homologs exhibited organ-specific expression patterns similar to those observed in other Papilionoideae. Duplicated lupin IFS homologs retained non-negligible levels of substitutions in conserved motifs, putatively due to positive selection acting during early evolution of the genus, before the whole-genome duplication. Strong purifying selection preserved newly arisen IFS duplicates from further nonsynonymous changes.
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Affiliation(s)
- Dorota Narożna
- Department of Biochemistry and Biotechnology, Faculty of Agronomy and Bioengineering, Poznań University of Life Sciences, Dojazd 11, 60-632, Poznań, Poland.
| | - Michał Książkiewicz
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland.
| | - Łucja Przysiecka
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland; NanoBioMedical Centre, Adam Mickiewicz University, Umultowska 85, 61-614, Poznań, Poland.
| | - Joanna Króliczak
- Department of Biochemistry and Biotechnology, Faculty of Agronomy and Bioengineering, Poznań University of Life Sciences, Dojazd 11, 60-632, Poznań, Poland.
| | - Bogdan Wolko
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland.
| | - Barbara Naganowska
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland.
| | - Cezary J Mądrzak
- Department of Biochemistry and Biotechnology, Faculty of Agronomy and Bioengineering, Poznań University of Life Sciences, Dojazd 11, 60-632, Poznań, Poland.
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33
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Moll KM, Zhou P, Ramaraj T, Fajardo D, Devitt NP, Sadowsky MJ, Stupar RM, Tiffin P, Miller JR, Young ND, Silverstein KAT, Mudge J. Strategies for optimizing BioNano and Dovetail explored through a second reference quality assembly for the legume model, Medicago truncatula. BMC Genomics 2017; 18:578. [PMID: 28778149 PMCID: PMC5545040 DOI: 10.1186/s12864-017-3971-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 07/31/2017] [Indexed: 12/16/2022] Open
Abstract
Background Third generation sequencing technologies, with sequencing reads in the tens- of kilo-bases, facilitate genome assembly by spanning ambiguous regions and improving continuity. This has been critical for plant genomes, which are difficult to assemble due to high repeat content, gene family expansions, segmental and tandem duplications, and polyploidy. Recently, high-throughput mapping and scaffolding strategies have further improved continuity. Together, these long-range technologies enable quality draft assemblies of complex genomes in a cost-effective and timely manner. Results Here, we present high quality genome assemblies of the model legume plant, Medicago truncatula (R108) using PacBio, Dovetail Chicago (hereafter, Dovetail) and BioNano technologies. To test these technologies for plant genome assembly, we generated five assemblies using all possible combinations and ordering of these three technologies in the R108 assembly. While the BioNano and Dovetail joins overlapped, they also showed complementary gains in continuity and join numbers. Both technologies spanned repetitive regions that PacBio alone was unable to bridge. Combining technologies, particularly Dovetail followed by BioNano, resulted in notable improvements compared to Dovetail or BioNano alone. A combination of PacBio, Dovetail, and BioNano was used to generate a high quality draft assembly of R108, a M. truncatula accession widely used in studies of functional genomics. As a test for the usefulness of the resulting genome sequence, the new R108 assembly was used to pinpoint breakpoints and characterize flanking sequence of a previously identified translocation between chromosomes 4 and 8, identifying more than 22.7 Mb of novel sequence not present in the earlier A17 reference assembly. Conclusions Adding Dovetail followed by BioNano data yielded complementary improvements in continuity over the original PacBio assembly. This strategy proved efficient and cost-effective for developing a quality draft assembly compared to traditional reference assemblies. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3971-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Karen M Moll
- National Center for Genome Resources, 2935 Rodeo Park Drive East, Santa Fe, NM, 87505, USA.,Montana State University, Center for Biofilm Engineering, Bozeman, MT, 59717, USA
| | - Peng Zhou
- Department of Plant Biology, University of Minnesota, Saint Paul, MN, USA
| | - Thiruvarangan Ramaraj
- National Center for Genome Resources, 2935 Rodeo Park Drive East, Santa Fe, NM, 87505, USA
| | - Diego Fajardo
- National Center for Genome Resources, 2935 Rodeo Park Drive East, Santa Fe, NM, 87505, USA
| | - Nicholas P Devitt
- National Center for Genome Resources, 2935 Rodeo Park Drive East, Santa Fe, NM, 87505, USA
| | - Michael J Sadowsky
- Department of Soil, Water & Climate, Plant and Microbial Biology and BioTechnology Institute, University of Minnesota, St. Paul, MN, USA
| | - Robert M Stupar
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, USA
| | - Peter Tiffin
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, USA
| | | | - Nevin D Young
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, USA
| | | | - Joann Mudge
- National Center for Genome Resources, 2935 Rodeo Park Drive East, Santa Fe, NM, 87505, USA.
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Cao Y, Han Y, Meng D, Li D, Jin Q, Lin Y, Cai Y. Genome-wide analysis suggests high level of microsynteny and purifying selection affect the evolution of EIN3/EIL family in Rosaceae. PeerJ 2017; 5:e3400. [PMID: 28584725 PMCID: PMC5455322 DOI: 10.7717/peerj.3400] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 05/10/2017] [Indexed: 11/20/2022] Open
Abstract
The ethylene-insensitive3/ethylene-insensitive3-like (EIN3/EIL) proteins are a type of nuclear-localized protein with DNA-binding activity in plants. Although the EIN3/EIL gene family has been studied in several plant species, little is known about comprehensive study of the EIN3/EIL gene family in Rosaceae. In this study, ten, five, four, and five EIN3/EIL genes were identified in the genomes of pear (Pyrus bretschneideri), mei (Prunus mume), peach (Prunus persica) and strawberry (Fragaria vesca), respectively. Twenty-eight chromosomal segments of EIL/EIN3 gene family were found in four Rosaceae species, and these segments could form seven orthologous or paralogous groups based on interspecies or intraspecies gene colinearity (microsynteny) analysis. Moreover, the highly conserved regions of microsynteny were found in four Rosaceae species. Subsequently it was found that both whole genome duplication and tandem duplication events significantly contributed to the EIL/EIN3 gene family expansion. Gene expression analysis of the EIL/EIN3 genes in the pear revealed subfunctionalization for several PbEIL genes derived from whole genome duplication. It is noteworthy that according to environmental selection pressure analysis, the strong purifying selection should dominate the maintenance of the EIL/EIN3 gene family in four Rosaceae species. These results provided useful information on Rosaceae EIL/EIN3 genes, as well as insights into the evolution of this gene family in four Rosaceae species. Furthermore, high level of microsynteny in the four Rosaceae plants suggested that a large-scale genome duplication event in the EIL/EIN3 gene family was predated to speciation.
