Annotation And Evolution Analysis Of LTR Retrotransposons In The Three Legumes Such As Common Bean

Phaseolus vulgaris,Vigna angularis and Vigna radiata all belong to legumes,which have high nutritional value and are important economic crops in China.As a major component of plant genome,LTR retrotransposons play an important role in the evolution of genes and genomes.This study systematically annotated the LTR retrotransposons of three legumes at the genomic level,and preliminarily clarified the number,type,classification,distribution,genetic relationship and relationship with functional genes of these LTR retrotransposons.It will provide better convenience for the further development of the three functional genes of legumes,the identification of active retrotransposons,the development of molecular markers and related work of molecular breeding.The main results are as follows:1.Annotation and analysis of LTR retrotransposons in the three legumesBased on the structure of de novo search and homology alignment method,we identified 9584 LTR retrotransposons from the Phaseolus vulgaris genome,including 3231 intact elements and 6353 solo LTR.These elements can be divided into 183 families,113 families belong to the Gypsy superfamily,and 68 families belong to the Copia superfamily.5311 LTR retrotransposons were identified from the Vigna angularis genome,including 2618 intact elements and 2693 solo LTR.These elements can be divided into 478 families,307 families belong to the Gypsy superfamily,and 167 families belong to the Copia superfamily.4809 LTR retrotransposons were identified from the Vigna radiata genome,including 1843 intact elements and 2966 solo LTR.These elements can be divided into 361 families,231 families belong to the Gypsy superfamily,and 126 families belong to the Copia superfamily.Most of the elements of the three legumes were inserted into the genome in the last 5 million years(Phaseolus vulgaris:98.0%;Vigna angularis:96.3%;Vigna radiata:94.2%).However,the transposable activities of these elements are very different in the same period.Each family’s S/I(number of solo LTR elements/number of intact elements)has nothing to do with evolution time,but has a significant positive correlation with the length of LTR.The LTR retrotransposons of the three legumes were unevenly distributed on each chromosome and showed a significant negative correlation with the distribution of functional genes.The ratio of the number of solo LTR elements to the number of intact elements in each family has nothing to do with the evolution time,but has a significant positive correlation with the length of LTR.The LTR retrotransposons of the three legumes were unevenly distributed on each chromosome and showed a significant negative correlation with the distribution of functional genes.Pvr3,Vanr2 and Vrar2 families are highly conserved,about 90%of the elements do not contain any coding sequence,the element length is generally about 380 bp,the distribution on the chromosome is random,and there are a lot of elements inserted into the gene region,these characteristics are consistent with those of typical TRIMs.2.Phylogenetic tree analysis of LTR retrotransposons in the three legumesThere are six Copia lineages in the genomes of three legumes,namely Angela,Ale,Bianca,Ivana,Maximus and TAR.In terms of Gypsy lineages,Galadriel lineage was not found in the three legumes.There were five lineages in Phaseolus vulgaris and Vigna angularis genomes,that is Tekay,CRM,Reina,Athila and Tat,only four of them existed in Vigna radiata genomes,and Tekay lineage was missing.In addition,there are great differences in the number of families and elements in different plant lineages.Ivana lineage and Ale lineage have the largest number of families and elements in Vigna angularis and Vigna radiata,while the largest number of families and elements in Phaseolus vulgaris are Ale lineage and Maximus lineage,respectively.3.The relationship between LTR retrotransposons and functional genes in the three legumes plantsThere are 1504 LTR retrotransposon elements inserted in the gene region(within the gene and adjacent 2kb)in Phaseolus vulgaris,and the largest number of elements were distributed in the gene adjacent to 2kb;1736 and 1486 elements inserted in the gene region in Vigna angularis and 1581 in Vigna radiata respectively,and both of them had the largest number of elements in the intron region.The functional enrichment analysis of these genes showed that the three legumes had similar enrichment characteristics.In terms of cell component,the annotation mainly focused on cell,cell part and organelle.In the aspect of molecular function,the annotation mainly focused on catalytic activity and binding.In the aspect of biological process,the annotation mainly focused on cell process and metabolic process.