Phylogenetic Relationship Among Local Legumes In Jiangsu Province Based On Analyses Of MatK Gene And ITS Sequence

Recently,many local varieties of legumes including common bean and other edible beans have been cultivated by breeders in Jiangsu Province.They are important source of vegetables.However,most of them are selected by different scientific research institutions in different years,and the nomenclature is lack of standard and systematicness,leading to the ambiguous relationship of local species.In order to study the genetic relationship among the local varieties of legumes in Jiangsu Province,we used the commonly used DNA barcode matK gene?the chloroplast genome gene?and ITS sequence?the nuclear genome gene?as the target sequences.Genetic relationships among 14 legumes were analyzed under the molecular level,in order to provide a theoretical basis for the germplasm innovation and genetic improvement in legumes.The main results are as follows:1.Sequence analysis of the matK gene and ITS sequenceWe compared and analyzed the matK gene and ITS sequence of 14 Jiangsu local varieties of legumes collected by our laboratory and another four legumes?Glycine max,Phaseolus vulgaris,Vigna angularis and Vigna radiata?from GenBank.The results showed that the length of matK gene in 18 legumes was 750 bp after alignment,including 85 variable sites and 82 informative sites.The length of ITS sequence was 795 bp after alignment,with 260 variable sites and 242 informative sites.The analysis of SNP and INDEL showed that the genetic distance between Suchanglifandou and Vigna angularis was closer than that of Phaseolus vulgaris and Vigna radiate.2.The analysis of genetic distance,relationship and divergence timesThe results of genetic distance showed that the range of genetic distance calculated by matK gene and ITS sequence was 0.000-0.099 and 0.000-0.292,respectively.The genetic distance was relatively small between intraspecies,and was relatively large among interspecies.A phylogenetic tree was constructed by matK gene and ITS sequence by using Lotus corniculatus as outgroup respectively.And the result showed that 18 legumes were divided into three groups,Vigna angularis and Vigna radiate were grouped to one branch,Glycine max and Phaseolus vulgaris were respectively grouped to the other two branches.The estimated divergence times were 19.02 Mya?Glycine max vs Phaseolus vulgaris?,13.50 Mya?Phaseolus vulgaris vs Vigna angularis?and 2.94 Mya?Vigna radiate vs Vigna angularis?for the three major groups.Sequence analyses and results from phylogenetic tree were consistent with the morphologic identification in these legumes,which suggested that both math gene and ITS sequence could be used for phylogenetic analysis among different genus of local legumes.3.Identification and functional analysis of tissue specific expression genes and orthologous genes in in four legumesUsing the homologous gene search tool inparanoid₄.1,we searched the genomic sequence of three legumes?Phaseolus vulgaris,Vigna radiate and Vigna radiate?according to the genes expressed in Glycine max flower?938?,green pod?408?and nodule?527?tissue.349,144 and 144 homologous genes were identified in the three legumes,respectively.The three tissue specific genes and orthologous genes were annotated by Gene Ontology?GO?in Glycine max,Phaseolus vulgaris,Vigna angularis,Vigna radiate,respectively.All results consist three parts i.e.biological process,cellular component and molecular function.The biological process mainly includes cellular process and metabolic process,the cellular process mainly includes cell and cell part,and the molecular function mainly includes binding and catalytic activity.In addition,the GO result show the same trend in three tissues of four legumes.A total of 41,17,30 tissue specific functional genes were found in orthologous genes of Phaseolus vulgaris compared with Glycine max flower,green pod,nodule,respectively.There are 14,5 and 29 tissue specific functional genes were matched to the KEGG database in flower,green pod and nodule of Phaseolus vulgaris,respectively.The endocytosis genes are enriched in flower belonging to the genes of cellular processes,and the biosynthesis of secondary metabolites genes are enriched in nodule belonging to the genes of metabolism.