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

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.

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De Novo Genome Sequence Assemblies of Gossypium raimondii and Gossypium turneri

G3 Genes|Genome|Genetics ◽

10.1534/g3.119.400392 ◽

2019 ◽

Vol 9 (10) ◽

pp. 3079-3085 ◽

Cited By ~ 8

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.

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Wheat genome structure and function: genome sequence data and the International Wheat Genome Sequencing Consortium

Australian Journal of Agricultural Research ◽

10.1071/ar06155 ◽

2007 ◽

Vol 58 (6) ◽

pp. 470 ◽

Cited By ~ 11

Author(s):

P. Moolhuijzen ◽

D. S. Dunn ◽

M. Bellgard ◽

M. Carter ◽

J. Jia ◽

...

Keyword(s):

Genome Sequencing ◽

Physical Map ◽

Genome Structure ◽

Genetic Research ◽

Structure And Function ◽

Wheat Genome ◽

D Genome ◽

Genome Sequencing Consortium ◽

And Function ◽

Bac Contigs

Genome sequencing and the associated bioinformatics is now a widely accepted research tool for accelerating genetic research and the analysis of genome structure and function of wheat because it leverages similar work from other crops and plants. The International Wheat Genome Sequencing Consortium addresses the challenge of wheat genome structure and function and builds on the research efforts of Professor Bob McIntosh in the genetics of wheat. Currently, expressed sequence tags (ESTs; ~500 000 to date) are the largest sequence resource for wheat genome analyses. It is estimated that the gene coverage of the wheat EST collection is ~60%, close to that of Arabidopsis, indicating that ~40% of wheat genes are not represented in EST collections. The physical map of the D-genome donor species Aegilops tauschii is under construction (http://wheat.pw.usda.gov/PhysicalMapping). The technologies developed in this analysis of the D genome provide a good model for the approach to the entire wheat genome, namely compiling BAC contigs, assigning these BAC contigs to addresses in a high resolution genetic map, filling in gaps to obtain the entire physical length of a chromosome, and then large-scale sequencing.

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A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii, the wheat D-genome progenitor

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1219082110 ◽

2013 ◽

Vol 110 (19) ◽

pp. 7940-7945 ◽

Cited By ~ 158

Author(s):

M.-C. Luo ◽

Y. Q. Gu ◽

F. M. You ◽

K. R. Deal ◽

Y. Ma ◽

...

Keyword(s):

Physical Map ◽

Aegilops Tauschii ◽

D Genome ◽

Complex Genome

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Genetic map construction and functional characterization of genes within the segregation distortion regions (SDRs) in the F2:3 populations derived from wild cotton species of the D genome

Journal of Cotton Research ◽

10.1186/s42397-020-00072-2 ◽

2020 ◽

Vol 3 (1) ◽

Author(s):

Joy Nyangasi KIRUNGU ◽

Richard Odongo MAGWANGA ◽

Margaret Linyerera SHIRAKU ◽

Pu LU ◽

Teame Gereziher MEHARI ◽

...

Keyword(s):

Transcription Factors ◽

Segregation Distortion ◽

Critical Role ◽

Functional Characterization ◽

Dominant Gene ◽

Regulatory Elements ◽

Consensus Map ◽

D Genome ◽

Cotton Species ◽

Wild Cotton

Abstract Background Segregation distortion (SD) is a common phenomenon among stable or segregating populations, and the principle behind it still puzzles many researchers. The F2:3 progenies developed from the wild cotton species of the D genomes were used to investigate the possible plant transcription factors within the segregation distortion regions (SDRs). A consensus map was developed between two maps from the four D genomes, map A derived from F2:3 progenies of Gossypium klotzschianum and G. davidsonii while Map B from G. thurberi and G. trilobum F2:3 generations. In each map, 188 individual plants were used. Results The consensus linkage map had 1 492 markers across the 13 linkage groups with a map size of 1 467.445 cM and an average marker distance of 1.037 0 cM. Chromosome D502 had the highest percentage of SD with 58.6%, followed by Chromosome D507 with 47.9%. Six thousand and thirty-eight genes were mined within the SDRs on chromosome D502 and D507 of the consensus map. Within chromosome D502 and D507, 2 308 and 3 730 genes were mined, respectively, and were found to belong to 1 117 gourp out of which 622 groups were common across the two chromosomes. Moreover, genes within the top 9 groups related to plant resistance genes (R genes), whereas 188 genes encoding protein kinase domain (PF00069) comprised the largest group. Further analysis of the dominant gene group revealed that 287 miRNAs were found to target various genes, such as the gra-miR398, gra-miR5207, miR164a, miR164b, miR164c among others, which have been found to target top-ranked stress-responsive transcription factors such as NAC genes. Moreover, some of the stress- responsive cis-regulatory elements were also detected. Furthermore, RNA profiling of the genes from the dominant family showed that higher numbers of genes were highly upregulated under salt and osmotic stress conditions, and also they were highly expressed at different stages of fiber development. Conclusion The results indicated the critical role of the SDRs in the evolution of the key regulatory genes in plants.

