scholarly journals Identification of a genome-specific repetitive element in the Gossypium D genome

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8344
Author(s):  
Hejun Lu ◽  
Xinglei Cui ◽  
Yanyan Zhao ◽  
Richard Odongo Magwanga ◽  
Pengcheng Li ◽  
...  
Keyword(s):  
Repetitive Element ◽  
Repetitive Sequences ◽  
Long Terminal Repeat Retrotransposons ◽  
Gossypium Arboreum ◽  
D Genome ◽  
Cotton Species ◽  
A Genome ◽  
Gossypium Raimondii ◽  
The Common

The activity of genome-specific repetitive sequences is the main cause of genome variation between Gossypium A and D genomes. Through comparative analysis of the two genomes, we retrieved a repetitive element termed ICRd motif, which appears frequently in the diploid Gossypium raimondii (D5) genome but rarely in the diploid Gossypium arboreum (A2) genome. We further explored the existence of the ICRd motif in chromosomes of G. raimondii, G. arboreum, and two tetraploid (AADD) cotton species, Gossypium hirsutum and Gossypium barbadense, by fluorescence in situ hybridization (FISH), and observed that the ICRd motif exists in the D5 and D-subgenomes but not in the A2 and A-subgenomes. The ICRd motif comprises two components, a variable tandem repeat (TR) region and a conservative sequence (CS). The two constituents each have hundreds of repeats that evenly distribute across 13 chromosomes of the D5genome. The ICRd motif (and its repeats) was revealed as the common conservative region harbored by ancient Long Terminal Repeat Retrotransposons. Identification and investigation of the ICRd motif promotes the study of A and D genome differences, facilitates research on Gossypium genome evolution, and provides assistance to subgenome identification and genome assembling.

scholarly journals Identification of a genome-specific repetitive element in the Gossypium D genome

2019 ◽  
Author(s):  
Hejun Lu ◽  
Xinglei Cui ◽  
Yanyan Zhao ◽  
Richard Odongo Magwang ◽  
Pengcheng Li ◽  
...  
Keyword(s):  
Repetitive Element ◽  
Gossypium Arboreum ◽  
Repeat Region ◽  
D Genome ◽  
A Genome ◽  
Tandem Repeat Region ◽  
Gossypium Raimondii ◽  
The Common ◽  
Length Variable

The activity of genome-specific repetitive sequence is the main cause of the genome variation between Gossypium A and D genomes. Through the comparative analysis of the two genomes, we got a repetitive element (ICRd motif), which repeats massively in the diploid Gossypium raimondii (D5) genome while almost absent in the diploid Gossypium arboreum (A2) genome. We further explored the existence of ICRd motif in G. raimondii, G. arboreum, and two tetraploids (AADD) cotton G. hirsutum and G. barbadense by fluorescence in situ hybridization (FISH), and observed the ICRd motif exists in D5 and D-subgenomes but not in A2 and A-subgenome. The ICRd motif was investigated through its two constituents , a length variable tandem repeat region (TR) and a conservative sequence (CS), which highly repeat and evenly distribute in chromosomes of D5 genome. The ICRd motif was revealed as the common conservative region of ancient LTR-TEs. The identifications and investigation of the ICRd motif promote the study on the A and D genome differences, facilitate the research on the Gossypium genome evolution, and provide assistance to subgenome identification and genome assembling.

scholarly journals Identification of a genome-specific repetitive element in the Gossypium D genome

2019 ◽  
Author(s):  
Hejun Lu ◽  
Xinglei Cui ◽  
Yanyan Zhao ◽  
Richard Odongo Magwang ◽  
Pengcheng Li ◽  
...  
Keyword(s):  
Repetitive Element ◽  
Gossypium Arboreum ◽  
Repeat Region ◽  
D Genome ◽  
A Genome ◽  
Tandem Repeat Region ◽  
Gossypium Raimondii ◽  
The Common ◽  
Length Variable

