Land-plant Phylogenomic and Pomegranate Transcriptomic Analyses Reveal an Evolutionary Scenario of CYP75 Genes Subsequent to Whole Genome Duplications
- 2 Downloads
Regulatory and developmental genes are retained following whole-genome duplication (WGD) events, and, thus, are central to elucidating the evolution of the gene family subsequent to WGDs. Among these genes, the CYP75 gene family is a key member of the biggest enzyme superfamily in land-plant lineages. Although the molecular genetics of the biological progress involved with CYP75 genes have been partly elucidated, the evolution after WGDs in landplant lineages are still largely unknown. Here, we identified CYP75 orthologues in pomegranate (Punica granatum) and other twenty-five representative species to explore the gene evolution under WGD shaping on a broad evolutionary scale. Phylogenomic analyses identified genome-wide CYP75 candidates and suggested that a recent duplication of the CYP75 genes in seed plants occurred prior to the split of gymnosperms and angiosperms approximately 400 million years ago. Molecular evolution analyses revealed that CYP75 gene lineages evolved under a different purifying selection pressure, and slight relaxations occurred in the recent duplication groups in gymnosperms and angiosperms. The syntenic analyses showed that WGDs together with segmental duplications contributed to the CYP75 gene evolution in pomegranate. RT-PCR, qRT-PCR and RNA-Seq verification suggested that pomegranate CYP75 genes evolved through exon fusion and had a fruit-specific expression pattern. Neo- or sub-functionalization is the main fate of CYP75 genes following duplication. The expression pattern of homologous copies of CYP75 in pomegranate supports the CYP75 family evolution contributing to species reproduction that showy fruit colours attracted birds and other animals to spread seeds. Integration of the above analyses generated a putative evolutionary scenario of the CYP75 family in land plants. Our data provided a potential reference model to further elucidate the evolution of the regulatory and developmental gene families after WGDs.
KeywordsCYP75 Gene family Expression pattern Land plant lineage-specific evolution Pomegranate genome Whole-genome duplication
Unable to display preview. Download preview PDF.
- Bowman JL, Kohchi T, Yamato KT, Jenkins J, Shu S, Ishizaki K, Yamaoka S, Nishihama R, Nakamura Y, Berger F, Adam C, Aki SS, Althoff F, Araki T, Arteaga-Vazquez MA, Balasubrmanian S, Barry K, Bauer D, Boehm CR, Briginshaw L, Caballero-Perez J, Catarino B, Chen F, Chiyoda S, Chovatia M, Davies KM, Delmans M, Demura T, Dierschke T, Dolan L, Dorantes-Acosta AE, Eklund DM, Florent SN, Flores-Sandoval E, Fujiyama A, Fukuzawa H, Galik B, Grimanelli D, Grimwood J, Grossniklaus U, Hamada T, Haseloff J, Hetherington AJ, Higo A, Hirakawa Y, Hundley HN, Ikeda Y, Inoue K, Inoue S-i, Ishida S, Jia Q, Kakita M, Kanazawa T, Kawai Y, Kawashima T, Kennedy M, Kinose K, Kinoshita T, Kohara Y, Koide E, Komatsu K, Kopischke S, Kubo M, Kyozuka J, Lagercrantz U, Lin S-S, Lindquist E, Lipzen AM, Lu C-W, De Luna E, Martienssen RA, Minamino N, Mizutani M, Mizutani M, Mochizuki N, Monte I, Mosher R, Nagasaki H, Nakagami H, Naramoto S, Nishitani K, Ohtani M, Okamoto T, Okumura M, Phillips J, Pollak B, Reinders A, Rövekamp M, Sano R, Sawa S, Schmid MW, Shirakawa M, Solano R, Spunde A, Suetsugu N, Sugano S, Sugiyama A, Sun R, Suzuki Y, Takenaka M, Takezawa D, Tomogane H, Tsuzuki M, Ueda T, Umeda M, Ward JM, Watanabe Y, Yazaki K, Yokoyama R, Yoshitake Y, Yotsui I, Zachgo S, Schmutz J (2017) Insights into land plant evolution garnered from the Marchantia polymorpha genome. Cell 171:287–304CrossRefGoogle Scholar
- Finn RD, Clements J, Eddy SR (2011) HMMER web server:interactive sequence similarity searching. Nucleic Acids Res 39:W29−W37Google Scholar
- Holland D, Hatib K, Bar-Ya'akov I (2009) Pomegranate:botany, horticulture, breeding, In Janick J ed, Hort Rev, Vol 35. John Wiley & Sons, Inc., Hoboken, NJ, USA pp 127−191Google Scholar
- Nelson DR, Schuler MA, Paquette SM, Werck-Reichhart D, Bak S (2004) Comparative genomics of rice and Arabidopsis. Analysis of 727 cytochrome P450 genes and pseudogenes from a monocot and a dicot. Plant Physiol 135:756–772Google Scholar
- Panchy N, Lehti-Shiu M, Shiu S-H (2016) Evolution of gene duplication in Plants. Plant Physiol 171:2294–2316Google Scholar
- Patel RK, Jain M (2012) NGS QC Toolkit:a toolkit for quality control of next generation sequencing data. PLoS One 7:e30619Google Scholar
- Wang Y, Tang H, DeBarry JD, Tan X, Li J, Wang X, Lee T-h, Jin H, Marler B, Guo H, Kissinger JC, Paterson AH (2012) MCScanX:a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res 40:e49Google Scholar
- Yuan Z, Fang Y, Zhang T, Fei Z, Han F, Liu C, Liu M, Xiao W, Zhang W, Wu S, Zhang M, Ju Y, Xu H, Dai H, Liu Y, Chen Y, Wang L, Zhou J, Guan D, Yan M, Xia Y, Huang X, Liu D, Wei H, Zheng H (2018) The pomegranate (Punica granatum L.) genome provides insights into fruit quality and ovule developmental biology. Plant Biotechnol J 16:1363–1374CrossRefGoogle Scholar
- Zhang T, Liu C, Zhang H, Yuan Z (2017) An integrated approach to identify Cytochrome P450 superfamilies in plant species within the Malvids, In Zhang D ed, Proceedings of the 5th International Conference on Bioinformatics and Computational Biology, ACM, New York, NY, USA pp 11−16Google Scholar
- Zhu FZ, Yuan ZH, Zhao XQ, Yin YL, Feng LJ (2015) Composition and contents of anthocyanins in different pomegranate cultivars. Acta Hortic 1089:35–41Google Scholar