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Affiliation(s)
- Yunpeng Cao
- College of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Yahui Han
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Dandan Meng
- College of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Dahui Li
- College of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Qing Jin
- College of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Yi Lin
- College of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Yongping Cai
- College of Life Sciences, Anhui Agricultural University, Hefei, China
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35
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Yano K, Aoki S, Liu M, Umehara Y, Suganuma N, Iwasaki W, Sato S, Soyano T, Kouchi H, Kawaguchi M. Function and evolution of a Lotus japonicus AP2/ERF family transcription factor that is required for development of infection threads. DNA Res 2017; 24:193-203. [PMID: 28028038 PMCID: PMC5397602 DOI: 10.1093/dnares/dsw052] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 10/25/2016] [Indexed: 01/05/2023] Open
Abstract
Legume-rhizobium symbiosis is achieved by two major events evolutionarily acquired: root hair infection and organogenesis. Infection thread (IT) development is a distinct element for rhizobial infection. Through ITs, rhizobia are efficiently transported from infection foci on root hairs to dividing meristematic cortical cells. To unveil this process, we performed genetic screening using Lotus japonicus MG-20 and isolated symbiotic mutant lines affecting nodulation, root hair morphology, and IT development. Map-based cloning identified an AP2/ERF transcription factor gene orthologous to Medicago truncatula ERN1. LjERN1 was activated in response to rhizobial infection and depended on CYCLOPS and NSP2. Legumes conserve an ERN1 homolog, ERN2, that functions redundantly with ERN1 in M. truncatula. Phylogenetic analysis showed that the lineages of ERN1 and ERN2 genes originated from a gene duplication event in the common ancestor of legume plants. However, genomic analysis suggested the lack of ERN2 gene in the L. japonicus genome, consistent with Ljern1 mutants exhibited a root hair phenotype that is observed in ern1/ern2 double mutants in M. truncatula. Molecular evolutionary analysis suggested that the nonsynonymous/synonymous rate ratios of legume ERN1 genes was almost identical to that of non-legume plants, whereas the ERN2 genes experienced a relaxed selective constraint.
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Affiliation(s)
- Koji Yano
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
- Division of Symbiotic Systems, National Institute for Basic Biology, National Institute for Natural Sciences, Okazaki 444-8585, Japan
| | - Seishiro Aoki
- Department of General Systems Studies, Graduate School of Arts and Sciences, the University of Tokyo, Meguro-ku, Tokyo 153-8902, Japan
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Meng Liu
- Division of Symbiotic Systems, National Institute for Basic Biology, National Institute for Natural Sciences, Okazaki 444-8585, Japan
- Department of Basic Biology, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), Okazaki 444-8585, Japan and
| | - Yosuke Umehara
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
| | - Norio Suganuma
- Department of Life Science, Aichi University of Education, Kariya, Aichi 448–8542, Japan
| | - Wataru Iwasaki
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Shusei Sato
- Kazusa DNA Research Institute, Kisarazu, Chiba 292–0812, Japan
- Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai 980-8577, Japan
| | - Takashi Soyano
- Division of Symbiotic Systems, National Institute for Basic Biology, National Institute for Natural Sciences, Okazaki 444-8585, Japan
- Department of Basic Biology, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), Okazaki 444-8585, Japan and
| | - Hiroshi Kouchi
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
| | - Masayoshi Kawaguchi
- Division of Symbiotic Systems, National Institute for Basic Biology, National Institute for Natural Sciences, Okazaki 444-8585, Japan
- Department of Basic Biology, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), Okazaki 444-8585, Japan and
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Książkiewicz M, Rychel S, Nelson MN, Wyrwa K, Naganowska B, Wolko B. Expansion of the phosphatidylethanolamine binding protein family in legumes: a case study of Lupinus angustifolius L. FLOWERING LOCUS T homologs, LanFTc1 and LanFTc2. BMC Genomics 2016; 17:820. [PMID: 27769166 PMCID: PMC5073747 DOI: 10.1186/s12864-016-3150-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 10/08/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Arabidopsis FLOWERING LOCUS T (FT) gene, a member of the phosphatidylethanolamine binding protein (PEBP) family, is a major controller of flowering in response to photoperiod, vernalization and light quality. In legumes, FT evolved into three, functionally diversified clades, FTa, FTb and FTc. A milestone achievement in narrow-leafed lupin (Lupinus angustifolius L.) domestication was the loss of vernalization responsiveness at the Ku locus. Recently, one of two existing L. angustifolius homologs of FTc, LanFTc1, was revealed to be the gene underlying Ku. It is the first recorded involvement of an FTc homologue in vernalization. The evolutionary basis of this phenomenon in lupin has not yet been deciphered. RESULTS Bacterial artificial chromosome (BAC) clones carrying LanFTc1 and LanFTc2 genes were localized in different mitotic chromosomes and constituted sequence-specific landmarks for linkage groups NLL-10 and NLL-17. BAC-derived superscaffolds containing LanFTc genes revealed clear microsyntenic patterns to genome sequences of nine legume species. Superscaffold-1 carrying LanFTc1 aligned to regions encoding one or more FT-like genes whereas superscaffold-2 mapped to a region lacking such a homolog. Comparative mapping of the L. angustifolius genome assembly anchored to linkage map localized superscaffold-1 in the middle of a 15 cM conserved, collinear region. In contrast, superscaffold-2 was found at the edge of a 20 cM syntenic block containing highly disrupted collinearity at the LanFTc2 locus. 118 PEBP-family full-length homologs were identified in 10 legume genomes. Bayesian phylogenetic inference provided novel evidence supporting the hypothesis that whole-genome and tandem duplications contributed to expansion of PEBP-family genes in legumes. Duplicated genes were subjected to strong purifying selection. Promoter analysis of FT genes revealed no statistically significant sequence similarity between duplicated copies; only RE-alpha and CCAAT-box motifs were found at conserved positions and orientations. CONCLUSIONS Numerous lineage-specific duplications occurred during the evolution of legume PEBP-family genes. Whole-genome duplications resulted in the origin of subclades FTa, FTb and FTc and in the multiplication of FTa and FTb copy number. LanFTc1 is located in the region conserved among all main lineages of Papilionoideae. LanFTc1 is a direct descendant of ancestral FTc, whereas LanFTc2 appeared by subsequent duplication.
