Genome-wide identification and characterization of the lateral organ boundaries domain gene family in Brassica rapa var. rapa

doi:10.1016/j.pld.2019.11.004

Plant Diversity ›› 2020, Vol. 42 ›› Issue (01): 52-60.DOI: 10.1016/j.pld.2019.11.004

Genome-wide identification and characterization of the lateral organ boundaries domain gene family in Brassica rapa var. rapa

Qin Yu^a,b,c,d, Simin Hu^a,b,c,d, Jiancan Du^a,b,c,d, Yongping Yang^a,b,c, Xudong Sun^a,b,c

a Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming 650201, China;
b Plant Germplasm and Genomics Center, The Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China;
c Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China;
d University of the Chinese Academy of Sciences, Beijing 100049, China

收稿日期:2018-01-15 修回日期:2019-11-15 出版日期:2020-02-25 发布日期:2020-02-29
通讯作者: Yongping Yang, Xudong Sun
基金资助:
This study was supported by the Major Program of National Natural Science Foundation of China,China (31590820 and 31590823), the National Natural Science Foundation of China, China (41771123 and 31400244) and the Natural Science Foundation of Yunnan Province (2017FB050).

Genome-wide identification and characterization of the lateral organ boundaries domain gene family in Brassica rapa var. rapa

Qin Yu^a,b,c,d, Simin Hu^a,b,c,d, Jiancan Du^a,b,c,d, Yongping Yang^a,b,c, Xudong Sun^a,b,c

a Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming 650201, China;
b Plant Germplasm and Genomics Center, The Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China;
c Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China;
d University of the Chinese Academy of Sciences, Beijing 100049, China

Received:2018-01-15 Revised:2019-11-15 Online:2020-02-25 Published:2020-02-29
Contact: Yongping Yang, Xudong Sun
Supported by:
This study was supported by the Major Program of National Natural Science Foundation of China,China (31590820 and 31590823), the National Natural Science Foundation of China, China (41771123 and 31400244) and the Natural Science Foundation of Yunnan Province (2017FB050).

摘要/Abstract

摘要： The Lateral Organ Boundaries Domain (LBD) genes encode highly conserved plant-specific LOB domain proteins which regulate growth and development in various species. However, members of the LBD gene family have yet to be identified in Brassica rapa var. rapa. In the present study, fifty-nine LBD genes were identified and distributed on 10 chromosomes. The BrrLBD proteins are predicted to encode hydrophobic polypeptides between 118 and 394 amino acids in length and with molecular weights ranging from 13.31 to 44.24 kDa; the theoretical pI for these proteins varies from 4.83 to 9.68. There were 17 paralogous gene pairs in the BrrLBD family, suggesting that the amplification of the BrrLBD gene family involved largescale gene duplication events. Members of the BrrLBD family were divided into 7 subclades (class I a to e, class II a and b). Analysis of gene structure and conserved domains revealed that most BrrLBD genes of the same subclade had similar gene structures and protein motifs. The expression profiles of 59 BrrLBD genes were determined through Quantitative Real-time fluorescent PCR (qRT-PCR). Most BrrLBD genes in the same subclade had similar gene expression profiles. However, the expression patterns of 7 genes differed from their duplicates, indicating that although the gene function of most BrrLBD genes has been conserved, some BrrLBD genes may have undergone evolutionary change.

关键词: LBD, Transcription factors, LBD gene sequence analysis, Expression profiles, Brassica rapa var. rapa

Abstract: The Lateral Organ Boundaries Domain (LBD) genes encode highly conserved plant-specific LOB domain proteins which regulate growth and development in various species. However, members of the LBD gene family have yet to be identified in Brassica rapa var. rapa. In the present study, fifty-nine LBD genes were identified and distributed on 10 chromosomes. The BrrLBD proteins are predicted to encode hydrophobic polypeptides between 118 and 394 amino acids in length and with molecular weights ranging from 13.31 to 44.24 kDa; the theoretical pI for these proteins varies from 4.83 to 9.68. There were 17 paralogous gene pairs in the BrrLBD family, suggesting that the amplification of the BrrLBD gene family involved largescale gene duplication events. Members of the BrrLBD family were divided into 7 subclades (class I a to e, class II a and b). Analysis of gene structure and conserved domains revealed that most BrrLBD genes of the same subclade had similar gene structures and protein motifs. The expression profiles of 59 BrrLBD genes were determined through Quantitative Real-time fluorescent PCR (qRT-PCR). Most BrrLBD genes in the same subclade had similar gene expression profiles. However, the expression patterns of 7 genes differed from their duplicates, indicating that although the gene function of most BrrLBD genes has been conserved, some BrrLBD genes may have undergone evolutionary change.

Key words: LBD, Transcription factors, LBD gene sequence analysis, Expression profiles, Brassica rapa var. rapa

Qin Yu, Simin Hu, Jiancan Du, Yongping Yang, Xudong Sun. Genome-wide identification and characterization of the lateral organ boundaries domain gene family in Brassica rapa var. rapa[J]. Plant Diversity, 2020, 42(01): 52-60.

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Genome-wide identification and characterization of the lateral organ boundaries domain gene family in Brassica rapa var. rapa

Genome-wide identification and characterization of the lateral organ boundaries domain gene family in Brassica rapa var. rapa

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