The activity of genome-specific repetitive sequence is the main cause of the genome variation between Gossypium A and D genomes. Through the comparative analysis of the two genomes, we got a repetitive element (ICRd motif), which repeats massively in the diploid Gossypium raimondii (D5) genome while almost absent in the diploid Gossypium arboreum (A2) genome. We further explored the existence of ICRd motif in G. raimondii, G. arboreum, and two tetraploids (AADD) cotton G. hirsutum and G. barbadense by fluorescence in situ hybridization (FISH), and observed the ICRd motif exists in D5 and D-subgenomes but not in A2 and A-subgenome. The ICRd motif was investigated through its two constituents , a length variable tandem repeat region (TR) and a conservative sequence (CS), which highly repeat and evenly distribute in chromosomes of D5 genome. The ICRd motif was revealed as the common conservative region of ancient LTR-TEs. The identifications and investigation of the ICRd motif promote the study on the A and D genome differences, facilitate the research on the Gossypium genome evolution, and provide assistance to subgenome identification and genome assembling.

scholarly journals De Novo Genome Sequence Assemblies of Gossypium raimondii and Gossypium turneri

2019 ◽  
Vol 9 (10) ◽  
pp. 3079-3085 ◽  
Author(s):  
Joshua A. Udall ◽  
Evan Long ◽  
Chris Hanson ◽  
Daojun Yuan ◽  
Thiruvarangan Ramaraj ◽  
...  
Keyword(s):  
Genome Sequence ◽  
De Novo ◽  
Close Relative ◽  
Sequencing Data ◽  
Genome Sequences ◽  
D Genome ◽  
Cotton Species ◽  
A Genome ◽  
Long Read ◽  
Gossypium Raimondii

Cotton is an agriculturally important crop. Because of its importance, a genome sequence of a diploid cotton species (Gossypium raimondii, D-genome) was first assembled using Sanger sequencing data in 2012. Improvements to DNA sequencing technology have improved accuracy and correctness of assembled genome sequences. Here we report a new de novo genome assembly of G. raimondii and its close relative G. turneri. The two genomes were assembled to a chromosome level using PacBio long-read technology, HiC, and Bionano optical mapping. This report corrects some minor assembly errors found in the Sanger assembly of G. raimondii. We also compare the genome sequences of these two species for gene composition, repetitive element composition, and collinearity. Most of the identified structural rearrangements between these two species are due to intra-chromosomal inversions. More inversions were found in the G. turneri genome sequence than the G. raimondii genome sequence. These findings and updates to the D-genome sequence will improve accuracy and translation of genomics to cotton breeding and genetics.

Chromosomal organization of a sequence related to LTR-like elements of Ty1-copia retrotransposons in Avena species

Genome ◽  
1999 ◽  
Vol 42 (4) ◽  
pp. 706-713 ◽  
Author(s):  
Concha Linares ◽  
Antonio Serna ◽  
Araceli Fominaya
Keyword(s):  
In Situ Hybridization ◽  
Diploid Species ◽  
D Genome ◽  
Specific Sequence ◽  
Chromosomal Organization ◽  
Intergenomic Translocations ◽  
A Genome ◽  
Slot Blot Analysis ◽  
Copia Retrotransposons

A repetitive sequence, pAs17, was isolated from Avena strigosa (As genome) and characterized. The insert was 646 bp in length and showed 54% AT content. Databank searches revealed its high homology to the long terminal repeat (LTR) sequences of the specific family of Ty1-copia retrotransposons represented by WIS2-1A and Bare. It was also found to be 70% identical to the LTR domain of the WIS2-1A retroelement of wheat and 67% identical to the Bare-1 retroelement of barley. Southern hybridizations of pAs17 to diploid (A or C genomes), tetraploid (AC genomes), and hexaploid (ACD genomes) oat species revealed that it was absent in the C diploid species. Slot-blot analysis suggested that both diploid and tetraploid oat species contained 1.3 × 104 copies, indicating that they are a component of the A-genome chromosomes. The hexaploid species contained 2.4 × 104 copies, indicating that they are a component of both A- and D-genome chromosomes. This was confirmed by fluorescent in situ hybridization analyses using pAs17, two ribosomal sequences, and a C-genome specific sequence as probes. Further, the chromosomes involved in three C-A and three C-D intergenomic translocations in Avena murphyi (AC genomes) and Avena sativa cv. Extra Klock (ACD genomes), respectively, were identified. Based on its physical distribution and Southern hybridization patterns, a parental retrotransposon represented by pAs17 appears to have been active at least once during the evolution of the A genome in species of the Avena genus.Key words: chromosomal organization, in situ hybridization, intergenomic translocations, LTR sequence, oats.

scholarly journals A draft physical map of a D-genome cotton species (Gossypium raimondii)