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Affiliation(s)
- Michał Książkiewicz
- Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland.
| | - Sandra Rychel
- Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Matthew N Nelson
- Natural Capital and Plant Health, Royal Botanic Gardens Kew, Wakehurst Place, Ardingly, West Sussex, RH17 6TN, UK.,School of Plant Biology, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.,The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Katarzyna Wyrwa
- Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Barbara Naganowska
- Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Bogdan Wolko
- Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
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Chen Z, Chen D, Chu W, Zhu D, Yan H, Xiang Y. Retention and Molecular Evolution of Lipoxygenase Genes in Modern Rosid Plants. Front Genet 2016; 7:176. [PMID: 27746812 PMCID: PMC5043136 DOI: 10.3389/fgene.2016.00176] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 09/16/2016] [Indexed: 11/13/2022] Open
Abstract
Whole-genome duplication events have occurred more than once in the genomes of some rosids and played a significant role over evolutionary time. Lipoxygenases (LOXs) are involved in many developmental and resistance processes in plants. Our study concerns the subject of the LOX gene family; we tracked the evolutionary process of ancestral LOX genes in four modern rosids. Here we show that some members of the LOX gene family in the Arabidopsis genome are likely to be lost during evolution, leading to a smaller size than that in Populus, Vitis, and Carica. Strong purifying selection acted as a critical role in almost all of the paralogous and orthologous genes. The structure of LOX genes in Carica and Populus are relatively stable, whereas Vitis and Arabidopsis have a difference. By searching conserved motifs of LOX genes, we found that each sub-family shared similar components. Research on intraspecies gene collinearity show that recent duplication holds an important position in Populus and Arabidopsis. Gene collinearity analysis within and between these four rosid plants revealed that all LOX genes in each modern rosid were the offspring from different ancestral genes. This study traces the evolution of LOX genes which have been differentially retained and expanded in rosid plants. Our results presented here may aid in the selection of special genes retained in the rosid plants for further analysis of biological function.
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Affiliation(s)
- Zhu Chen
- Laboratory of Modern Biotechnology, Anhui Agricultural University Hefei, China
| | - Danmei Chen
- Laboratory of Modern Biotechnology, Anhui Agricultural University Hefei, China
| | - Wenyuan Chu
- Laboratory of Modern Biotechnology, Anhui Agricultural University Hefei, China
| | - Dongyue Zhu
- Laboratory of Modern Biotechnology, Anhui Agricultural University Hefei, China
| | - Hanwei Yan
- Laboratory of Modern Biotechnology, Anhui Agricultural UniversityHefei, China; Key Laboratory of Biomass Improvement and Conversion, Anhui Agriculture UniversityHefei, China
| | - Yan Xiang
- Laboratory of Modern Biotechnology, Anhui Agricultural UniversityHefei, China; Key Laboratory of Biomass Improvement and Conversion, Anhui Agriculture UniversityHefei, China
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Devos N, Szövényi P, Weston DJ, Rothfels CJ, Johnson MG, Shaw AJ. Analyses of transcriptome sequences reveal multiple ancient large-scale duplication events in the ancestor of Sphagnopsida (Bryophyta). THE NEW PHYTOLOGIST 2016; 211:300-18. [PMID: 26900928 DOI: 10.1111/nph.13887] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 01/04/2016] [Indexed: 05/07/2023]
Abstract
The goal of this research was to investigate whether there has been a whole-genome duplication (WGD) in the ancestry of Sphagnum (peatmoss) or the class Sphagnopsida, and to determine if the timing of any such duplication(s) and patterns of paralog retention could help explain the rapid radiation and current ecological dominance of peatmosses. RNA sequencing (RNA-seq) data were generated for nine taxa in Sphagnopsida (Bryophyta). Analyses of frequency plots for synonymous substitutions per synonymous site (Ks ) between paralogous gene pairs and reconciliation of 578 gene trees were conducted to assess evidence of large-scale or genome-wide duplication events in each transcriptome. Both Ks frequency plots and gene tree-based analyses indicate multiple duplication events in the history of the Sphagnopsida. The most recent WGD event predates divergence of Sphagnum from the two other genera of Sphagnopsida. Duplicate retention is highly variable across species, which might be best explained by local adaptation. Our analyses indicate that the last WGD could have been an important factor underlying the diversification of peatmosses and facilitated their rise to ecological dominance in peatlands. The timing of the duplication events and their significance in the evolutionary history of peat mosses are discussed.
