Comparative bioinformatics analyses of the chloroplast genome of a diploid Cotton (G. herbaceum) with two allotetraploid species

Nasrollahi, Hajar; Talat, Farshid; Bernousi, Iraj; Badri Anarjan, Mehdi

Comparative bioinformatics analyses of the chloroplast genome of a diploid Cotton (G. herbaceum) with two allotetraploid species

Document Type : Research Paper

Authors

¹ Former M.Sc. Student of Plant Breeding, Urmia University, Urmia, Iran

² Assistant Professor, Seed and Plant Improvement Research Department, West Azarbaijan Agricultural and Natural Resources Research and Education Center, AREEO, Urmia, Iran.

³ Associate Professor, Department of Plant Breeding and Plant Biotechnology, Faculty of Agriculture, Urmia University, Urmia, Iran

Abstract

Diploid genome contains 8 genomes designated as A, B, C, D, E, F, G and K which have been identified in the genus Gossypium. The genome of A is limited only in two species as G. herbaceum and G.arboreum, and it is transferred from G. herbaceum to other species. The chloroplast genome (CP) of G. herbaceum has 160,140 bp lengths with protected quadripartite structure. Single copy regions of chloroplast genome are separated by two inverted repeat regions with a large copy region with 88,709 bp also the single copy region and each small inverted repeat regions have 20,221 and 25,605bp. The plastidic' s genome has 113 single copy genes and 19 duplicated copy genes. Single copy genes are encoding of 79 genes for protein production, four ribosomal RNA genes and 31 transfer RNA genes. Result showed that among all plastid genes only 18 genes appeared to have 1-2 intron/s and when compared with chloroplast genome of two allotetraploid species. Ycf15 gene as the only duplicated gene, rpl22 was in G. herbaceum and in the two species has studied G. herbaceum, G. barbadense. But ycf15 gene in G. barbadense and both ycf15 and rpl22 genes were lost in G. barbadense and G. hirsutum. Though the high level of SSR protection in the chloroplast genome. SSRs are useful for genetic variation analysis since they have high efficiency against genomic SSRs.

Keywords

20.1001.1.22520783.1396.7.20.1.4

Main Subjects

Bioinformatics

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