scholarly journals A Survey of Alternative Splicing in Allotetraploid Cotton (Gossypium hirsutum L.)

2018 ◽  
Author(s):  
Xiang Jia Min
Keyword(s):  
Alternative Splicing ◽  
Gossypium Hirsutum ◽  
Allotetraploid Cotton

scholarly journals Characterization and Stress Response of the JmjC Domain-Containing Histone Demethylase Gene Family in the Allotetraploid Cotton Species Gossypium hirsutum

Plants ◽  
2020 ◽  
Vol 9 (11) ◽  
pp. 1617
Author(s):  
Jie Zhang ◽  
Junping Feng ◽  
Wei Liu ◽  
Zhongying Ren ◽  
Junjie Zhao ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Stress Response ◽  
Gossypium Hirsutum ◽  
Gene Family ◽  
Function Analysis ◽  
Histone Demethylase ◽  
Abiotic Stress Response ◽  
Cotton Species ◽  
Jmjc Domain ◽  
Allotetraploid Cotton

Histone modification is an important epigenetic modification that controls gene transcriptional regulation in eukaryotes. Histone methylation is accomplished by histone methyltransferase and can occur on two amino acid residues, arginine and lysine. JumonjiC (JmjC) domain-containing histone demethylase regulates gene transcription and chromatin structure by changing the methylation state of the lysine residue site and plays an important role in plant growth and development. In this study, we carried out genome-wide identification and comprehensive analysis of JmjC genes in the allotetraploid cotton species Gossypium hirsutum. In total, 50 JmjC genes were identified and in G. hirsutum, and 25 JmjC genes were identified in its two diploid progenitors, G. arboreum and G. raimondii, respectively. Phylogenetic analysis divided these JmjC genes into five subfamilies. A collinearity analysis of the two subgenomes of G. hirsutum and the genomes of G. arboreum and G. raimondii uncovered a one-to-one relationship between homologous genes of the JmjC gene family. Most homologs in the JmjC gene family between A and D subgenomes of G. hirsutum have similar exon-intron structures, which indicated that JmjC family genes were conserved after the polyploidization. All G. hirsutumJmjC genes were found to have a typical JmjC domain, and some genes also possess other special domains important for their function. Analysis of promoter regions revealed that cis-acting elements, such as those related to hormone and abiotic stress response, were enriched in G. hirsutum JmjC genes. According to a reverse transcription-quantitative polymerase chain reaction (RT-qPCR) analysis, most G. hirsutumJmjC genes had high abundance expression at developmental stages of fibers, suggesting that they might participate in cotton fiber development. In addition, some G. hirsutumJmjC genes were found to have different degrees of response to cold or osmotic stress, thus indicating their potential role in these types of abiotic stress response. Our results provide useful information for understanding the evolutionary history and biological function of JmjC genes in cotton.

Characteristics and analysis of simple sequence repeats in the cotton genome based on a linkage map constructed from a BC1 population between Gossypium hirsutum and G. barbadense

Genome ◽  
2008 ◽  
Vol 51 (7) ◽  
pp. 534-546 ◽  
Author(s):  
Yanxin Zhang ◽  
Zhongxu Lin ◽  
Qizhong Xia ◽  
Mingju Zhang ◽  
Xianlong Zhang
Keyword(s):  
Gossypium Hirsutum ◽  
Linkage Map ◽  
Expressed Sequence Tag ◽  
Average Distance ◽  
Dinucleotide Repeats ◽  
Genome Wide ◽  
Size Type ◽  
Simple Sequence ◽  
Mapping Populations ◽  
Allotetraploid Cotton

In the past decade, several molecular maps of cotton have been constructed using diverse DNA molecular markers and mapping populations. In this study, an interspecific linkage map of allotetraploid cotton was developed using a BC1 population ((Gossypium hirsutum × G. barbadense) × G. hirsutum). This map was genome-wide and was based entirely on simple sequence repeat (SSR) markers. Forty-four linkage groups were assigned to 26 chromosomes, with 917 loci spanning 5452.2 cM of the genome. The average distance between loci was 5.9 cM, providing uniform coverage of the A subgenome and D subgenome. Characteristics of this map were analyzed in detail, including the distributions of genomic SSRs, expressed sequence tag (EST)-SSRs, and distorted markers. Furthermore, the relationships between motif characteristics (size, type, length) and the level of polymorphism in EST-SSRs were also surveyed. The results showed that tetranucleotide and dinucleotide repeats had similar levels of polymorphism, and ACAT, AC, and ACT repeats had the highest polymorphism rates. Loci with lengths of 27 bp, 33 bp, and 24 bp were more likely to be polymorphic. This work will provide information to assist in designing future EST-SSRs.