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Affiliation(s)
- Nicolas Devos
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - Péter Szövényi
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, 8008, Zurich, Switzerland
- Institute of Systematic Botany, University of Zurich, 8057, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge-Batiment Genopode, 1015, Lausanne, Switzerland
- MTA ELTE-MTM Ecology Research Group, ELTE, Biological Institute, H1117, Budapest, Hungary
| | - David J Weston
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, 37831, USA
| | - Carl J Rothfels
- University Herbarium & Department of Integrative Biology, University of California, Berkeley, CA, 24720, USA
| | - Matthew G Johnson
- Chicago Botanic Garden, 1000 Lake Cook Road, Glencoe, IL, 60022, USA
| | - A Jonathan Shaw
- Department of Biology, Duke University, Durham, NC, 27708, USA
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Hou J, Ye N, Dong Z, Lu M, Li L, Yin T. Major Chromosomal Rearrangements Distinguish Willow and Poplar After the Ancestral "Salicoid" Genome Duplication. Genome Biol Evol 2016; 8:1868-75. [PMID: 27352946 PMCID: PMC4943198 DOI: 10.1093/gbe/evw127] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Populus (poplar) and Salix (willow) are sister genera in the Salicaceae family. In both lineages extant species are predominantly diploid. Genome analysis previously revealed that the two lineages originated from a common tetraploid ancestor. In this study, we conducted a syntenic comparison of the corresponding 19 chromosome members of the poplar and willow genomes. Our observations revealed that almost every chromosomal segment had a parallel paralogous segment elsewhere in the genomes, and the two lineages shared a similar syntenic pinwheel pattern for most of the chromosomes, which indicated that the two lineages diverged after the genome reorganization in the common progenitor. The pinwheel patterns showed distinct differences for two chromosome pairs in each lineage. Further analysis detected two major interchromosomal rearrangements that distinguished the karyotypes of willow and poplar. Chromosome I of willow was a conjunction of poplar chromosome XVI and the lower portion of poplar chromosome I, whereas willow chromosome XVI corresponded to the upper portion of poplar chromosome I. Scientists have suggested that Populus is evolutionarily more primitive than Salix. Therefore, we propose that, after the “salicoid” duplication event, fission and fusion of the ancestral chromosomes first give rise to the diploid progenitor of extant Populus species. During the evolutionary process, fission and fusion of poplar chromosomes I and XVI subsequently give rise to the progenitor of extant Salix species. This study contributes to an improved understanding of genome divergence after ancient genome duplication in closely related lineages of higher plants.
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Affiliation(s)
- Jing Hou
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Ning Ye
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Zhongyuan Dong
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Mengzhu Lu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Laigeng Li
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Tongming Yin
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
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Zheng F, Wu H, Zhang R, Li S, He W, Wong FL, Li G, Zhao S, Lam HM. Molecular phylogeny and dynamic evolution of disease resistance genes in the legume family. BMC Genomics 2016; 17:402. [PMID: 27229309 PMCID: PMC4881053 DOI: 10.1186/s12864-016-2736-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Accepted: 05/12/2016] [Indexed: 02/06/2023] Open
Abstract
Background Legumes are the second-most important crop family in agriculture for its economic and nutritional values. Disease resistance (R-) genes play an important role in responding to pathogen infections in plants. To further increase the yield of legume crops, we need a comprehensive understanding of the evolution of R-genes in the legume family. Results In this study, we developed a robust pipeline and identified a total of 4,217 R-genes in the genomes of seven sequenced legume species. A dramatic diversity of R-genes with structural variances indicated a rapid birth-and-death rate during the R-gene evolution in legumes. The number of R-genes transiently expanded and then quickly contracted after whole-genome duplications, which meant that R-genes were sensitive to subsequent diploidization. R proteins with the Coiled-coil (CC) domain are more conserved than others in legumes. Meanwhile, other types of legume R proteins with only one or two typical domains were subjected to higher rates of loss during evolution. Although R-genes evolved quickly in legumes, they tended to undergo purifying selection instead of positive selection during evolution. In addition, domestication events in some legume species preferentially selected for the genes directly involved in the plant-pathogen interaction pathway while suppressing those R-genes with low occurrence rates. Conclusions Our results provide insights into the dynamic evolution of R-genes in the legume family, which will be valuable for facilitating genetic improvements in the disease resistance of legume cultivars. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2736-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fengya Zheng
- Centre for Soybean Research, Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, New Territories, Hong Kong
| | - Haiyang Wu
- BGI-Shenzhen, Shenzhen, 518083, China.,HKU-BGI Bioinformatics Laboratory and Department of Computer Science, University of Hong Kong, Pofulam, Hong Kong
| | - Rongzhi Zhang
- Crop research institution, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | | | | | - Fuk-Ling Wong
- Centre for Soybean Research, Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, New Territories, Hong Kong
| | - Genying Li
- Crop research institution, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Shancen Zhao
- Centre for Soybean Research, Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, New Territories, Hong Kong. .,BGI-Shenzhen, Shenzhen, 518083, China.
| | - Hon-Ming Lam
- Centre for Soybean Research, Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, New Territories, Hong Kong.
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Wyrwa K, Książkiewicz M, Szczepaniak A, Susek K, Podkowiński J, Naganowska B. Integration of Lupinus angustifolius L. (narrow-leafed lupin) genome maps and comparative mapping within legumes. Chromosome Res 2016; 24:355-78. [PMID: 27168155 PMCID: PMC4969343 DOI: 10.1007/s10577-016-9526-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 04/14/2016] [Accepted: 04/24/2016] [Indexed: 11/30/2022]
Abstract
Narrow-leafed lupin (Lupinus angustifolius L.) has recently been considered a reference genome for the Lupinus genus. In the present work, genetic and cytogenetic maps of L. angustifolius were supplemented with 30 new molecular markers representing lupin genome regions, harboring genes involved in nitrogen fixation during the symbiotic interaction of legumes and soil bacteria (Rhizobiaceae). Our studies resulted in the precise localization of bacterial artificial chromosomes (BACs) carrying sequence variants for early nodulin 40, nodulin 26, nodulin 45, aspartate aminotransferase P2, asparagine synthetase, cytosolic glutamine synthetase, and phosphoenolpyruvate carboxylase. Together with previously mapped chromosomes, the integrated L. angustifolius map encompasses 73 chromosome markers, including 5S ribosomal DNA (rDNA) and 45S rDNA, and anchors 20 L. angustifolius linkage groups to corresponding chromosomes. Chromosomal identification using BAC fluorescence in situ hybridization identified two BAC clones as narrow-leafed lupin centromere-specific markers, which served as templates for preliminary studies of centromere composition within the genus. Bioinformatic analysis of these two BACs revealed that centromeric/pericentromeric regions of narrow-leafed lupin chromosomes consisted of simple sequence repeats ordered into tandem repeats containing the trinucleotide and pentanucleotide simple sequence repeats AGG and GATAC, structured into long arrays. Moreover, cross-genus microsynteny analysis revealed syntenic patterns of 31 single-locus BAC clones among several legume species. The gene and chromosome level findings provide evidence of ancient duplication events that must have occurred very early in the divergence of papilionoid lineages. This work provides a strong foundation for future comparative mapping among legumes and may facilitate understanding of mechanisms involved in shaping legume chromosomes.
