Next-Generation Sequencing Facilitates Centromere Position Analysis of Gossypium barbadense and Gossypium hirsutum
Ontology highlight
ABSTRACT:
ORGANISM(S): Gossypium hirsutum Gossypium barbadense
PROVIDER: GSE119184 | GEO | 2019/01/17
REPOSITORIES: GEO
Similar Datasets
Project description:Next-Generation Sequencing Facilitates Centromere Position Analysis of Gossypium barbadense and Gossypium hirsutum
| PRJNA488416 | ENA
Project description:MBI9915 is an introgression cotton line with excellent fiber quality. It was obtained by advanced backcrossing and continuous inbreeding from an interspecific cross between the upland cotton (Gossypium hirsutum) cultivar CCRI36 as the recurrent parent and the sea island cotton (G. barbadense) cultivar Hai1, as the donor parent. To study the genetic effects of the introgressed chromosome segments in G. hirsutum, an F2 secondary segregating population of 1537 individuals was created by crossing MBI9915 and CCRI36, and an F2:3 population was created by randomly selecting 347 individuals from the F2 generation. Quantitative trait locus (QTL) mapping and interaction for fiber length and strength were identified using IciMapping software. The genotype analysis showed that the recovery rate for MBI9915 was 97.9%, with a total 6 heterozygous segments and 13 homozygous segments. A total of 18 QTLs for fiber quality and 6 QTLs for yield related traits were detected using the two segregating generations. These QTLs were distributed across 7 chromosomes and collectively explained 0.81%-9.51% of the observed phenotypic variations. Six QTLs were consistently detected in two generations and 6 QTLs were identified in previous studies. A total of 13 pairs of interaction for fiber length and 13 pairs of interaction for fiber strength were identified in two generations. Among them, 3 pairs of interaction for fiber length and 3 pairs of interaction for fiber strength could be identified in all generations; 4 pairs of interactions affected fiber length and fiber strength simultaneously. The results clearly showed that 5 chromosome segments (Seg-5-1, Seg-7-1, Seg-8-1, Seg-20-2 and Seg-20-3) have important effects on fiber yield and quality. This study provides the useful information for gene cloning and marker-assisted breeding for excellent fiber related quality.
| S-EPMC5607130 | biostudies-literature
Project description:BackgroundThe mitochondrial genome from upland cotton, G. hirsutum, was previously sequenced. To elucidate the evolution of mitochondrial genomic diversity within a single genus, we sequenced the mitochondrial genome from Sea Island cotton (Gossypium barbadense L.).MethodsMitochondrial DNA from week-old etiolated seedlings was extracted from isolated organelles using discontinuous sucrose density gradient method. Mitochondrial genome was sequenced with Solexa using paired-end, 90 bp read. The clean reads were assembled into contigs using ABySS and finished via additional fosmid and BAC sequencing. Finally, the genome was annotated and analyzed using different softwares.ResultsThe G. barbadense (Sea Island cotton) mitochondrial genome was fully sequenced (677,434-bp) and compared to the mitogenome of upland cotton. The G. barbadense mitochondrial DNA contains seven more genes than that of upland cotton, with a total of 40 protein coding genes (excluding possible pseudogenes), 6 rRNA genes, and 29 tRNA genes. Of these 75 genes, atp1, mttB, nad4, nad9, rrn5, rrn18, and trnD(GTC)-cp were each represented by two identical copies. A single 64 kb repeat was largely responsible for the 9 % difference in genome size between the two mtDNAs. Comparison of genome structures between the two mitochondrial genomes revealed 8 rearranged syntenic regions and several large repeats. The largest repeat was missing from the master chromosome in G. hirsutum. Both mitochondrial genomes contain a duplicated copy of rps3 (rps3-2) in conjunction with a duplication of repeated sequences. Phylogenetic and divergence considerations suggest that a 544-bp fragment of rps3 was transferred to the nuclear genome shortly after divergence of the A- and D- genome diploid cottons.ConclusionThese results highlight the insights to the evolution of structural variation between Sea Island and upland cotton mitochondrial genomes.
