Evolution and Functional Analysis of Gene Clusters in Anther Tapetum Cells of Arabidopsis thaliana
Received date: 2019-05-30
Accepted date: 2019-09-19
Online published: 2019-09-24
In plant genome, in addition to the discovery of homologous gene clustering, it has been known that some heterologous genes with co-expression characteristics can exist as gene clusters, however, the evolution and biological function of these heterogeneous gene clusters remain elusive. The development of anthers and the formation of pollen are unique reproductive biology processes evolved in seed plants. In this process, some gene cluster genes that specifically express and function in the anther tapetum are evolved. This study screened for some clustered genes expressed during anther development, and analyzed their molecular characteristics, expression regulation, gene age, as well as explored the relationship between the clustered genes and plant flowering function evolution. In Arabidopsis thaliana, we screened 84 clustered genes (which belong to 13 gene clusters), which are mainly expressed in tandem repeat events, and 76% of these genes appear in the latter stage of flowering plant evolution, that mainly involved in biological processes such as reproductive development, pollen sheath composition and lipid metabolism. This study has thus provided preliminary analysis on the basic characteristics, biological functions and mechanisms of the evolution of the clustered genes in the anther tapetum of Arabidopsis thaliana, which laid a foundation for future study on the function of the clustered genes.
Key words: Arabidopsis thaliana; gene cluster; anther tapetum; gene duplication; evolution
Zeyuan Zuo,Wanlin Liu,Jie Xu . Evolution and Functional Analysis of Gene Clusters in Anther Tapetum Cells of Arabidopsis thaliana[J]. Chinese Bulletin of Botany, 2020 , 55(2) : 147 -162 . DOI: 10.11983/CBB19103
[1] | 李鸿健, 谭军 ( 2006). 基因倍增研究进展. 生命科学 18, 150-154. |
[2] | 吕海舟, 刘琬菁, 何柳, 徐志超, 罗红梅 ( 2017). 植物次生代谢基因簇研究进展. 植物科学学报 35, 609-621. |
[3] | 孙红正, 葛颂 ( 2010). 重复基因的进化——回顾与进展. 植物学报 45, 13-22. |
[4] | 朱子超, 柴友荣, 杨光伟 ( 2009). 查尔酮合酶基因重复-歧化的遗传学效应. 安徽农学通报 15, 25-30. |
[5] | Carbon S, Ireland A, Mungall CJ, Shu SQ, Marshall B, Lewis S , the AmiGO Hub, the Web Presence Working Group ( 2009). AmiGO: online access to ontology and annotation data. Bioinformatics 25, 288-289. |
[6] | Chen CJ, Xia R, Chen H, He YH ( 2018). TBtools, a toolkit for biologists integrating various HTS-data handling tools with a user-friendly interface. bioRxiv. doi: 10.1101/289660. |
[7] | Cimermancic P, Medema MH, Claesen J, Kurita K, Brown LCW, Mavrommatis K, Pati A, Godfrey PA, Koehrsen M, Clardy J, Birren BW, Takano E, Sali A, Linington RG, Fischbach MA ( 2014). Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters. Cell 158, 412-421. |
[8] | Cui X, Lv Y, Chen ML, Nikoloski Z, Twell D, Zhang DB ( 2015). Young genes out of the male: an insight from evolutionary age analysis of the pollen transcriptome. Mol Plant 8, 935-945. |
[9] | De Bodt S, Maere S, Van de Peer Y ( 2005). Genome duplication and the origin of angiosperms. Trends Ecol Evol 20, 591-597. |
[10] | Díez B, Gutiérrez S, Barredo JL, van Solingen P, van der Voort LH, Martín JF ( 1990). The cluster of penicillin biosynthetic genes. Identification and characterization of the pcbAB gene encoding the alpha-aminoadipyl-cysteinyl- valine synthetase and linkage to the pcbC and penDE genes. J Biol Chem 265, 16358-16365. |
[11] | Domazet-Lo?o T, Brajkovi? J, Tautz D ( 2007). A phylostratigraphy approach to uncover the genomic history of major adaptations in metazoan lineages. Trends Genet 23, 533-539. |
[12] | Domazet-Lo?o T, Tautz D ( 2010). A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns. Nature 468, 815-818. |
[13] | Falara V, Akhtar TA, Nguyen TTH, Spyropoulou EA, Bleeker PM, Schauvinhold I, Matsuba Y, Bonini ME, Schilmiller AL, Last RL, Schuurink RC, Pichersky E ( 2011). The tomato terpene synthase gene family. Plant Physiol 157, 770-789. |
[14] | Force A, Lynch M, Pickett FB, Amores A, Yan YL, Postlethwait J ( 1999). Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151, 1531-1545. |