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Affiliation(s)
- Katarzyna Wyrwa
- Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, Poznań, 60-479, Poland.
| | - Michał Książkiewicz
- Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, Poznań, 60-479, Poland
| | - Anna Szczepaniak
- Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, Poznań, 60-479, Poland
| | - Karolina Susek
- Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, Poznań, 60-479, Poland
| | - Jan Podkowiński
- Institute of Bioorganic Chemistry of the Polish Academy of Sciences, Z. Noskowskiego 12/14, Poznań, 61-704, Poland
| | - Barbara Naganowska
- Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, Poznań, 60-479, Poland
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Roque E, Fares MA, Yenush L, Rochina MC, Wen J, Mysore KS, Gómez-Mena C, Beltrán JP, Cañas LA. Evolution by gene duplication of Medicago truncatula PISTILLATA-like transcription factors. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:1805-1817. [PMID: 26773809 PMCID: PMC4783364 DOI: 10.1093/jxb/erv571] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
PISTILLATA (PI) is a member of the B-function MADS-box gene family, which controls the identity of both petals and stamens in Arabidopsis thaliana. In Medicago truncatula (Mt), there are two PI-like paralogs, known as MtPI and MtNGL9. These genes differ in their expression patterns, but it is not known whether their functions have also diverged. Describing the evolution of certain duplicated genes, such as transcription factors, remains a challenge owing to the complex expression patterns and functional divergence between the gene copies. Here, we report a number of functional studies, including analyses of gene expression, protein-protein interactions, and reverse genetic approaches designed to demonstrate the respective contributions of each M. truncatula PI-like paralog to the B-function in this species. Also, we have integrated molecular evolution approaches to determine the mode of evolution of Mt PI-like genes after duplication. Our results demonstrate that MtPI functions as a master regulator of B-function in M. truncatula, maintaining the overall ancestral function, while MtNGL9 does not seem to have a role in this regard, suggesting that the pseudogenization could be the functional evolutionary fate for this gene. However, we provide evidence that purifying selection is the primary evolutionary force acting on this paralog, pinpointing the conservation of its biochemical function and, alternatively, the acquisition of a new role for this gene.
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Affiliation(s)
- Edelín Roque
- Instituto de Biología Molecular y Celular de Plantas Consejo Superior de Investigaciones Científicas & Universidad Politécnica de Valencia (CSIC-UPV), Ciudad Politécnica de la Innovación, Edf. 8E, C/ Ingeniero Fausto Elio s/n, E-46011 Valencia, Spain
| | - Mario A Fares
- Instituto de Biología Molecular y Celular de Plantas Consejo Superior de Investigaciones Científicas & Universidad Politécnica de Valencia (CSIC-UPV), Ciudad Politécnica de la Innovación, Edf. 8E, C/ Ingeniero Fausto Elio s/n, E-46011 Valencia, Spain
| | - Lynne Yenush
- Instituto de Biología Molecular y Celular de Plantas Consejo Superior de Investigaciones Científicas & Universidad Politécnica de Valencia (CSIC-UPV), Ciudad Politécnica de la Innovación, Edf. 8E, C/ Ingeniero Fausto Elio s/n, E-46011 Valencia, Spain
| | - Mari Cruz Rochina
- Instituto de Biología Molecular y Celular de Plantas Consejo Superior de Investigaciones Científicas & Universidad Politécnica de Valencia (CSIC-UPV), Ciudad Politécnica de la Innovación, Edf. 8E, C/ Ingeniero Fausto Elio s/n, E-46011 Valencia, Spain
| | - Jiangqi Wen
- Plant Biology Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA
| | - Kirankumar S Mysore
- Plant Biology Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA
| | - Concepción Gómez-Mena
- Instituto de Biología Molecular y Celular de Plantas Consejo Superior de Investigaciones Científicas & Universidad Politécnica de Valencia (CSIC-UPV), Ciudad Politécnica de la Innovación, Edf. 8E, C/ Ingeniero Fausto Elio s/n, E-46011 Valencia, Spain
| | - José Pío Beltrán
- Instituto de Biología Molecular y Celular de Plantas Consejo Superior de Investigaciones Científicas & Universidad Politécnica de Valencia (CSIC-UPV), Ciudad Politécnica de la Innovación, Edf. 8E, C/ Ingeniero Fausto Elio s/n, E-46011 Valencia, Spain
| | - Luis A Cañas
- Instituto de Biología Molecular y Celular de Plantas Consejo Superior de Investigaciones Científicas & Universidad Politécnica de Valencia (CSIC-UPV), Ciudad Politécnica de la Innovación, Edf. 8E, C/ Ingeniero Fausto Elio s/n, E-46011 Valencia, Spain
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Vlasova A, Capella-Gutiérrez S, Rendón-Anaya M, Hernández-Oñate M, Minoche AE, Erb I, Câmara F, Prieto-Barja P, Corvelo A, Sanseverino W, Westergaard G, Dohm JC, Pappas GJ, Saburido-Alvarez S, Kedra D, Gonzalez I, Cozzuto L, Gómez-Garrido J, Aguilar-Morón MA, Andreu N, Aguilar OM, Garcia-Mas J, Zehnsdorf M, Vázquez MP, Delgado-Salinas A, Delaye L, Lowy E, Mentaberry A, Vianello-Brondani RP, García JL, Alioto T, Sánchez F, Himmelbauer H, Santalla M, Notredame C, Gabaldón T, Herrera-Estrella A, Guigó R. Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes. Genome Biol 2016; 17:32. [PMID: 26911872 PMCID: PMC4766624 DOI: 10.1186/s13059-016-0883-6] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2015] [Accepted: 01/22/2016] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Legumes are the third largest family of angiosperms and the second most important crop class. Legume genomes have been shaped by extensive large-scale gene duplications, including an approximately 58 million year old whole genome duplication shared by most crop legumes. RESULTS We report the genome and the transcription atlas of coding and non-coding genes of a Mesoamerican genotype of common bean (Phaseolus vulgaris L., BAT93). Using a comprehensive phylogenomics analysis, we assessed the past and recent evolution of common bean, and traced the diversification of patterns of gene expression following duplication. We find that successive rounds of gene duplications in legumes have shaped tissue and developmental expression, leading to increased levels of specialization in larger gene families. We also find that many long non-coding RNAs are preferentially expressed in germ-line-related tissues (pods and seeds), suggesting that they play a significant role in fruit development. Our results also suggest that most bean-specific gene family expansions, including resistance gene clusters, predate the split of the Mesoamerican and Andean gene pools. CONCLUSIONS The genome and transcriptome data herein generated for a Mesoamerican genotype represent a counterpart to the genomic resources already available for the Andean gene pool. Altogether, this information will allow the genetic dissection of the characters involved in the domestication and adaptation of the crop, and their further implementation in breeding strategies for this important crop.