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Functional divergence of cellulose synthase orthologs in between wild Gossypium raimondii and domesticated G. arboreum diploid cotton species

Cellulose ◽

10.1007/s10570-019-02744-y ◽

2019 ◽

Vol 26 (18) ◽

pp. 9483-9501

Author(s):

Hee Jin Kim ◽

Gregory N. Thyssen ◽

Xianliang Song ◽

Christopher D. Delhom ◽

Yongliang Liu

Keyword(s):

Functional Divergence ◽

Cellulose Synthase ◽

Cotton Species ◽

Gossypium Raimondii ◽

Diploid Cotton

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Cotton D genome assemblies built with long-read data unveil mechanisms of centromere evolution and stress tolerance divergence

BMC Biology ◽

10.1186/s12915-021-01041-0 ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Zhaoen Yang ◽

Xiaoyang Ge ◽

Weinan Li ◽

Yuying Jin ◽

Lisen Liu ◽

...

Keyword(s):

Stress Tolerance ◽

Crop Improvement ◽

Gene Activation ◽

Regulatory Region ◽

Rapid Evolution ◽

Ethylene Biosynthesis ◽

D Genome ◽

3D Genome ◽

Cotton Species ◽

Long Read

Abstract Background Many of genome features which could help unravel the often complex post-speciation evolution of closely related species are obscured because of their location in chromosomal regions difficult to accurately characterize using standard genome analysis methods, including centromeres and repeat regions. Results Here, we analyze the genome evolution and diversification of two recently diverged sister cotton species based on nanopore long-read sequence assemblies and Hi-C 3D genome data. Although D genomes are conserved in gene content, they have diversified in gene order, gene structure, gene family diversification, 3D chromatin structure, long-range regulation, and stress-related traits. Inversions predominate among D genome rearrangements. Our results support roles for 5mC and 6mA in gene activation, and 3D chromatin analysis showed that diversification in proximal-vs-distal regulatory-region interactions shape the regulation of defense-related-gene expression. Using a newly developed method, we accurately positioned cotton centromeres and found that these regions have undergone obviously more rapid evolution relative to chromosome arms. We also discovered a cotton-specific LTR class that clarifies evolutionary trajectories among diverse cotton species and identified genetic networks underlying the Verticillium tolerance of Gossypium thurberi (e.g., SA signaling) and salt-stress tolerance of Gossypium davidsonii (e.g., ethylene biosynthesis). Finally, overexpression of G. thurberi genes in upland cotton demonstrated how wild cottons can be exploited for crop improvement. Conclusions Our study substantially deepens understanding about how centromeres have developed and evolutionarily impacted the divergence among closely related cotton species and reveals genes and 3D genome structures which can guide basic investigations and applied efforts to improve crops.

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Genetic map construction and functional characterization of genes within the segregation distortion regions (SDRs) in the F2:3 generation derived from wild cotton species of the D genome

10.7287/peerj.preprints.27845 ◽

2019 ◽

Author(s):

Joy Nyangasi Kirungu ◽

Richard Odongo Magwanga ◽

Margaret Linyerera Shiraku ◽

Pu Lu ◽

Teame Gereziher Mehari ◽

...

