Analysis And Application Of Colinearity Relationship In Genome Of Cruciferous Plants

Cruciferae crops, the largest growing area of vegetable crops in China, are the subjects ofeconomic value in the flowering plants. There are many important vegetables, flowers, fuel, fodder andmedicinal crops, agricultural production in Cruciferae in China, which take a very important position inthe agricultural area. It is of great theoretical and practical significantly important for us to understandthe origin, evolution and classification of cruciferous crops, and take full advantage of the rich geneticresources of cruciferous species, nurture and create cruciferous superior strains by using thecomparative genomics approach to deeply analysis of co-linear relationship among the plants genome.Brassica crops belong to cruciferous plants, which is the the largest area under cultivation and thehighest total output. Brassica rapa and Brassica oleracea all belong to the Brassica crops. Brassicarapa is an economically important crop. In2008, next generation sequencing technology was used tosequence the genome of B. rapa accession Chiifu. The result has shown that B. rapa has experiencedonly the second genome triplication reported to date. It provide the raw material for the analysis of geneevolution after WGT. The ancestral species of B. rapa has the close relationship with the modelspecies Arabidopsis thaliana, which it divergence from the A. thaliana lineage at least13-17MYA. So,the genomes of these two species still retain near-perfect collinearity between them. It is reported thatthe auxin-related genes that affect the organ morphological variation are amplified. But the impact of genome triplication on tandem gene evolution in B. rapa hasn’t researched indepth.This study concerns the sequenced genome of Cruciferae plant, that is Arabidopsis thaliana,Arabidopsis lyrata, Thellungiella parvula, Brassica rapa, Brassica oleracea. The genome ofArabidopsis thaliana is considered as the central species. The colinear relationship between the otherspecies and A. thaliana are analysised. The result of the colinearity of B. rapa and A. thaliana can beused as the material to work on the gene retention and the tandem gene evolution after WGT. Theresults we got are listed as follows:1. We used five sequenced genome of Cruciferae plant to get the collinear relationship between A.thaliana and the other species. Comparative studies have confirmed genome triplication in a commonancestor of B. oleracea and B. rapa since its divergence from the A. thaliana lineage. The origin andevolution of Cruciferae plant can be comfirmed by the phylogenetic tree of gene families. The result hasshown that the A. thaliana and A. lyrata have the close relationship. B. rapa and B. oleracea belong toBrassica and both of them genome had undergone WGT, so they have the close relationship. In contrastto the Arabidopsis, T. parvular has the close relationship with Brassica.2. The gene retention after WGD and TD can be analysised based on the colinear relationshipbetween B. rapa and A. thaliana and the Gene Ontology (GO). Genes with GO terms associated withresponse to important environmental factors and plant hormones were also over retained after WGT,which had not been reported in other species. It can be regarded as the specific over-retained genes in B.rapa. The gene retention after TD is the same as the reported other species, the genes that are response to abiotic and biotic stress had been extanded.3. The tandemly arrayed gene that we researched can be grouped into two types—conservedtandemly duplicated genes and the specific tandemly duplicated genes. The evolution of conservedtandemly duplicated genes in B. rapa may be affected WGT. The tandem gene number in most sharedtandem arrays in B. rapa is decreased compared to that in A. thalina, A. lyrata and T. parvula. After thewhole genome triplication, the redundant genes in tandem arrays are then prone to be lost. But, thespecific tandemly arrayed genes don’t affect by the WGT. Then, the environment between B. rapa and T.parvula are different that lead to the tandem gene that response to the environment stimulus variedgreatly.