The genome of a wild Medicago species provides insights into the tolerant mechanisms of legume forage to environmental stress
Abstract Background Medicago ruthenica, a wild and perennial legume forage widely distributed in semi-arid grasslands, is distinguished by its outstanding tolerance to environmental stress. It is a close relative of commonly cultivated forage of alfalfa (Medicago sativa). The high tolerance of M. ru...
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2021-05-01
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| Series: | BMC Biology |
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| Online Access: | https://doi.org/10.1186/s12915-021-01033-0 |
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doaj-b3f7b19e638d41958a8770367372750d2021-05-09T11:29:51ZengBMCBMC Biology1741-70072021-05-0119111710.1186/s12915-021-01033-0The genome of a wild Medicago species provides insights into the tolerant mechanisms of legume forage to environmental stressTianzuo Wang0Lifei Ren1Caihong Li2Di Zhang3Xiuxiu Zhang4Gang Zhou5Dan Gao6Rujin Chen7Yuhui Chen8Zhaolan Wang9Fengling Shi10Andrew D. Farmer11Yansu Li12Mengyan Zhou13Nevin D. Young14Wen-Hao Zhang15State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, The Chinese Academy of SciencesState Key Laboratory of Vegetation and Environmental Change, Institute of Botany, The Chinese Academy of SciencesState Key Laboratory of Vegetation and Environmental Change, Institute of Botany, The Chinese Academy of SciencesState Key Laboratory of Vegetation and Environmental Change, Institute of Botany, The Chinese Academy of SciencesState Key Laboratory of Vegetation and Environmental Change, Institute of Botany, The Chinese Academy of SciencesNovogene Bioinformatics InstituteNovogene Bioinformatics InstituteSchool of Life Sciences, Lanzhou UniversitySchool of Life Sciences, Lanzhou UniversityInstitute of Grassland Research, Chinese Academy of Agricultural SciencesCollege of Ecology and Environmental Science, Inner Mongolia Agricultural UniversityNational Centre for Genome ResourcesInstitute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesNovogene Bioinformatics InstituteDepartments of Plant Pathology and Plant Biology, University of MinnesotaState Key Laboratory of Vegetation and Environmental Change, Institute of Botany, The Chinese Academy of SciencesAbstract Background Medicago ruthenica, a wild and perennial legume forage widely distributed in semi-arid grasslands, is distinguished by its outstanding tolerance to environmental stress. It is a close relative of commonly cultivated forage of alfalfa (Medicago sativa). The high tolerance of M. ruthenica to environmental stress makes this species a valuable genetic resource for understanding and improving traits associated with tolerance to harsh environments. Results We sequenced and assembled genome of M. ruthenica using an integrated approach, including PacBio, Illumina, 10×Genomics, and Hi-C. The assembled genome was 904.13 Mb with scaffold N50 of 99.39 Mb, and 50,162 protein-coding genes were annotated. Comparative genomics and transcriptomic analyses were used to elucidate mechanisms underlying its tolerance to environmental stress. The expanded FHY3/FAR1 family was identified to be involved in tolerance of M. ruthenica to drought stress. Many genes involved in tolerance to abiotic stress were retained in M. ruthenica compared to other cultivated Medicago species. Hundreds of candidate genes associated with drought tolerance were identified by analyzing variations in single nucleotide polymorphism using accessions of M. ruthenica with varying tolerance to drought. Transcriptomic data demonstrated the involvements of genes related to transcriptional regulation, stress response, and metabolic regulation in tolerance of M. ruthenica. Conclusions We present a high-quality genome assembly and identification of drought-related genes in the wild species of M. ruthenica, providing a valuable resource for genomic studies on perennial legume forages.https://doi.org/10.1186/s12915-021-01033-0Wild genetic resourceGenomeEvolutionDomesticationComparative genomicsTranscriptome |
| collection |
DOAJ |
| language |
English |
| format |
Article |
| sources |
DOAJ |
| author |
Tianzuo Wang Lifei Ren Caihong Li Di Zhang Xiuxiu Zhang Gang Zhou Dan Gao Rujin Chen Yuhui Chen Zhaolan Wang Fengling Shi Andrew D. Farmer Yansu Li Mengyan Zhou Nevin D. Young Wen-Hao Zhang |
| spellingShingle |
Tianzuo Wang Lifei Ren Caihong Li Di Zhang Xiuxiu Zhang Gang Zhou Dan Gao Rujin Chen Yuhui Chen Zhaolan Wang Fengling Shi Andrew D. Farmer Yansu Li Mengyan Zhou Nevin D. Young Wen-Hao Zhang The genome of a wild Medicago species provides insights into the tolerant mechanisms of legume forage to environmental stress BMC Biology Wild genetic resource Genome Evolution Domestication Comparative genomics Transcriptome |
| author_facet |
Tianzuo Wang Lifei Ren Caihong Li Di Zhang Xiuxiu Zhang Gang Zhou Dan Gao Rujin Chen Yuhui Chen Zhaolan Wang Fengling Shi Andrew D. Farmer Yansu Li Mengyan Zhou Nevin D. Young Wen-Hao Zhang |
| author_sort |
Tianzuo Wang |
| title |
The genome of a wild Medicago species provides insights into the tolerant mechanisms of legume forage to environmental stress |
| title_short |
The genome of a wild Medicago species provides insights into the tolerant mechanisms of legume forage to environmental stress |
| title_full |
The genome of a wild Medicago species provides insights into the tolerant mechanisms of legume forage to environmental stress |
| title_fullStr |
The genome of a wild Medicago species provides insights into the tolerant mechanisms of legume forage to environmental stress |
| title_full_unstemmed |
The genome of a wild Medicago species provides insights into the tolerant mechanisms of legume forage to environmental stress |
| title_sort |
genome of a wild medicago species provides insights into the tolerant mechanisms of legume forage to environmental stress |
| publisher |
BMC |
| series |
BMC Biology |
| issn |
1741-7007 |
| publishDate |
2021-05-01 |
| description |
Abstract Background Medicago ruthenica, a wild and perennial legume forage widely distributed in semi-arid grasslands, is distinguished by its outstanding tolerance to environmental stress. It is a close relative of commonly cultivated forage of alfalfa (Medicago sativa). The high tolerance of M. ruthenica to environmental stress makes this species a valuable genetic resource for understanding and improving traits associated with tolerance to harsh environments. Results We sequenced and assembled genome of M. ruthenica using an integrated approach, including PacBio, Illumina, 10×Genomics, and Hi-C. The assembled genome was 904.13 Mb with scaffold N50 of 99.39 Mb, and 50,162 protein-coding genes were annotated. Comparative genomics and transcriptomic analyses were used to elucidate mechanisms underlying its tolerance to environmental stress. The expanded FHY3/FAR1 family was identified to be involved in tolerance of M. ruthenica to drought stress. Many genes involved in tolerance to abiotic stress were retained in M. ruthenica compared to other cultivated Medicago species. Hundreds of candidate genes associated with drought tolerance were identified by analyzing variations in single nucleotide polymorphism using accessions of M. ruthenica with varying tolerance to drought. Transcriptomic data demonstrated the involvements of genes related to transcriptional regulation, stress response, and metabolic regulation in tolerance of M. ruthenica. Conclusions We present a high-quality genome assembly and identification of drought-related genes in the wild species of M. ruthenica, providing a valuable resource for genomic studies on perennial legume forages. |
| topic |
Wild genetic resource Genome Evolution Domestication Comparative genomics Transcriptome |
| url |
https://doi.org/10.1186/s12915-021-01033-0 |
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