Keyword(s):

Transcription Factors ◽

Segregation Distortion ◽

Functional Characterization ◽

Regulatory Elements ◽

D Genome ◽

Rna Profiling ◽

Cotton Species ◽

Wild Cotton ◽

Gossypium Thurberi ◽

Marker Distance

Segregation distortion (SD) is a phenomenon common among stable or segregating populations, and the principle behind it is still an issue that puzzles many researchers. An F2:3 generations developed from the wild cotton species of the D genomes was applied to investigate the possible plant transcription factors within the segregation distortion regions (SDRs). We constructed a consensus map between two maps in the D genome, map A; Gossypium klotzschianum and Gossypium davidsonii and Map B; Gossypium thurberi and Gossypium trilobum. The two maps were developed from 188 F2:3 populations for each map, a total of 1492 markers, were linked to the 13 linkage groups. The consensus linkage map size was 1467.445 cM with an average marker distance of 1.0370cM. Chr02 had the highest percentage of segregation distortion with 58.621% followed by Chr07 with 47.887%. A total of 6,038 genes were mined within the segregation distortion regions (SDR region) of Chr02 and Chr07 with 2,308 gene in Chr02 and 3,730 genes in Chr07, we obtained a total of 1,117 domains within the SDR with a total of 622 domains shared between the two chromosomes, the first 9 domains all belonged to the plant resistance genes (R genes), the largest domain was PF00069 with a total of 188 genes. A total of 287 miRNAs were found to target the various genes, such as gr-miR398, gra-miR5207, miR164a, miR164b, miR164c among others which have been found to target top-ranked stress-responsive transcription factors such as NAC genes. Moreover, the genes were found to be regulated by various stress responsive cis-regulatory elements. RNA profiling showed that higher numbers of genes were highly upregulated in abiotic and different fiber development stages. The result shows that the SDR regions could be playing an important role in the evolution of significant genes in plants.

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Genetic map construction and functional characterization of genes within the segregation distortion regions (SDRs) in the F2:3 generation derived from wild cotton species of the D genome

10.7287/peerj.preprints.27845v1 ◽

2019 ◽

Author(s):

Joy Nyangasi Kirungu ◽

Richard Odongo Magwanga ◽

Margaret Linyerera Shiraku ◽

Pu Lu ◽

Teame Gereziher Mehari ◽

...

Keyword(s):

Transcription Factors ◽

Segregation Distortion ◽

Functional Characterization ◽

Regulatory Elements ◽

D Genome ◽

Rna Profiling ◽

Cotton Species ◽

Wild Cotton ◽

Gossypium Thurberi ◽

Marker Distance

Segregation distortion (SD) is a phenomenon common among stable or segregating populations, and the principle behind it is still an issue that puzzles many researchers. An F2:3 generations developed from the wild cotton species of the D genomes was applied to investigate the possible plant transcription factors within the segregation distortion regions (SDRs). We constructed a consensus map between two maps in the D genome, map A; Gossypium klotzschianum and Gossypium davidsonii and Map B; Gossypium thurberi and Gossypium trilobum. The two maps were developed from 188 F2:3 populations for each map, a total of 1492 markers, were linked to the 13 linkage groups. The consensus linkage map size was 1467.445 cM with an average marker distance of 1.0370cM. Chr02 had the highest percentage of segregation distortion with 58.621% followed by Chr07 with 47.887%. A total of 6,038 genes were mined within the segregation distortion regions (SDR region) of Chr02 and Chr07 with 2,308 gene in Chr02 and 3,730 genes in Chr07, we obtained a total of 1,117 domains within the SDR with a total of 622 domains shared between the two chromosomes, the first 9 domains all belonged to the plant resistance genes (R genes), the largest domain was PF00069 with a total of 188 genes. A total of 287 miRNAs were found to target the various genes, such as gr-miR398, gra-miR5207, miR164a, miR164b, miR164c among others which have been found to target top-ranked stress-responsive transcription factors such as NAC genes. Moreover, the genes were found to be regulated by various stress responsive cis-regulatory elements. RNA profiling showed that higher numbers of genes were highly upregulated in abiotic and different fiber development stages. The result shows that the SDR regions could be playing an important role in the evolution of significant genes in plants.

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

10.7287/peerj.preprints.27806v1 ◽

2019 ◽

Cited By ~ 1

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.

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