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Affiliation(s)
- Anna Vlasova
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Salvador Capella-Gutiérrez
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
- Yeast and Basidiomycete Research Group, CBS Fungal Biodiversity Centre, Uppsalalaan 8, 3584 LT, Utrecht, The Netherlands
| | - Martha Rendón-Anaya
- Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav-Irapuato, CP 36821, Irapuato, Guanajuato, Mexico
| | - Miguel Hernández-Oñate
- Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav-Irapuato, CP 36821, Irapuato, Guanajuato, Mexico
| | - André E Minoche
- Garvan Institute of Medical Research, 384 Victoria Street, Sydney, NSW, 2010, Australia
| | - Ionas Erb
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Francisco Câmara
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Pablo Prieto-Barja
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - André Corvelo
- New York Genome Center, 101 Avenue of the Americas, New York, NY, 10013, USA
| | - Walter Sanseverino
- IRTA, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, 08193 Bellaterra, Barcelona, Catalonia, Spain
| | - Gastón Westergaard
- Instituto de Agrobiotecnología Rosario (INDEAR), Rosario, Santa Fe, 2000, Argentina
| | - Juliane C Dohm
- Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190, Vienna, Austria
| | - Georgios J Pappas
- Department of Cellular Biology, University of Brasilia, Biological Science Institute, Brasília, DF, 70790-160, Brazil
| | - Soledad Saburido-Alvarez
- Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav-Irapuato, CP 36821, Irapuato, Guanajuato, Mexico
| | - Darek Kedra
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Irene Gonzalez
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
- Genomics Unit, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Catalonia, Spain
| | - Luca Cozzuto
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Jessica Gómez-Garrido
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - María A Aguilar-Morón
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
- Genomics Unit, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Catalonia, Spain
| | - Nuria Andreu
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
- Genomics Unit, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Catalonia, Spain
| | - O Mario Aguilar
- Instituto de Biotecnología y Biología Molecular (IBBM), UNLP-CONICET, 1900, La Plata, Argentina
| | - Jordi Garcia-Mas
- IRTA, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, 08193 Bellaterra, Barcelona, Catalonia, Spain
| | - Maik Zehnsdorf
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
- Genomics Unit, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Catalonia, Spain
| | - Martín P Vázquez
- Instituto de Agrobiotecnología Rosario (INDEAR), Rosario, Santa Fe, 2000, Argentina
| | - Alfonso Delgado-Salinas
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Luis Delaye
- Departamento de Ingeniería Genética, Unidad Irapuato, Cinvestav, 36821, Irapuato, Guanajuato, Mexico
| | - Ernesto Lowy
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Alejandro Mentaberry
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (UBA), C1428EGA, Buenos Aires, Argentina
| | | | - José Luís García
- Environmental Biology Department, Centro de Investigaciones Biológicas, (CSIC), 28040, Madrid, Spain
| | - Tyler Alioto
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Federico Sánchez
- Depto. de Biología Molecular de Plantas, Instituto Biotecnología, Universidad Nacional Autónoma de México, 62210, Cuernavaca, Morelos, Mexico
| | - Heinz Himmelbauer
- Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190, Vienna, Austria
| | - Marta Santalla
- Mision Biológica de Galicia (MBG)-National Spanish Research Council (CSIC), 36080, Pontevedra, Spain
| | - Cedric Notredame
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Toni Gabaldón
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010, Barcelona, Spain.
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav-Irapuato, CP 36821, Irapuato, Guanajuato, Mexico.
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain.
- IMIM (Hospital del Mar Medical Research Institute), 08003, Barcelona, Spain.
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Gil-Quintana E, Lyon D, Staudinger C, Wienkoop S, González EM. Medicago truncatula and Glycine max: Different Drought Tolerance and Similar Local Response of the Root Nodule Proteome. J Proteome Res 2015; 14:5240-51. [PMID: 26503705 PMCID: PMC4673605 DOI: 10.1021/acs.jproteome.5b00617] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2015] [Indexed: 12/14/2022]
Abstract
Legume crops present important agronomical and environmental advantages mainly due to their capacity to reduce atmospheric N2 to ammonium via symbiotic nitrogen fixation (SNF). This process is very sensitive to abiotic stresses such as drought, but the mechanism underlying this response is not fully understood. The goal of the current work is to compare the drought response of two legumes with high economic impact and research importance, Medicago truncatula and Glycine max, by characterizing their root nodule proteomes. Our results show that, although M. truncatula exhibits lower water potential values under drought conditions compared to G. max, SNF declined analogously in the two legumes. Both of their nodule proteomes are very similar, and comparable down-regulation responses in the diverse protein functional groups were identified (mainly proteins related to the metabolism of carbon, nitrogen, and sulfur). We suggest lipoxygenases and protein turnover as newly recognized players in SNF regulation. Partial drought conditions applied to a split-root system resulted in the local down-regulation of the entire proteome of drought-stressed nodules in both legumes. The high degree of similarity between both legume proteomes suggests that the vast amount of research conducted on M. truncatula could be applied to economically important legume crops, such as soybean.