| S-EPMC4603758 | biostudies-literature
Project description:We identified a newly formed dicentric chromosome (sDic-15) in maize from intrachromosomal recombination and BFB cycles, in which only one centromere is active. The centromeres lost CentC sequences and dramatic reduced the CRM sequences, but when the molecular features of functional centromeres such as CENH3 was examined, they were present. Immunolocalization analysis of phosphorylation of H3T3, H3ser-10 and H2A levels on this new centromere shows a pattern typical of a functional centromere. Meiotic analysis revealed that this dicentric chromosome is table and transmit very well. To examine the new sequences associated with CENH3 in this centromere, chromatin immunoprecipitation (ChIP) was carried out with anti-CENH3 antibodies and material from young seedlings with or without dicentric chromosome. We mapped the ChIP-Seq reads to the reference genome and found a 723kb region from the short arm of maize chromosome 9 involve the new centromere formation. This region is gene-poor and full of TEs, but genes in this region are transcribed. The original 723kb region shows a high DNA methylation level as native centromeres but had no significant change when it involved into new centromere formation. The reactivation of this newly formed centromere indicated that centromere reactivation may not dependent on the relatively intact DNA sequences or topology of original inactive centromere. ChIP-seq was carried out with anti-CENH3 antibodies using material from young seedlings with and without sDic-15 chromosome. For sDic-15, some ChIPed DNA was treated with sodium bisulfite and prepared for Illumina sequencing to test its methylation level.
2013-06-25 | E-GEOD-43140 | biostudies-arrayexpress
Project description:We identified a newly formed dicentric chromosome (sDic-15) in maize from intrachromosomal recombination and BFB cycles, in which only one centromere is active. The centromeres lost CentC sequences and dramatic reduced the CRM sequences, but when the molecular features of functional centromeres such as CENH3 was examined, they were present. Immunolocalization analysis of phosphorylation of H3T3, H3ser-10 and H2A levels on this new centromere shows a pattern typical of a functional centromere. Meiotic analysis revealed that this dicentric chromosome is table and transmit very well. To examine the new sequences associated with CENH3 in this centromere, chromatin immunoprecipitation (ChIP) was carried out with anti-CENH3 antibodies and material from young seedlings with or without dicentric chromosome. We mapped the ChIP-Seq reads to the reference genome and found a 723kb region from the short arm of maize chromosome 9 involve the new centromere formation. This region is gene-poor and full of TEs, but genes in this region are transcribed. The original 723kb region shows a high DNA methylation level as native centromeres but had no significant change when it involved into new centromere formation. The reactivation of this newly formed centromere indicated that centromere reactivation may not dependent on the relatively intact DNA sequences or topology of original inactive centromere.
2013-06-25 | GSE43140 | GEO
Project description:The centromere is the chromosomal site for assembly of the kinetochore where spindle fibers attach during cell division. In most muticellular eukaryotes, centromeres are composed of long tracks of satellite repeats that are recalcitrant to sequencing and fine scale genetic mapping. Here we report the genomic and genetic characterization of the complete centromere of rice chromosome 3. Using a DNA fiber-fluorescence in situ hybridization approach, we demonstrated that the centromere of chromosome 3 (Cen3) contains ~414 kb of the centromeric satellite repeat CentO. Cen3 includes a ~1,851-kb domain associated with CENH3, the centromere-specific histone H3 variant. This CENH3-associated chromatin domain is embedded within a 3,083-kb region that lacks genetic recombination. We detected several active genes within the CENH3-binding domain based on a comprehensive annotation and a survey for matches with mRNA signatures. However, the gene density in the CENH3-binding domain is significantly lower than in the pericentromeric domains. In contrast, the CENH3-binding domain contains a higher percentage of repetitive DNA sequences than the pericentromeric regions. These results suggest that Cen3 is in the process of evolving from a genic region toward an accumulation of satellite repeats and transposable elements that is more characteristic of centromeres in most complex eukaryotic species. Keywords: MPSS, mRNA, transcriptome, rice, centromere, Cen3, chromosome 3
2006-05-26 | GSE4920 | GEO
Project description:The centromere is the chromosomal site for assembly of the kinetochore where spindle fibers attach during cell division. In most muticellular eukaryotes, centromeres are composed of long tracks of satellite repeats that are recalcitrant to sequencing and fine scale genetic mapping. Here we report the genomic and genetic characterization of the complete centromere of rice chromosome 3. Using a DNA fiber-fluorescence in situ hybridization approach, we demonstrated that the centromere of chromosome 3 (Cen3) contains ~414 kb of the centromeric satellite repeat CentO. Cen3 includes a ~1,851-kb domain associated with CENH3, the centromere-specific histone H3 variant. This CENH3-associated chromatin domain is embedded within a 3,083-kb region that lacks genetic recombination. We detected several active genes within the CENH3-binding domain based on a comprehensive annotation and a survey for matches with mRNA signatures. However, the gene density in the CENH3-binding domain is significantly lower than in the pericentromeric domains. In contrast, the CENH3-binding domain contains a higher percentage of repetitive DNA sequences than the pericentromeric regions. These results suggest that Cen3 is in the process of evolving from a genic region toward an accumulation of satellite repeats and transposable elements that is more characteristic of centromeres in most complex eukaryotic species. Keywords: MPSS, small RNA, rice, centromere, Cen3, chromosome 3
