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. 2006 Mar 23:7:61.
doi: 10.1186/1471-2164-7-61.

The complete chloroplast genome sequence of Gossypium hirsutum: organization and phylogenetic relationships to other angiosperms

Seung-Bum Lee  1 , Charalambos Kaittanis, Robert K Jansen, Jessica B Hostetler, Luke J Tallon, Christopher D Town, Henry Daniell
Affiliations

The complete chloroplast genome sequence of Gossypium hirsutum: organization and phylogenetic relationships to other angiosperms

Seung-Bum Lee et al. BMC Genomics. .

Abstract

Background: Cotton (Gossypium hirsutum) is the most important fiber crop grown in 90 countries. In 2004-2005, US farmers planted 79% of the 5.7-million hectares of nuclear transgenic cotton. Unfortunately, genetically modified cotton has the potential to hybridize with other cultivated and wild relatives, resulting in geographical restrictions to cultivation. However, chloroplast genetic engineering offers the possibility of containment because of maternal inheritance of transgenes. The complete chloroplast genome of cotton provides essential information required for genetic engineering. In addition, the sequence data were used to assess phylogenetic relationships among the major clades of rosids using cotton and 25 other completely sequenced angiosperm chloroplast genomes.

Results: The complete cotton chloroplast genome is 160,301 bp in length, with 112 unique genes and 19 duplicated genes within the IR, containing a total of 131 genes. There are four ribosomal RNAs, 30 distinct tRNA genes and 17 intron-containing genes. The gene order in cotton is identical to that of tobacco but lacks rpl22 and infA. There are 30 direct and 24 inverted repeats 30 bp or longer with a sequence identity > or = 90%. Most of the direct repeats are within intergenic spacer regions, introns and a 72 bp-long direct repeat is within the psaA and psaB genes. Comparison of protein coding sequences with expressed sequence tags (ESTs) revealed nucleotide substitutions resulting in amino acid changes in ndhC, rpl23, rpl20, rps3 and clpP. Phylogenetic analysis of a data set including 61 protein-coding genes using both maximum likelihood and maximum parsimony were performed for 28 taxa, including cotton and five other angiosperm chloroplast genomes that were not included in any previous phylogenies.

Conclusion: Cotton chloroplast genome lacks rpl22 and infA and contains a number of dispersed direct and inverted repeats. RNA editing resulted in amino acid changes with significant impact on their hydropathy. Phylogenetic analysis provides strong support for the position of cotton in the Malvales in the eurosids II clade sister to Arabidopsis in the Brassicales. Furthermore, there is strong support for the placement of the Myrtales sister to the eurosid I clade, although expanded taxon sampling is needed to further test this relationship.

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Figures

Figure 1
Figure 1
Gene map of the Gossypium hirsutum chloroplast genome. The thick lines indicate the extent of the inverted repeats (IRa and IRb), which separate the genome into small (SSC) and large (LSC) single copy regions. Genes on the outside of the map are transcribed in the clockwise direction and genes on the inside of the map are transcribed in the counterclockwise direction. Numbered lines around the map indicate the location of repeated sequences found in the cotton genome (see Table 1 for details). The SSC region is in the reverse orientation relative to tobacco [80]. This does not reflect any differences in gene order for cotton but simply reflects the well-known phenomenon that the SSC exists in two orientations in chloroplast genomes [84].
Figure 2
Figure 2
Histogram showing the number of repeated sequences ≥ 30 bp long with a sequence identity ≥ 90% in the cotton chloroplast genome.
Figure 3
Figure 3
Parsimony tree based on 61 chloroplast protein-coding genes. The tree has a length of 49,957, a consistency index of 0.46 (excluding uninformative characters) and a retention index of 0.6. Numbers above node indicate number of changes along each branch and numbers below nodes are bootstrap support values. Taxa in red are those which have not appeared in any previous phylogenetic studies using 61 genes from complete chloroplast genome sequences. Ordinal and higher level group names follow APG II [85]. The maximum likelihood tree has the same topology but is not shown.
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