Genome-Wide Identification And Phylogenetic Analysis Of Key Gene Families For Terpene Biosynthesis In Gossypium Raimondii And Gossypium Arboreum

Terpenes represent the largest and most diverse class of plant secondary metabolites, which are important in plant growth and development. In plant cells, two independent pathways are responsible for the biosynthesis of terpenes, the cytosolic mevalonate pathway (MVA pathway) and the plastidial2-C-methyl-D-erythritol-4-phosphate pathway (MEP pathway). The3-hydroxy-3-methylglutaryl-CoA reductase (HMGR) is a rate-limiting enzyme in the MVA pathway. The terpene synthases (TPSs) catalyze the synthesis of the backbone of various terpene molecules, which contribute to the variation and plasticity of terpene formation. Gossypol and its derivatives, which are a unique group of terpenes produced by Gossypium species, serve as an important phytoalexin in defense against pathogens and pests. In the process of adaptive selection, the evolution of the special ability to synthesize gossypol and related sesquiterpenes was attributed to special evolutionaly pattern of genes involved in the terpene biosynthesis pathway in cotton. Genome sequences of various plant species, especially two diploid cottons, Gossypium raimondii and Gossypium arboreum, have become available recently, offering an opportunity to investigate the molecular mechanism of gossypol biosynthesis in cotton through comparative analysis. Gossypol and related sesquiterpenes are derived from a cytosolic branch of terpene biosynthesis via the MVA pathway. So the HMGR is a key enzyme in regulation of gossypol biosynthesis. The (+)-δ-cadinene synthase (CDNS), as a kind of terpene synthases, is another key enzyme in the process of gossypol biosynthesis. In this study, to detect the molecular basis of the gossypol biosynthesis in cotton, the genome data of the two diploid cottons and other plant species were used, and the HMGR and TPS gene families were analyzed at the genome-wide level. The main results were as follows:1. A genome-wide identification of MVA pathway genes from20representative species ranging from unicellular algae to higher plants was carried out, and then the phylogenetic relationships of HMGR genes were further studied. The results indicated that the Chlorophyta had abandoned the MVA pathway, while the land plants simultaneously retained the MVA and MEP pathways. The plant HMGR genes might be derived from one ancestor gene and finally developed into two distinct groups within the monocots and eudicots, respectively. The HMGR gene family underwent species-specific expansions in Zea mays, G. raimondii, Populus trichocarpa and Glycine max. Segmental duplication appeared to be the dominant mechanism for the gene expasion in Z. mays, P. trichocarpa and G. max, whereas segmental duplication and tandem duplication played similar roles in the expansion of the HMGR gene family in G. raimondii. It could be dudced that the species-specific expansion of HMGR genes in G. raimondii might due to the large production for gossypol and its derivatives in its growth and development. The functional divergence after the gene duplications was restricted, which confirmed the key-regulating role of HMGR in terpene biosynthesis.2. A comparative analysis of HMGR genes in G. raimondii and G. arboreum was performed. The results indicated that the HMGR genes underwent gene expansion and a gene cluster including four HMGR genes was found in both two diploid cotton genomes. The phylogenetic analysis suggested that the expansion of HMGR genes had occurred in their common ancestor. Most of HMGR genes showed relatively high expression in roots in G. raimondii and G. arboreum, which fit well with the fact that gossypol is synthesized in cotton roots. The expression patterns of the orthologous gene pairs between two diploid cotton genomes were divergent, which might be caused by adapting to their surrounding environment. For this important enzyme, the existence of a HMGR pseudogene was revealed in G. arboreum.3. A systematic analysis of TPS gene family in G. raimondii and G. arboreum was conducted. The results indicated that the tandem duplication might contribute to expansion of the TPS genes, especially the TPS genes in TPS-a subfamily, in Gossypium genomes. The TPS genes have evolved differently in the two cotton genomes after gene expansion. The cotton CDNS genes were derived from functional divergence after the tandem duplications of ancestral genes in TPS-a subfamily, and some CDNS genes also might undergo tandem duplications later, which lead to more members of CDNS genes. Athough CDNS genes underwent species-specific evolution after the speciation of G. raimondii and G. arboreum, there was a CDNS gene cluster which was conserved in both two Gossypium genomes, suggesting that the CDNS genes in the gene cluster mingt play important roles in the gossypol biosynthesis.In summary, the study showed that there were several special evolutionary patterns, such as the specific expansion of HMGR genes, and the emergence of CDNS genes from tandem gene duplications and functional divergence, in G. raimondii and G. arboreum. These results can lay an important foundation for understanding the molecular basis of gossypol biosynthesis in cotton.