2006-05-26 | GSE4912 | GEO
Project description:Centromeres typically contain repeat sequences, but centromere function does not necessarily depend on these sequences. In aneuploid wheat (Triticum aestivum) and wheat distant hybridization offspring, we found functional centromeres with dramatic changes to centromeric retrotransposon of wheat (CRW) sequences. CRW sequences were greatly reduced in the ditelosomic lines 1BS, 5DS, 5DL, and a wheat-Thinopyrum elongatum addition line. CRWs were completely lost in the ditelosomic line 4DS, but a 994 kb ectopic genomic DNA sequence was involved in de novo centromere formation on the 4DS chromosome. In addition, two ectopic sequences were incorporated in a de novo centromere in a wheat-Th. intermedium addition line. Centromeric sequences were also expanded to the chromosome arm in wide hybridizations. Stable alien chromosomes with two and three regions containing centromeric sequences were found in wheat-Th. elongatum hybrid derivatives, but only one is functional. In wheat-rye (Secale cereale) hybrids, rye centromere specific sequences spread to the chromosome arm and may cause centromere expansion. Thus, distant wheat hybridizations cause frequent and significant changes to the centromere via centromere misdivision, which may affect retention or loss of alien chromosomes in hybrids. ChIP-seq was carried out with anti-CENH3 antibody using material 4DS and control (Chinese Spring, CS as short).
2016-04-02 | E-GEOD-63752 | biostudies-arrayexpress
Project description:The ability of centromeres to alternate between active and inactive states indicates significant epigenetic elements controlling centromere assembly and centromere function. In maize (Zea mays), misdivision of the B chromosome centromere on a translocation with the short arm of chromosome 9 (TB-9Sb) can produce many variants with varying centromere sizes and centromeric DNA sequences. In derivatives of TB-9Sb, we found a de novo centromere on chromosome telo-3-3, which has no canonical centromeric repeat sequences. This centromere is derived from a 288-kb region on the short arm of chromosome 9, and is 19 megabases (Mb) removed from the translocation breakpoint of chromosome 9 in TB-9Sb. This centromere is much smaller than normal ones but can be maintained through meiosis. The functional B centromere in progenitor telo2-2 is deleted from telo3-3 but some B-repeat sequences remain. The de novo centromere of telo3-3 becomes inactive in three further derivatives with new centromeres being formed elsewhere on the chromosomes. One such de novo centromere contains only 200-kb CENH3 binding domain. This 200-kb centromere is located 3 Mb removed from the translocation breakpoint in a new location. The deleted B centromere in telo3-3 is activated in two derivatives. Our results suggest that de novo centromere formation is more common than previously thought and can persist on chromosomal fragments without a canonical centromere providing implications for karyotype evolution. ChIP-seq was carried out with anti-CENH3 antibodies using material from young leaves with control, telo3-3 and its derivate.
2015-03-03 | E-GEOD-59124 | biostudies-arrayexpress
Project description:The centromere is the chromosomal site for assembly of the kinetochore where spindle fibers attach during cell division. In most muticellular eukaryotes, centromeres are composed of long tracks of satellite repeats that are recalcitrant to sequencing and fine scale genetic mapping. Here we report the genomic and genetic characterization of the complete centromere of rice chromosome 3. Using a DNA fiber-fluorescence in situ hybridization approach, we demonstrated that the centromere of chromosome 3 (Cen3) contains ~414 kb of the centromeric satellite repeat CentO. Cen3 includes a ~1,851-kb domain associated with CENH3, the centromere-specific histone H3 variant. This CENH3-associated chromatin domain is embedded within a 3,083-kb region that lacks genetic recombination. We detected several active genes within the CENH3-binding domain based on a comprehensive annotation and a survey for matches with mRNA signatures. However, the gene density in the CENH3-binding domain is significantly lower than in the pericentromeric domains. In contrast, the CENH3-binding domain contains a higher percentage of repetitive DNA sequences than the pericentromeric regions. These results suggest that Cen3 is in the process of evolving from a genic region toward an accumulation of satellite repeats and transposable elements that is more characteristic of centromeres in most complex eukaryotic species. MPSS was performed to sequence small RNAs that derived from 16 untreated and 6 abiotic-treated diverse tissue libraries. The method for the MPSS sequencing of mRNAs is described in Brenner et al. (Nat Biotechnol. 2000 18:630).
2006-05-26 | E-GEOD-4920 | biostudies-arrayexpress