[15] | Guenzi E, Galli G, Grgurina I, Gross DC, Grandi G ( 1998). Characterization of the syringomycin synthetase gene cluster. A link between prokaryotic and eukaryotic peptide synthetases. J Biol Chem 273, 32857-32863. |
[16] | Itkin M, Heinig U, Tzfadia O, Bhide AJ, Shinde B, Cardenas PD, Bocobza SE, Unger T, Malitsky S, Finkers R, Tikunov Y, Bovy A, Chikate Y, Singh P, Rogachev I, Beekwilder J, Giri AP, Aharoni A ( 2013). Biosynthesis of antinutritional alkaloids in solanaceous crops is mediated by clustered genes. Science 341, 175-179. |
[17] | Klein J, Figueroa F ( 1986). Evolution of the major histocompatibility complex. Crit Rev Immunol 6, 295-386. |
[18] | Koch MA, Haubold B, Mitchell-Olds T ( 2000). Comparative evolutionary analysis of chalcone synthase and alcohol dehydrogenase loci in Arabidopsis, Arabis, and related genera (Brassicaceae). Mol Biol Evol 17, 1483-1498. |
[19] | Kondrashov FA, Rogozin IB, Wolf YI, Koonin EV ( 2002). Selection in the evolution of gene duplications. Genome Biol 3, research0008. |
[20] | Kumar S, Stecher G, Tamura K ( 2016). MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33, 1870-1874. |
[21] | Li DD, Xue JS, Zhu J, Yang ZN ( 2017). Gene regulatory network for tapetum development in Arabidopsis thaliana. Front Plant Sci 8, 1559. |
[22] | Lora J, Testillano PS, Risue?o MC, Hormaza JI, Herrero M ( 2009). Pollen development in Annona cherimola Mill.(Annonaceae). Implications for the evolution of aggregated pollen. BMC Plant Biol 9, 129. |
[23] | MacCabe AP, Riach MB, Unkles SE, Kinghorn JR ( 1990). The Aspergillus nidulans npeA locus consists of three contiguous genes required for penicillin biosynthesis. EMBO J 9, 279-287. |
[24] | Mascarenhas JP ( 1990). Gene activity during pollen development. Annu Rev Plant Physiol Plant Mol Biol 41, 317-338. |
[25] | Mi HY, Huang XS, Muruganujan A, Tang HM, Mills C, Kang D, Thomas PD ( 2017). PANTHER version 11: expanded annotation data from gene ontology and reactome pathways, and data analysis tool enhancements. Nucleic Acids Res 45, D183-D189. |
[26] | Nishida H, Nishiyama M, Kobashi N, Kosuge T, Hoshino T, Yamane H ( 1999). A prokaryotic gene cluster involved in synthesis of lysine through the amino adipate pathway: a key to the evolution of amino acid biosynthesis. Genome Res 9, 1175-1183. |
[27] | Prince VE, Pickett FB ( 2002). Splitting pairs: the diverging fates of duplicated genes. Nat Rev Genet 3, 827-837. |
[28] | Qi X, Bakht S, Leggett M, Maxwell C, Melton R, Osbourn A ( 2004). A gene cluster for secondary metabolism in oat: implications for the evolution of metabolic diversity in plants. Proc Natl Acad Sci USA 101, 8233-8238. |
[29] | Slot JC ( 2017). Fungal gene cluster diversity and evolution. Adv Genet 100, 141-178. |
[30] | Thornton J ( 2006). New genes, new functions: gene family evolution and phylogenetics. In: Fox CW, Wolf JB, eds. Evolutionary Genetics: Concepts and Case Studies. New York: Oxford University Press. pp. 157-172. |
[31] | Wang YP, Tang HB, DeBarry JD, Tan X, Li JP, Wang XY, Lee TH, Jin HZ, 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, e49. |
[32] | Wilson ZA, Zhang DB ( 2009). From Arabidopsis to rice: pathways in pollen development. J Exp Bot 60, 1479-1492. |
[33] | Worthen DB ( 2008). Streptomyces in nature and medicine: the antibiotic makers. J History Med Allied Sci 63, 273-274. |
[34] | Yang SL, Xie LF, Mao HZ, San Puah C, Yang WC, Jiang LX, Sundaresan V, Ye D ( 2003). TAPETUM DETERMINANT 1 is required for cell specialization in the Arabidopsis anther. Plant Cell 15, 2792-2804. |
[35] | Zhang JZ ( 2003). Evolution by gene duplication: an update. Trend Ecol Evol 18, 292-298. |
[36] | Zhu YG, Fu P, Lin QH, Zhang GT, Zhang HB, Li SM, Ju JH, Zhu WM, Zhang CS ( 2012). Identification of caerulomycin A gene cluster implicates a tailoring amidohydrolase. Org Lett 14, 2666-2669. |
[37] | Zhu YG, Picard ME, Zhang QB, Barma J, Després XM, Mei XG, Zhang LP, Duvignaud JB, Couture M, Zhu WM, Shi R, Zhang CS ( 2016). Flavoenzyme CrmK-mediated substrate recycling in caerulomycin biosynthesis. Chem Sci 7, 4867-4874. |
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