Genome-Wide Analysis Of AP2/EREBP Gene Family In Cotton

Cotton is the most important economic crops in the world and its fiber is the natural raw materialof textile industry. The cotton seeds can be used for extracting oil. Currently, the conflict in use of landbetween grain and cotton in more and more appears due to the limitation of cultivated land In China.Cotton, as a relatively drought-resistant and salt-tolerant crops compared with food crops, was moved toplant in inland arid environment. Cotton verticillium wilt is also one of the most important problems inrestricting the cotton production. So the research of resistance to adversity in cotton is still the importantdirection of current cotton research.AP2/EREBP is a super transcription factors gene family specific in plants, including three sub genefamilies which are AP2, EREBP, and RAV. The members of this gene family are very active in responseto biotic and abiotic stresses for plants. AP2genes mainly play an important role in the processmediated by ABA, JA, and ET involved in resistance to various stresses to plants. EREBP, response tomany stress such as drought, cold, high temperature, and plant diseases. RAV gene family is mainlyinvolved in abiotic stress such as chilling injury and infection by verticillium wilt. In this study, weidentified and classified the AP2/EREBP super family genes from the two diploid cotton speciesGossypium raimondii, Gossypium arboreum, containing A, D genome, respectively, according to thewhole genome sequencing data. We also do the analysis of phylogenetic evolution of RAV subfamily.We analyzed the differentially expressed of RAV family genes between control group and drought groupof Gossypium darwinii, according to the RPKM value by RNA sequencing. The RAV genes weresearched in the EST and unigene database of upland cotton in NCBI and then their expression patternsof different organizations were analysed. Using RT-PCR technic, the different expressions of RAV genein the upland cotton subjected to verticillium wilt fungus stress were detected. The main results are asfollows:1. There are271and274AP2/EREBP family members in the whole genome of Gossypiumraimondii and Gossypium arboreum were detected respectively. The subfamily classification resultsshowed that the two diploid cottons almost have same numbers. We speculated that the commonancestor of A and D cotton also had the similar distribution of these gene family members just like in Aand D sub genome. And we also speculate that after the A and D diploid cottons were divided from thecommon ancestor, the AP2/EREBP family may not have experienced a single duplicate in theirrespective evolution.2. The distribution of AP2/EREBP family genes in Gossypium raimondii and Gossypiumarboretum showed that the distribution of these family members on each couple homologychromosomes were not consistent, which present differences of location and numbers. We speculatedthat genome recombination or translocation events had happened at least on one of the two diploidgenomes, after they divided from a common ancestor.3. The cotton genome AP2/EREBP were involved in cotton-specific duplication event after they divided from a common ancestor with cocoa, according to the comparison of the whole genome sizeand AP2/EREBP family numbers among cotton, Arabidopsis thaliana and cocoa.4. The phylogeny development analysis of RAV gene from cotton and other plants showed that, theplants RAV subfamily could be divided into four groups regularly. We also found that an evidence thecotton RAV family members may be involved in a cotton-specific whole-genome duplication.5. The transcriptome sequencing data of G. darwinii under drought stress showed that there were58960EST sequences whose lengths were more than500bp in G. darwinii. There were11773and7392unigenes were up-regulated and down-regulated in drought-stress group compared with the control,respectively. Two RAV genes were all down-regulated.6. The results of real-time fluorescent quantitative PCR detection showed that3RAV genes wereall down-regulated obviously in stress plant sample compared with the control, which were deducedmay be related to the response to the Verticillium wilt in cotton.