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Genome-wide analysis of the AP2/ERF family in Musa species reveals divergence and neofunctionalisation during evolution.
Sci Rep. 2016 Jan 06; 6:18878.SR

Abstract

AP2/ERF domain containing transcription factor super family is one of the important regulators in the plant kingdom. The involvement of AP2/ERF family members has been elucidated in various processes associated with plant growth, development as well as in response to hormones, biotic and abiotic stresses. In this study, we carried out genome-wide analysis to identify members of AP2/ERF family in Musa acuminata (A genome) and Musa balbisiana (B genome) and changes leading to neofunctionalisation of genes. Analysis identified 265 and 318 AP2/ERF encoding genes in M. acuminata and M. balbisiana respectively which were further classified into ERF, DREB, AP2, RAV and Soloist groups. Comparative analysis indicated that AP2/ERF family has undergone duplication, loss and divergence during evolution and speciation of the Musa A and B genomes. We identified nine genes which are up-regulated during fruit ripening and might be components of the regulatory machinery operating during ethylene-dependent ripening in banana. Tissue-specific expression analysis of the genes suggests that different regulatory mechanisms might be involved in peel and pulp ripening process through recruiting specific ERFs in these tissues. Analysis also suggests that MaRAV-6 and MaERF026 have structurally diverged from their M. balbisiana counterparts and have attained new functions during ripening.

Authors+Show Affiliations

CSIR-National Botanical Research Institute, Council of Scientific and Industrial Research (CSIR-NBRI), Rana Pratap Marg, Lucknow-226001, INDIA. Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi-110 001, India.CSIR-National Botanical Research Institute, Council of Scientific and Industrial Research (CSIR-NBRI), Rana Pratap Marg, Lucknow-226001, INDIA.CSIR-National Botanical Research Institute, Council of Scientific and Industrial Research (CSIR-NBRI), Rana Pratap Marg, Lucknow-226001, INDIA.CSIR-National Botanical Research Institute, Council of Scientific and Industrial Research (CSIR-NBRI), Rana Pratap Marg, Lucknow-226001, INDIA. Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi-110 001, India.CSIR-National Botanical Research Institute, Council of Scientific and Industrial Research (CSIR-NBRI), Rana Pratap Marg, Lucknow-226001, INDIA. Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi-110 001, India.CSIR-National Botanical Research Institute, Council of Scientific and Industrial Research (CSIR-NBRI), Rana Pratap Marg, Lucknow-226001, INDIA. Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi-110 001, India.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

26733055

Citation

Lakhwani, Deepika, et al. "Genome-wide Analysis of the AP2/ERF Family in Musa Species Reveals Divergence and Neofunctionalisation During Evolution." Scientific Reports, vol. 6, 2016, p. 18878.
Lakhwani D, Pandey A, Dhar YV, et al. Genome-wide analysis of the AP2/ERF family in Musa species reveals divergence and neofunctionalisation during evolution. Sci Rep. 2016;6:18878.
Lakhwani, D., Pandey, A., Dhar, Y. V., Bag, S. K., Trivedi, P. K., & Asif, M. H. (2016). Genome-wide analysis of the AP2/ERF family in Musa species reveals divergence and neofunctionalisation during evolution. Scientific Reports, 6, 18878. https://doi.org/10.1038/srep18878
Lakhwani D, et al. Genome-wide Analysis of the AP2/ERF Family in Musa Species Reveals Divergence and Neofunctionalisation During Evolution. Sci Rep. 2016 Jan 6;6:18878. PubMed PMID: 26733055.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Genome-wide analysis of the AP2/ERF family in Musa species reveals divergence and neofunctionalisation during evolution. AU - Lakhwani,Deepika, AU - Pandey,Ashutosh, AU - Dhar,Yogeshwar Vikram, AU - Bag,Sumit Kumar, AU - Trivedi,Prabodh Kumar, AU - Asif,Mehar Hasan, Y1 - 2016/01/06/ PY - 2015/08/19/received PY - 2015/11/09/accepted PY - 2016/1/7/entrez PY - 2016/1/7/pubmed PY - 2016/12/15/medline SP - 18878 EP - 18878 JF - Scientific reports JO - Sci Rep VL - 6 N2 - AP2/ERF domain containing transcription factor super family is one of the important regulators in the plant kingdom. The involvement of AP2/ERF family members has been elucidated in various processes associated with plant growth, development as well as in response to hormones, biotic and abiotic stresses. In this study, we carried out genome-wide analysis to identify members of AP2/ERF family in Musa acuminata (A genome) and Musa balbisiana (B genome) and changes leading to neofunctionalisation of genes. Analysis identified 265 and 318 AP2/ERF encoding genes in M. acuminata and M. balbisiana respectively which were further classified into ERF, DREB, AP2, RAV and Soloist groups. Comparative analysis indicated that AP2/ERF family has undergone duplication, loss and divergence during evolution and speciation of the Musa A and B genomes. We identified nine genes which are up-regulated during fruit ripening and might be components of the regulatory machinery operating during ethylene-dependent ripening in banana. Tissue-specific expression analysis of the genes suggests that different regulatory mechanisms might be involved in peel and pulp ripening process through recruiting specific ERFs in these tissues. Analysis also suggests that MaRAV-6 and MaERF026 have structurally diverged from their M. balbisiana counterparts and have attained new functions during ripening. SN - 2045-2322 UR - https://www.unboundmedicine.com/medline/citation/26733055/Genome_wide_analysis_of_the_AP2/ERF_family_in_Musa_species_reveals_divergence_and_neofunctionalisation_during_evolution_ L2 - https://doi.org/10.1038/srep18878 DB - PRIME DP - Unbound Medicine ER -