Sequence and expression variation in SUPPRESSOR of OVEREXPRESSION of CONSTANS 1 (SOC1): homeolog evolution in Indian Brassicas

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• 作者：Tanu Sri ; Pratiksha Mayee ; Anandita Singh
• 关键词：SOC1 ; Gene fractionation ; Homeolog divergence ; MIKC transcription factors ; Regulatory evolution
• 刊名：Development Genes and Evolution
• 出版年：2015
• 出版时间：September 2015
• 年：2015
• 卷：225
• 期：5
• 页码：287-303
• 全文大小：1,503 KB
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• 作者单位：Tanu Sri (1)
  Pratiksha Mayee (1) (2)
  Anandita Singh (1)
  
  1. Department of Biotechnology, TERI University, 10 Institutional Area, Vasant Kunj, New Delhi, 110070, India
  2. Department of Research, Ankur Seeds Pvt. Ltd., Nagpur, 440018, India
  
• 刊物类别：Biomedical and Life Sciences
• 刊物主题：Life Sciences
  Developmental Biology
  Neurosciences
  Cell Biology
  
• 出版者：Springer Berlin / Heidelberg
• ISSN：1432-041X

文摘

Whole genome sequence analyses allow unravelling such evolutionary consequences of meso-triplication event in Brassicaceae (?4-0 million years ago (MYA)) as differential gene fractionation and diversification in homeologous sub-genomes. This study presents a simple gene-centric approach involving microsynteny and natural genetic variation analysis for understanding SUPPRESSOR of OVEREXPRESSION of CONSTANS 1 (SOC1) homeolog evolution in Brassica. Analysis of microsynteny in Brassica rapa homeologous regions containing SOC1 revealed differential gene fractionation correlating to reported fractionation status of sub-genomes of origin, viz. least fractionated (LF), moderately fractionated 1 (MF1) and most fractionated (MF2), respectively. Screening 18 cultivars of 6 Brassica species led to the identification of 8 genomic and 27 transcript variants of SOC1, including splice-forms. Co-occurrence of both interrupted and intronless SOC1 genes was detected in few Brassica species. In silico analysis characterised Brassica SOC1 as MADS intervening, K-box, C-terminal (MIKCC) transcription factor, with highly conserved MADS and I domains relative to K-box and C-terminal domain. Phylogenetic analyses and multiple sequence alignments depicting shared pattern of silent/non-silent mutations assigned Brassica SOC1 homologs into groups based on shared diploid base genome. In addition, a sub-genome structure in uncharacterised Brassica genomes was inferred. Expression analysis of putative MF2 and LF (Brassica diploid base genome A (AA)) sub-genome-specific SOC1 homeologs of Brassica juncea revealed near identical expression pattern. However, MF2-specific homeolog exhibited significantly higher expression implying regulatory diversification. In conclusion, evidence for polyploidy-induced sequence and regulatory evolution in Brassica SOC1 is being presented wherein differential homeolog expression is implied in functional diversification. Keywords SOC1 Gene fractionation Homeolog divergence MIKC transcription factors Regulatory evolution