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Affiliation(s)
- Erena Gil-Quintana
- Department
of Environmental Sciences, Public University
of Navarra, E-31006 Pamplona, Spain
| | - David Lyon
- Department
of Molecular Systems Biology, University
of Vienna, Althanstrasse
14, 1090 Vienna, Austria
| | - Christiana Staudinger
- Department
of Molecular Systems Biology, University
of Vienna, Althanstrasse
14, 1090 Vienna, Austria
| | - Stefanie Wienkoop
- Department
of Molecular Systems Biology, University
of Vienna, Althanstrasse
14, 1090 Vienna, Austria
| | - Esther M. González
- Department
of Environmental Sciences, Public University
of Navarra, E-31006 Pamplona, Spain
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Development and Validation of EST-SSR Markers from the Transcriptome of Adzuki Bean (Vigna angularis). PLoS One 2015; 10:e0131939. [PMID: 26146990 PMCID: PMC4492930 DOI: 10.1371/journal.pone.0131939] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 06/08/2015] [Indexed: 11/28/2022] Open
Abstract
The adzuki bean (Vigna angularis (Ohwi) Ohwi and Ohashi) is an important grain legume of Asia. It is cultivated mainly in China, Japan and Korea. Despite its importance, few genomic resources are available for molecular genetic research of adzuki bean. In this study, we developed EST-SSR markers for the adzuki bean through next-generation sequencing. More than 112 million high-quality cDNA sequence reads were obtained from adzuki bean using Illumina paired-end sequencing technology, and the sequences were de novo assembled into 65,950 unigenes. The average length of the unigenes was 1,213 bp. Among the unigenes, 14,547 sequences contained a unique simple sequence repeat (SSR) and 3,350 sequences contained more than one SSR. A total of 7,947 EST-SSRs were identified as potential molecular markers, with mono-nucleotide A/T repeats (99.0%) as the most abundant motif class, followed by AG/CT (68.4%), AAG/CTT (30.0%), AAAG/CTTT (26.2%), AAAAG/CTTTT (16.1%), and AACGGG/CCCGTT (6.0%). A total of 500 SSR markers were randomly selected for validation, of which 296 markers produced reproducible amplicons with 38 polymorphic markers among the 32 adzuki bean genotypes selected from diverse geographical locations across China. The large number of SSR-containing sequences and EST-SSR markers will be valuable for genetic analysis of the adzuki bean and related Vigna species.
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Raudaskoski M, Kothe E. Novel findings on the role of signal exchange in arbuscular and ectomycorrhizal symbioses. MYCORRHIZA 2015; 25:243-52. [PMID: 25260351 DOI: 10.1007/s00572-014-0607-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 09/16/2014] [Indexed: 05/11/2023]
Abstract
The availability of genome sequences from both arbuscular and ectomycorrhizal fungi and their hosts has, together with elegant biochemical and molecular biological analyses, provided new information on signal exchange between the partners in mycorrhizal associations. The progress in understanding cellular processes has been more rapid in arbuscular than ectomycorrhizal symbiosis due to its similarities of early processes with Rhizobium-legume symbiosis. In ectomycorrhiza, the role of auxin and ethylene produced by both fungus and host plant is becoming understood at the molecular level, although the actual ligands and receptors leading to ectomycorrhizal symbiosis have not yet been discovered. For both systems, the functions of small effector proteins secreted from the respective fungus and taken up into the plant cell may be pivotal in understanding the attenuation of host defense. We review the subject by comparing cross-talk between fungal and plant partners during formation and establishment of arbuscular and ectomycorrhizal symbioses.
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Affiliation(s)
- Marjatta Raudaskoski
- Department of Biochemistry, Molecular Plant Biology, University of Turku, 20014, Turku, Finland
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Pankievicz VCS, do Amaral FP, Santos KFDN, Agtuca B, Xu Y, Schueller MJ, Arisi ACM, Steffens MBR, de Souza EM, Pedrosa FO, Stacey G, Ferrieri RA. Robust biological nitrogen fixation in a model grass-bacterial association. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 81:907-19. [PMID: 25645593 DOI: 10.1111/tpj.12777] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 01/15/2015] [Accepted: 01/20/2015] [Indexed: 05/18/2023]
Abstract
Nitrogen-fixing rhizobacteria can promote plant growth; however, it is controversial whether biological nitrogen fixation (BNF) from associative interaction contributes to growth promotion. The roots of Setaria viridis, a model C4 grass, were effectively colonized by bacterial inoculants resulting in a significant enhancement of growth. Nitrogen-13 tracer studies provided direct evidence for tracer uptake by the host plant and incorporation into protein. Indeed, plants showed robust growth under nitrogen-limiting conditions when inoculated with an ammonium-excreting strain of Azospirillum brasilense. (11)C-labeling experiments showed that patterns in central carbon metabolism and resource allocation exhibited by nitrogen-starved plants were largely reversed by bacterial inoculation, such that they resembled plants grown under nitrogen-sufficient conditions. Adoption of S. viridis as a model should promote research into the mechanisms of associative nitrogen fixation with the ultimate goal of greater adoption of BNF for sustainable crop production.
