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. 2008 Jul 1;9:314.
doi: 10.1186/1471-2164-9-314.

A Preliminary Analysis of Genome Structure and Composition in Gossypium Hirsutum

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Free PMC article

A Preliminary Analysis of Genome Structure and Composition in Gossypium Hirsutum

Wangzhen Guo et al. BMC Genomics. .
Free PMC article

Abstract

Background: Upland cotton has the highest yield, and accounts for > 95% of world cotton production. Decoding upland cotton genomes will undoubtedly provide the ultimate reference and resource for structural, functional, and evolutionary studies of the species. Here, we employed GeneTrek and BAC tagging information approaches to predict the general composition and structure of the allotetraploid cotton genome.

Results: 142 BAC sequences from Gossypium hirsutum cv. Maxxa were downloaded http://www.ncbi.nlm.nih.gov and confirmed. These BAC sequence analysis revealed that the tetraploid cotton genome contains over 70,000 candidate genes with duplicated gene copies in homoeologous A- and D-subgenome regions. Gene distribution is uneven, with gene-rich and gene-free regions of the genome. Twenty-one percent of the 142 BACs lacked genes. BAC gene density ranged from 0 to 33.2 per 100 kb, whereas most gene islands contained only one gene with an average of 1.5 genes per island. Retro-elements were found to be a major component, first an enriched LTR/gypsy and second LTR/copia. Most LTR retrotransposons were truncated and in nested structures. In addition, 166 polymorphic loci amplified with SSRs developed from 70 BAC clones were tagged on our backbone genetic map. Seventy-five percent (125/166) of the polymorphic loci were tagged on the D-subgenome. By comprehensively analyzing the molecular size of amplified products among tetraploid G. hirsutum cv. Maxxa, acc. TM-1, and G. barbadense cv. Hai7124, and diploid G. herbaceum var. africanum and G. raimondii, 37 BACs, 12 from the A- and 25 from the D-subgenome, were further anchored to their corresponding subgenome chromosomes. After a large amount of genes sequence comparison from different subgenome BACs, the result showed that introns might have no contribution to different subgenome size in Gossypium.

Conclusion: This study provides us with the first glimpse of cotton genome complexity and serves as a foundation for tetraploid cotton whole genomesequencing in the future.

Figures

Figure 1
Figure 1
Gene density variation among BACs. The BACs are sorted by overall gene density.
Figure 2
Figure 2
Gene distribution in gene islands.
Figure 3
Figure 3
A updated genetic map of A1/D1 and A6/D6 homoeologous pairs. Note: Genetic map was constructed using a BC1 population obtained from the interspecific cross: G. hirsutum L. acc. TM-1 × G. barbadense L. cv. Hai7124. Chromosomes and linkage groups are arranged by homoeologous pairs and their corresponding conventional chromosome numbers denoted in bracket. Positions of loci are given in centiMorgans. Fragment sizes from Hai7124 allele (in base pair) are given next to the marker name, and the marker loci unmarked fragment size indicate tagged genes unpublished. Deviated loci are underlined. All SSR-derived BAC clones markers are indicated in bold. Homoeologous loci identified are connected by a bar.
Figure 4
Figure 4
A updated genetic map of A2/D2 and A3/D3 homoeologous pairs. All legends are same as described for Figure 3.
Figure 5
Figure 5
A updated genetic map of A4/D4 and A5/D5 homoeologous pairs. All legends are same as described for Figure 3.
Figure 6
Figure 6
A updated genetic map of A7/D7 and A8/D8 homoeologous pairs. All legends are same as described for Figure 3. Deviated interval in A7 and D7 is boxed.
Figure 7
Figure 7
A updated genetic map of A9/D9 and A10/D10 homoeologous pairs. All legends are same as described for Figure 3.
Figure 8
Figure 8
A updated genetic map of A11/D11 and A12/D12 homoeologous pairs. All legends are same as described for Figure 3.
Figure 9
Figure 9
A updated genetic map of A13/D13 homoeologous pairs. All legends are same as described for Figure 3.
Figure 10
Figure 10
Identification of three BACs (AC187848, AC190263 and AC188140) belongings by amplified size analysis. Note: 1. G. hirsutum cv. Maxxa; 2. G. hirsutum acc. TM-1; 3. G. barbadense cv. Hai7124; 4. G. herbaceum var. africanum; 5. G. raimondii Arrow: amplified product with expected size from Maxxa. A: NAU6627 for AC187848 with expected size 247 bp. SSR tagging position was consistent with BAC clone belongings. B: NAU6202 for AC190263 with expected size 349 bp. BAC clone belongings is in homoeologous chromosome of SSR tagging position. C: NAU6465 for AC188140 with expected size 171 bp. BAC clone belongings is confirmed by comparing amplified product size in tetraploid with that in their diploid progenitors G. herbaceum and G. raimondii.

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