Genome−wide identification and analysis of LEA_2 gene family in alfalfa (Medicago sativa L.) under aluminum stress
Late embryonic development abundant proteins (LEAs) are a large family of proteins commonly existing in plants. LEA_2 is the largest subfamily in the LEA, it plays an important role in plant resistance to abiotic stress. In order to explore the characteristics of LEA_2 gene family members in alfalfa...
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| Format: | Article |
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Frontiers Media S.A.
2022-11-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2022.976160/full |
| _version_ | 1811211871550701568 |
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| author | Yujing Zhang Nana Fan Wuwu Wen Siyan Liu Xin Mo Yuan An Yuan An Peng Zhou |
| author_facet | Yujing Zhang Nana Fan Wuwu Wen Siyan Liu Xin Mo Yuan An Yuan An Peng Zhou |
| author_sort | Yujing Zhang |
| collection | DOAJ |
| description | Late embryonic development abundant proteins (LEAs) are a large family of proteins commonly existing in plants. LEA_2 is the largest subfamily in the LEA, it plays an important role in plant resistance to abiotic stress. In order to explore the characteristics of LEA_2 gene family members in alfalfa (Medicago sativa L.), 155 members of LEA_2 (MsLEA_2) family were identified from alfalfa genome. Bioinformatics analysis was conducted from the aspects of phylogenetic relationship, chromosome distribution, chromosome colinearity, physical and chemical properties, motif composition, exon-intron structure, cis-element and so on. Expression profiles of MsLEA_2 gene were obtained based on Real-time fluorescent quantitative PCR (qRT-PCR) analysis and previous RNA-seq data under aluminum (Al) stress. Bioinformatics results were shown that the MsLEA_2 genes are distributed on all 32 chromosomes. Among them, 85 genes were present in the gene clusters, accounting for 54.83%, and chromosome Chr7.3 carries the largest number of MsLEA_2 (19 LEA_2 genes on Chr7.3). Chr7.3 has a unique structure of MsLEA_2 distribution, which reveals a possible special role of Chr7.3 in ensuring the function of MsLEA_2. Transcriptional structure analysis revealed that the number of exons in each gene varies from 1 to 3, and introns varies from 0 to 2. Cis-element analysis identified that the promoter region of MsLEA_2 is rich in ABRE, MBS, LTR, and MeJARE, indicating MsLEA_2 has stress resistance potential under abiotic stress. RNA-seq data and qRT-PCR analyses showed that most of the MsLEA_2 members were up-regulated when alfalfa exposed to Al stress. This study revealed that phylogenetic relationship and possible function of LEA_ 2 gene in alfalfa, which were helpful for the functional analysis of LEA_ 2 proteins in the future and provided a new theoretical basis for improving Al tolerance of alfalfa. |
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| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-04-12T05:20:41Z |
| publishDate | 2022-11-01 |
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| series | Frontiers in Plant Science |
| spelling | doaj.art-e92012fc14174a7c909821bba642e2ab2022-12-22T03:46:29ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2022-11-011310.3389/fpls.2022.976160976160Genome−wide identification and analysis of LEA_2 gene family in alfalfa (Medicago sativa L.) under aluminum stressYujing Zhang0Nana Fan1Wuwu Wen2Siyan Liu3Xin Mo4Yuan An5Yuan An6Peng Zhou7School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, ChinaSchool of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, ChinaSchool of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, ChinaSchool of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, ChinaSchool of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, ChinaSchool of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, ChinaKey Laboratory of Urban Agriculture, Ministry of Agriculture, Shanghai, ChinaSchool of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, ChinaLate embryonic development abundant proteins (LEAs) are a large family of proteins commonly existing in plants. LEA_2 is the largest subfamily in the LEA, it plays an important role in plant resistance to abiotic stress. In order to explore the characteristics of LEA_2 gene family members in alfalfa (Medicago sativa L.), 155 members of LEA_2 (MsLEA_2) family were identified from alfalfa genome. Bioinformatics analysis was conducted from the aspects of phylogenetic relationship, chromosome distribution, chromosome colinearity, physical and chemical properties, motif composition, exon-intron structure, cis-element and so on. Expression profiles of MsLEA_2 gene were obtained based on Real-time fluorescent quantitative PCR (qRT-PCR) analysis and previous RNA-seq data under aluminum (Al) stress. Bioinformatics results were shown that the MsLEA_2 genes are distributed on all 32 chromosomes. Among them, 85 genes were present in the gene clusters, accounting for 54.83%, and chromosome Chr7.3 carries the largest number of MsLEA_2 (19 LEA_2 genes on Chr7.3). Chr7.3 has a unique structure of MsLEA_2 distribution, which reveals a possible special role of Chr7.3 in ensuring the function of MsLEA_2. Transcriptional structure analysis revealed that the number of exons in each gene varies from 1 to 3, and introns varies from 0 to 2. Cis-element analysis identified that the promoter region of MsLEA_2 is rich in ABRE, MBS, LTR, and MeJARE, indicating MsLEA_2 has stress resistance potential under abiotic stress. RNA-seq data and qRT-PCR analyses showed that most of the MsLEA_2 members were up-regulated when alfalfa exposed to Al stress. This study revealed that phylogenetic relationship and possible function of LEA_ 2 gene in alfalfa, which were helpful for the functional analysis of LEA_ 2 proteins in the future and provided a new theoretical basis for improving Al tolerance of alfalfa.https://www.frontiersin.org/articles/10.3389/fpls.2022.976160/fullalfalfaLEAgene familychromosomegene structurealuminum stress |
| spellingShingle | Yujing Zhang Nana Fan Wuwu Wen Siyan Liu Xin Mo Yuan An Yuan An Peng Zhou Genome−wide identification and analysis of LEA_2 gene family in alfalfa (Medicago sativa L.) under aluminum stress Frontiers in Plant Science alfalfa LEA gene family chromosome gene structure aluminum stress |
| title | Genome−wide identification and analysis of LEA_2 gene family in alfalfa (Medicago sativa L.) under aluminum stress |
| title_full | Genome−wide identification and analysis of LEA_2 gene family in alfalfa (Medicago sativa L.) under aluminum stress |
| title_fullStr | Genome−wide identification and analysis of LEA_2 gene family in alfalfa (Medicago sativa L.) under aluminum stress |
| title_full_unstemmed | Genome−wide identification and analysis of LEA_2 gene family in alfalfa (Medicago sativa L.) under aluminum stress |
| title_short | Genome−wide identification and analysis of LEA_2 gene family in alfalfa (Medicago sativa L.) under aluminum stress |
| title_sort | genome wide identification and analysis of lea 2 gene family in alfalfa medicago sativa l under aluminum stress |
| topic | alfalfa LEA gene family chromosome gene structure aluminum stress |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2022.976160/full |
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