comparative bioinformatics analysis of a wild diploid gossypium with two cultivated allotetraploid species

نویسندگان

farshid talat

kunbo wang

چکیده

background: gossypium thurberi is a wild diploid species that has been used to improve cultivated allotetraploid cotton. g. thurberi belongs to d genome, which is an important wild bio-source for the cotton breeding and genetic research. to a certain degree, chloroplast dna sequence information are a versatile tool for species identification and phylogenetic implications in plants. different chloroplast loci have been utilized for evaluating phylogenetic relationships at each classification level among plant species, including at the interspecies and intraspecies levels. present study was conducted in order to analyse the sequence of its chloroplast.objectives: present study was conducted to study and compare the complete chloroplast sequence of g. thurberi, analyses of its genome structure, gene content and organization, repeat sequence and codon usage and comparison with two cultivated allotetraploid sequenced cotton species.materials and methods: the available sequence was assembled by dnaman (version 8.1.2.378). gene annotation was mainly performed by dogma. the map of genome structure and gene distribution were carried out using ogdraw v1.1. relative synonymous codon usage (rscu) of different codons in each gene sample was calculated by codonw in mobyle. to determine the repeat sequence and location, an online version of reputer was used.results: the g. thurberi chloroplast (cp) genome is 160264 bp in length with conserved quadripartite structure. single copy region of cp genome is separated by the two inverted regions. the large single copy region is 88,737 bp, and the small single copy region is 20,271 bp whereas the inverted repeat is 25,628 bp each. the plastidic genome has 113 single genes and 20 duplicated genes. the singletones encode 79 proteins, 4 ribosomal rna genes and 30 transfer rna genes.conclusions: amongst all plastidic genes only 18 genes appeared to have 1-2 introns and when compared with cpdna of two cultivated allotetraploid, rps18 was the only duplicated gene in g.thurberi. despite the high level of conservation in cp genome ssrs ,these are useful in analysis of genetic diversity due to their greater efficiency as opposed to genomic ssrs. low gc content is a significant feature of plastidic genomes, which is possibly formed after endosymbiosis by dna replication and repair.

برای دانلود باید عضویت طلایی داشته باشید

برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

منابع مشابه

Comparative bioinformatics analysis of a wild diploid Gossypium with two cultivated allotetraploid species

Background: Gossypium thurberi is a wild diploid species that has been used to improve cultivated allotetraploid cotton. G. thurberi belongs to D genome, which is an important wild bio-source for the cotton breeding and genetic research. To a certain degree, chloroplast DNA sequence information are a versatile tool for species identification and phylogenetic implications in plants. Different ch...

متن کامل

Comparative Bioinformatics Analysis of the Chloroplast Genomes of a Wild Diploid Gossypium and Two Cultivated Allotetraploid Species.

BACKGROUND Gossypium thurberi is a wild diploid species that has been used to improve cultivated allotetraploid cotton.G. thurberi belongs to D genome, which is an important wild bio-source for the cotton breeding and genetic research. To a certain degree, chloroplast DNA sequence information are a versatile tool for species identification and phylogenetic implications in plants. Different chlo...

متن کامل

Bayesian phylogenetic analysis for diploid and allotetraploid species networks

Allopolyploid species are formed by genome doubling after hybridization between otherwise intersterile parental species. Allopolyploidy is the second most common speciation mechanism in land plants, after ordinary speciation. Here we describe and evaluate a Bayesian approach to the phylogenetic analysis of species relationships when both ordinary speciation and allopolyploidy are present. The a...

متن کامل

Collinearity analysis of allotetraploid Gossypium tomentosum and Gossypium darwinii.

Gossypium tomentosum and G. darwinii are wild allotetraploid cotton species, characterized by many excellent traits, including fiber fineness, drought tolerance, and Fusarium and Verticillium wilt resistance. Based on the construction of F2 linkage groups of G. hirsutum x G. tomentosum and G. hirsutum x G. darwinii, two genetic linkage maps were compared. As a result, we found a total of seven ...

متن کامل

Comparative genetic mapping of allotetraploid cotton and its diploid progenitors

Allotetraploid cotton species (Gossypium) belong to a 1–2 million year old lineage that reunited diploid genomes that diverged from each other 5–10 million years ago. To characterize genome evolution in the diploids and allotetraploids, comparative RFLP mapping was used to construct genetic maps for the allotetraploids (AD genome; n = 26) and diploids (A and D genomes; n = 13). Comparisons amon...

متن کامل

منابع من

با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید


عنوان ژورنال:
iranian journal of biotechnology

ناشر: national institute of genetic engineering and biotechnology

ISSN 1728-3043

دوره 13

شماره 3 2015

میزبانی شده توسط پلتفرم ابری doprax.com

copyright © 2015-2023