Abstract
BackgroundDissecting genome organization is indispensable for further functional and applied studies. As genome sequences data shown, cotton genomes contain more than 60 % repetitive sequences, so study on repetitive sequences composition, structure, and distribution is the key step to dissect cotton genome.ResultsIn this study, a bacterial artificial chromosome (BAC) clone enriched in repetitive sequences, was discovered initiatively by fluorescence in situ hybridization (FISH). FISHing with allotetraploidy cotton as target DNA, dispersed signals on most regions of all A sub-genome chromosomes, and only middle regions of all D sub-genome chromosomes were detected. Further FISHing with other cotton species bearing A or D genome as target DNA, specific signals were viewed. After BAC sequencing and bioinformational analysis, 129 repeat elements, size about 57,172 bp were found, accounting for more than 62 % of the BAC sequence (91,238 bp). Among them, a type of long terminal repeat-retrotransposon (LTR-RT), LTR/Gypsy was the key element causing the specific FISH results. Using the fragments of BAC matching with the identified Gypsy-like LTR as probes, the BAC-57I23-like FISH signals were reappeared. Running BLASTN, the fragments had good match with all chromosomes of G. arboreum (A2) genome and A sub-genome of G. hirsutum (AD1), and had relatively inferior match with all chromosomes of D sub-genome of AD1, but had little match with the chromosomes of G. raimondii (D5) genome, which was consistent with the FISH results.ConclusionA repeats-enriched cytogenetic marker to identify A and D sub-genomes of Gossypium was discovered by FISH. Combined sequences analysis with FISH verification, the assembly quality of repetitive sequences in the allotetraploidy cotton draft genome was assessed, and better chromosome belonging was verified. We also found the genomic distribution of the identified Gypsy-LTR-RT was similar to the distribution of heterochromatin. The expansion of this type of Gypsy-LTR-RT in heterochromatic regions may be one of the major reasons for the size gap between A and D genome. The findings showed here will help to understand the composition, structure, and evolution of cotton genome, and contribute to the further perfection of the draft genomes of cotton.
Highlights
Dissecting genome organization is indispensable for further functional and applied studies
bacterial artificial chromosome (BAC) clone screening During the screening of the 1th chromosome-specific BACs from the BAC library of G. herbaceum var. africanum, with SSR markers derived from a whole-genome marker map [41], the BAC clone 57I23 enriched in repeats was found
After comparing the distribution of the ten fragments in different cotton genomes, it was found that the copy number was the highest in A2 genome, but 10–25 times lower in D5 genome (Fig. 2), and with very bad match hits, which maybe partially explain the fluorescence in situ hybridization (FISH) results in D genome species
Summary
Dissecting genome organization is indispensable for further functional and applied studies. As one of the best-characterized allopolyploid species, is divided into eight diploid genome groups (2n = 2× = 26), namely A-G and K, and one allotetraploidy genome group (2n = 4× = 52), which is allotetraploid bearing. What’s more, there is a wide range in genome size across closely related diploid species (from 880 Mb to 2572 Mb per haploid nucleus) and well-established phylogeny in Gossypium [8]. To dissect the genomic complexity in allotetraploidy cotton, extensive efforts have been performed. In early years, based on some classic cytogenetic and cytological studies, genome composition of the polyploids was investigated, which confirmed that the American allotetraploidy species are allopolyploids containing two resident genomes, an A-genome from Africa or Asia, and a D-genome similar to those found in the American diploids [9,10,11]. With the extensive application of FISH, more evidences that allotetraploidy cottons may be polyphyly have been obtained [12, 13]
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