Complete Nucleotide Sequence of the Cotton (Gossypium barbadense L.) Chloroplast Genome with a Comparative Analysis of Sequences among 9 Dicot Plants

Abstract

Recently, the complete chloroplast genome sequences of many important crop plants were determined, and this can be considered a major step forward toward exploiting the usefulness of chloroplast genetic engineering technology. Economically, cotton is one of the most important crop plants for many countries. To further our understanding of this important crop, we determined the complete nucleotide sequence of the chloroplast genome from cotton ( Gossypium barbadense L.). The chloroplast genome of cotton is 160,317 base pairs (bp) in length, and is composed of a large single copy (LSC) of 88,841 bp, a small single copy (SSC) of 20,294 bp, and two identical inverted repeat (IR) regions of 25,591 bp each. The genome contains 114 unique genes, of which 17 genes are duplicated in the IRs. In addition, many open reading frames (ORFs) and hypothetical chloroplast reading frames ( ycf s) with unknown functions were deduced. Compared to the chloroplast genomes from 8 other dicot plants, the cotton chloroplast genome showed a high degree of similarity of the overall structure, gene organization, and gene content. Furthermore, the sequences of the genes showed high degrees of identity at the DNA and amino acid levels. The cotton chloroplast genome was somewhat longer than the chloroplast genomes of most of the other dicot plants compared here. However, this elongation of the cotton chloroplast genome was found to be due mainly to expansions of the intergenic regions and introns (noncoding DNA). Moreover, these expansions occurred predominantly in the LSC and SSC regions.

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

“…In our study similar to cassava (19) G. hirsutum (18), the infA was absent. However, some others had the infA as a pseudogene (17,22), while in others infA appeared as an intact gene (21). Similar to G. hirsutum (18) and G. barbadense (17) and angiosperms, trnP-GGG was absent in G. thurberi.…”

“…Total genome is a circular DNA molecule of 160,264 bp, which is shorter than G. barbadnese (17) and G. hirsutum (18). The two single copy regions are separated by the two inverted repeats.…”

Chloroplast genome of tetraploid cultivated cotton Gossypium barbadense L. and G. hirsutum L.

“…Resulted PCR-amplifi ed fragments were cloned and sequenced. The sequences obtained were aligned that revealed the presence of an A+T-rich region, 17 bp direct repeat insert/deletion in G. hirsutum, 129 bp and 6 bp insertion/deletion in G. barbadense, many simple sequence repeats, direct and inverted repeats, and 2 transversions (Ibrahim et al 2006, Lee et al 2006. Insertions/deletions of 17, 129, 6 bp are shown as groups of (-).…”

“…Extracted DNA was kept at -25°C and used as a template for PCR amplifi cation. on the chloroplast genome sequence of G. barbadense (Ibrahim et al 2006) as a reference. The following factors were carefully considered, length of primer, primer position, C+G content of at least 50%, melting temperature, and primer-dimer formation.…”

Safety Assessment of Transgenic Organisms, Volume 4

“…An international coalition of researchers has plans underway to completely sequence the nuclear genome of G. hirsutum , first by sequencing the ancestrally close D-genome relative G. raimondii, which has a much smaller genome (1C of 880 Mbp) (Hendrix and Stewart, 2005). The complete nucleotide sequences of the chloroplast genomes of G. hirsutum (Lee et al, 2006) and G. barbadense (Ibrahim et al, 2006) have been determined.The complexity in the Gossypium genome occurs in a multitude of diverse dimensions. The diploid genus itself is considered a paleopolyploid (as is possibly the case for most angiosperms).…”