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Affiliation(s)
- Vânia C S Pankievicz
- Department of Biochemistry and Molecular Biology, Federal University of Paraná, 81531-980, Curitiba, Brazil
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Cserhati M. Motif content comparison between monocot and dicot species. GENOMICS DATA 2015; 3:128-36. [PMID: 26484161 PMCID: PMC4535654 DOI: 10.1016/j.gdata.2014.12.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 12/29/2014] [Accepted: 12/30/2014] [Indexed: 01/04/2023]
Abstract
While a number of DNA sequence motifs have been functionally characterized, the full repertoire of motifs in an organism (the motifome) is yet to be characterized. The present study wishes to widen the scope of motif content analysis in different monocot and dicot species that include both rice species, Brachypodium, corn, wheat as monocots and Arabidopsis, Lotus japonica, Medicago truncatula, and Populus tremula as dicots. All possible existing motifs were analyzed in different regions of genomes such as were found in different sets of sequences in these species: the whole genome, core proximal and distal promoters, 5′ and 3′ UTRs, and the 1st introns. Due to the increased number of species involved in this study compared to previous works, species relationships were analyzed based on the similarity of common motif content. Certain secondary structure elements were inferred in the genomes of these species as well as new unknown motifs. The distribution of 20 motifs common to the studied species were found to have a significantly larger occurrence within the promoters and 3′ UTRs of genes, both being regulatory regions. Motifs common to the promoter regions of japonica rice, Brachypodium, and corn were also found in a number of orthologous and paralogous genes. Some of our motifs were found to be complementary to miRNA elements in Brachypodium distachyon and japonica rice.
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Affiliation(s)
- Matyas Cserhati
- Department of Genetics, Cell Biology, and Anatomy, 985805 Nebraska Medical Center, Omaha, NE, 68198-5805, United States
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Kim SK, Nair RM, Lee J, Lee SH. Genomic resources in mungbean for future breeding programs. FRONTIERS IN PLANT SCIENCE 2015; 6:626. [PMID: 26322067 PMCID: PMC4530597 DOI: 10.3389/fpls.2015.00626] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 07/28/2015] [Indexed: 05/03/2023]
Abstract
Among the legume family, mungbean (Vigna radiata) has become one of the important crops in Asia, showing a steady increase in global production. It provides a good source of protein and contains most notably folate and iron. Beyond the nutritional value of mungbean, certain features make it a well-suited model organism among legume plants because of its small genome size, short life-cycle, self-pollinating, and close genetic relationship to other legumes. In the past, there have been several efforts to develop molecular markers and linkage maps associated with agronomic traits for the genetic improvement of mungbean and, ultimately, breeding for cultivar development to increase the average yields of mungbean. The recent release of a reference genome of the cultivated mungbean (V. radiata var. radiata VC1973A) and an additional de novo sequencing of a wild relative mungbean (V. radiata var. sublobata) has provided a framework for mungbean genetic and genome research, that can further be used for genome-wide association and functional studies to identify genes related to specific agronomic traits. Moreover, the diverse gene pool of wild mungbean comprises valuable genetic resources of beneficial genes that may be helpful in widening the genetic diversity of cultivated mungbean. This review paper covers the research progress on molecular and genomics approaches and the current status of breeding programs that have developed to move toward the ultimate goal of mungbean improvement.
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Affiliation(s)
- Sue K. Kim
- Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National UniversitySeoul, South Korea
| | | | - Jayern Lee
- Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National UniversitySeoul, South Korea
| | - Suk-Ha Lee
- Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National UniversitySeoul, South Korea
- Plant Genomics and Breeding Institute, Seoul National UniversitySeoul, South Korea
- *Correspondence: Suk-Ha Lee, Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, South Korea,
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Gujaria-Verma N, Vail SL, Carrasquilla-Garcia N, Penmetsa RV, Cook DR, Farmer AD, Vandenberg A, Bett KE. Genetic mapping of legume orthologs reveals high conservation of synteny between lentil species and the sequenced genomes of Medicago and chickpea. FRONTIERS IN PLANT SCIENCE 2014; 5:676. [PMID: 25538716 PMCID: PMC4256995 DOI: 10.3389/fpls.2014.00676] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 11/13/2014] [Indexed: 05/23/2023]
Abstract
Lentil (Lens culinaris Medik.) is a global food crop with increasing importance for food security in south Asia and other regions. Lens ervoides, a wild relative of cultivated lentil, is an important source of agronomic trait variation. Lens is a member of the galegoid clade of the Papilionoideae family, which includes other important dietary legumes such as chickpea (Cicer arietinum) and pea (Pisum sativum), and the sequenced model legume Medicago truncatula. Understanding the genetic structure of Lens spp. in relation to more fully sequenced legumes would allow leveraging of genomic resources. A set of 1107 TOG-based amplicons were identified in L. ervoides and a subset thereof used to design SNP markers for mapping. A map of L. ervoides consisting of 377 SNP markers spread across seven linkage groups was developed using a GoldenGate genotyping array and single SNP marker assays. Comparison with maps of M. truncatula and L. culinaris documented considerable shared synteny and led to the identification of a few major translocations and a major inversion that distinguish Lens from M. truncatula, as well as a translocation that distinguishes L. culinaris from L. ervoides. The identification of chromosome-level differences among Lens spp. will aid in the understanding of introgression of genes from L. ervoides into cultivated L. culinaris, furthering genetic research and breeding applications in lentil.
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Affiliation(s)
- Neha Gujaria-Verma
- Department of Plant Sciences, University of SaskatchewanSaskatoon, SK, Canada
| | - Sally L. Vail
- Department of Plant Sciences, University of SaskatchewanSaskatoon, SK, Canada
- Department of Plant Pathology, University of California, DavisDavis, CA, USA
| | | | - R. Varma Penmetsa
- Department of Plant Pathology, University of California, DavisDavis, CA, USA
| | - Douglas R. Cook
- Department of Plant Pathology, University of California, DavisDavis, CA, USA
| | - Andrew D. Farmer
- Bioinformatics, National Centre for Genomic ResourcesSanta Fe, NM, USA
| | - Albert Vandenberg
- Department of Plant Sciences, University of SaskatchewanSaskatoon, SK, Canada
| | - Kirstin E. Bett
- Department of Plant Sciences, University of SaskatchewanSaskatoon, SK, Canada
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