Abstract
BACKGROUND:
Dissecting 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 keystep to dissect cotton genome.
RESULTS:
In 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.
CONCLUSION:
A
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.
http://www.ncbi.nlm.nih.gov/pubmed/?term=A%20Gossypium%20BAC%20clone%20contains%20key%20repeat%20components%20distinguishing%20sub-genome%20of%20allotetraploidy%20cottons
doi: 10.1186/s13039-016-0235-y.(IF=2.14)
PMID:27006694