BMC Genomics ◽  
2010 ◽  
Vol 11 (1) ◽  
pp. 395 ◽  
Author(s):  
Lifeng Lin ◽  
Gary J Pierce ◽  
John E Bowers ◽  
James C Estill ◽  
Rosana O Compton ◽  
...  
Keyword(s):  
Physical Map ◽  
D Genome ◽  
Cotton Species ◽  
Gossypium Raimondii

Fluorescence in situ hybridization mapping of Avena sativa L. cv. SunII and its monosomic lines using cloned repetitive DNA sequences

Genome ◽  
2002 ◽  
Vol 45 (6) ◽  
pp. 1230-1237 ◽  
Author(s):  
M L Irigoyen ◽  
C Linares ◽  
E Ferrer ◽  
A Fominaya
Keyword(s):  
In Situ Hybridization ◽  
Dna Sequences ◽  
Avena Sativa ◽  
Meiotic Chromosome ◽  
D Genome ◽  
Fish Mapping ◽  
Intergenomic Translocations ◽  
A Genome ◽  
C Genome

Fluorescent in situ hybridization (FISH) employing multiple probes was used with mitotic or meiotic chromosome spreads of Avena sativa L. cv. SunII and its monosomic lines to produce physical chromosome maps. The probes used were Avena strigosa pAs120a (which hybridizes exclusively to A-genome chromosomes), Avena murphyi pAm1 (which hybridizes exclusively to C-genome chromosomes), A. strigosa pAs121 (which hybridizes exclusively to A- and D-genome chromosomes), and the wheat rDNA probes pTa71 and pTa794. Simultaneous and sequential FISH employing two-by-two combinations of these probes allowed the unequivocal identification and genome assignation of all chromosomes. Ten pairs were found carrying intergenomic translocations: (i) between the A and C genomes (chromosome pair 5A); (ii) between the C and D genomes (pairs 1C, 2C, 4C, 10C, and 16C); and (iii) between the D and C genomes (pairs 9D, 11D, 13D, and 14D). The existence of a reciprocal intergenomic translocation (10C–14D) is also proposed. Comparing these results with those of other hexaploids, three intergenomic translocations (10C, 9D, and 14D) were found to be unique to A. sativa cv. SunII, supporting the view that 'SunII' is genetically distinct from other hexaploid Avena species and from cultivars of the A. sativa species. FISH mapping using meiotic and mitotic metaphases facilitated the genomic and chromosomal identification of the aneuploid chromosome in each monosomic line. Of the 18 analyzed, only 11 distinct monosomic lines were actually found, corresponding to 5 lines of the A genome, 2 lines of the C genome, and 4 lines of the D genome. The presence or absence of the 10C–14D interchange was also monitored in these lines.Key words: Avena sativa, monosomics, FISH mapping, genomic identification, intergenomic translocations.

scholarly journals Germline-Restricted Chromosome (GRC) is Widespread among Songbirds

2018 ◽  
Author(s):  
Anna A. Torgasheva ◽  
Lyubov P. Malinovskaya ◽  
Kira S. Zadesenets ◽  
Tatyana V. Karamysheva ◽  
Elena A. Kizilova ◽  
...  
Keyword(s):  
Zebra Finch ◽  
Common Ancestor ◽  
Germ Line ◽  
Repetitive Sequences ◽  
Genetic Element ◽  
Selfish Genetic Elements ◽  
Dna Loss ◽  
The Common ◽  
And Function

AbstractThe genome of flying birds, the smallest among amniotes, reflects overweight of the extensive DNA loss over the unrestricted proliferation of selfish genetic elements, resulted in a shortage of repeated sequences and lack of B-chromosomes. The only exception of this rule has been described in zebra finch, which possesses a large germ-line restricted chromosome (GRC), transmitted via oocytes, eliminated from male postmeiotic cells and absent in somatic cell. It is considered as a rarity and its origin, content and function remain unclear. We discovered that all songbirds possess GRC: in various size and genetic content it is present in all fifteen songbird species investigated and absent from germ-line genomes of all eight species of other bird orders examined. Our data based on fluorescent in situ hybridization of DNA probes derived from GRCs of four different Passeri species and their sequencing indicate that the GRCs show low homology between avian species. They contain fragments of the somatic genomes, which include various unique and repetitive sequences. We propose that the GRC has formed in the common ancestor of the extant songbirds and undergone subsequent divergence. GRC presence in the germ line of every songbird studied indicate that it could contain genetic element(s) indispensable for gametogenesis, which are yet to be discovered.

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