Cloning and characterization of homeologous cellulose synthase catalytic subunit 2 genes from allotetraploid cotton (Gossypium hirsutum L.)

Gene ◽  
2012 ◽  
Vol 494 (2) ◽  
pp. 181-189 ◽  
Author(s):  
Hee Jin Kim ◽  
Barbara A. Triplett ◽  
Hong-Bin Zhang ◽  
Mi-Kyung Lee ◽  
Doug J. Hinchliffe ◽  
...  
Keyword(s):  
Gossypium Hirsutum ◽  
Cellulose Synthase ◽  
Catalytic Subunit ◽  
Gossypium Hirsutum L ◽  
Allotetraploid Cotton

scholarly journals Gossypium barbadense and Gossypium hirsutum genomes provide insights into the origin and evolution of allotetraploid cotton

2019 ◽  
Vol 51 (4) ◽  
pp. 739-748 ◽  
Author(s):  
Yan Hu ◽  
Jiedan Chen ◽  
Lei Fang ◽  
Zhiyuan Zhang ◽  
Wei Ma ◽  
...  
Keyword(s):  
Gossypium Hirsutum ◽  
Gossypium Barbadense ◽  
Origin And Evolution ◽  
Allotetraploid Cotton

scholarly journals High efficient multisites genome editing in allotetraploid cotton (Gossypium hirsutum ) using CRISPR/Cas9 system

2017 ◽  
Vol 16 (1) ◽  
pp. 137-150 ◽  
Author(s):  
Pengcheng Wang ◽  
Jun Zhang ◽  
Lin Sun ◽  
Yizan Ma ◽  
Jiao Xu ◽  
...  
Keyword(s):  
Gossypium Hirsutum ◽  
Genome Editing ◽  
High Efficient ◽  
Allotetraploid Cotton

scholarly journals Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement

2015 ◽  
Vol 33 (5) ◽  
pp. 531-537 ◽  
Author(s):  
Tianzhen Zhang ◽  
Yan Hu ◽  
Wenkai Jiang ◽  
Lei Fang ◽  
Xueying Guan ◽  
...  
Keyword(s):  
Gossypium Hirsutum ◽  
Gossypium Hirsutum L ◽  
Allotetraploid Cotton

scholarly journals Evolutionary Conservation and Divergence of Genes Encoding 3-Hydroxy-3-methylglutaryl Coenzyme A Synthase in the Allotetraploid Cotton Species Gossypium hirsutum

Cells ◽  
2019 ◽  
Vol 8 (5) ◽  
pp. 412 ◽  
Author(s):  
Wei Liu ◽  
Zhiqiang Zhang ◽  
Wei Zhu ◽  
Zhongying Ren ◽  
Lin Jia ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Gossypium Hirsutum ◽  
Plant Species ◽  
Coenzyme A ◽  
Mevalonate Pathway ◽  
Expression Patterns ◽  
Duplicated Genes ◽  
Ancestral Gene ◽  
Cotton Species ◽  
Allotetraploid Cotton

Polyploidization is important for the speciation and subsequent evolution of many plant species. Analyses of the duplicated genes produced via polyploidization events may clarify the origin and evolution of gene families. During terpene biosynthesis, 3-hydroxy-3-methylglutaryl coenzyme A synthase (HMGS) functions as a key enzyme in the mevalonate pathway. In this study, we first identified a total of 53 HMGS genes in 23 land plant species, while no HMGS genes were detected in three green algae species. The phylogenetic analysis suggested that plant HMGS genes may have originated from a common ancestral gene before clustering in different branches during the divergence of plant lineages. Then, we detected six HMGS genes in the allotetraploid cotton species (Gossypium hirsutum), which was twice that of the two diploid cotton species (Gossypium raimondii and Gossypium arboreum). The comparison of gene structures and phylogenetic analysis of HMGS genes revealed conserved evolution during polyploidization in Gossypium. Moreover, the expression patterns indicated that six GhHMGS genes were expressed in all tested tissues, with most genes considerably expressed in the roots, and they were responsive to various phytohormone treatments and abiotic stresses. The sequence and expression divergence of duplicated genes in G. hirsutum implied the sub-functionalization of GhHMGS1A and GhHMGS1D as well as GhHMGS3A and GhHMGS3D, whereas it implied the pseudogenization of GhHMGS2A and GhHMGS2D. Collectively, our study unraveled the evolutionary history of HMGS genes in green plants and from diploid to allotetraploid in cotton and illustrated the different evolutionary fates of duplicated HMGS genes resulting from polyploidization.

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