scholarly journals Genome-Wide Identification of Cyclophilin Gene Family in Cotton and Expression Analysis of the Fibre Development in Gossypium barbadense

2019 ◽  
Vol 20 (2) ◽  
pp. 349 ◽  
Author(s):  
Qin Chen ◽  
Quan-Jia Chen ◽  
Guo-Qing Sun ◽  
Kai Zheng ◽  
Zheng-Pei Yao ◽  
...  
Keyword(s):  
Gene Family ◽  
Significant Role ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Composition Analysis ◽  
Rna Recognition Motif ◽  
Rna Recognition ◽  
Recognition Motif ◽  
Genome Wide ◽  
Fibre Development

Cyclophilins (CYPs) are a member of the immunophilin superfamily (in addition to FKBPs and parvulins) and play a significant role in peptidyl-prolyl cis-trans isomerase (PPIase) activity. Previous studies have shown that CYPs have important functions in plants, but no genome-wide analysis of the cotton CYP gene family has been reported, and the specific biological function of this gene is still elusive. Based on the release of the cotton genome sequence, we identified 75, 78, 40 and 38 CYP gene sequences from G. barbadense, G. hirsutum, G. arboreum, and G. raimondii, respectively; 221 CYP genes were unequally located on chromosomes. Phylogenetic analysis showed that 231 CYP genes clustered into three major groups and eight subgroups. Collinearity analysis showed that segmental duplications played a significant role in the expansion of CYP members in cotton. There were light-responsiveness, abiotic-stress and hormone-response elements upstream of most of the CYPs. In addition, the motif composition analysis revealed that 49 cyclophilin proteins had extra domains, including TPR (tetratricopeptide repeat), coiled coil, U-box, RRM (RNA recognition motif), WD40 (RNA recognition motif) and zinc finger domains, along with the cyclophilin-like domain (CLD). The expression patterns based on qRT-PCR showed that six CYP expression levels showed greater differences between Xinhai21 (long fibres, G. barbadense) and Ashmon (short fibres, G. barbadense) at 10 and 20 days postanthesis (DPA). These results signified that CYP genes are involved in the elongation stage of cotton fibre development. This study provides a valuable resource for further investigations of CYP gene functions and molecular mechanisms in cotton.

scholarly journals Genome-wide identification of expansin gene family reveals expansin genes are involved in fibre cells growth in cotton

2019 ◽  
Author(s):  
Limin Lv ◽  
Dongyun Zuo ◽  
Xingfen Wang ◽  
Hailiang Cheng ◽  
Youping Zhang ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Patterns ◽  
Crop Improvement ◽  
Cotton Fibre ◽  
Plant Cell Walls ◽  
Biological Functions ◽  
Qpcr Analysis ◽  
Genome Wide ◽  
Fibre Development ◽  
Initiation Stage

Abstract Background : Expansins ( EXPs ), a group of proteins that loosen plant cell walls and cellulosic materials, are involved in regulating cell growth and diverse developmental processes in plants. However, the biological functions of this gene family are still unknown in cotton. Results: In this paper, we identified a total of 93 expansin genes in Gossypium hirsutum . These genes were classified into four subfamilies, including 67 GhEXPAs , eight GhEXPBs , six GhEXLAs , and 12 GhEXLBs , and divided into 15 subgroups. All 93 expansin genes are distributed over 24 chromosomes excluding Ghir_A02 and Ghir_D06. All GhEXP genes contain multiple exons and each GhEXP protein has multiple conserved motifs. Transcript profiling and qPCR analysis revealed that the expansin genes have distinct expression patterns in different stages of cotton fibre development. Among them, three genes ( GhEXPA4o , GhEXPA1A , and GhEXPA8h ) were highly expressed in the initiation stage, nine genes ( GhEXPA4a , GhEXPA13a , GhEXPA4f , GhEXPA4q , GhEXPA8f , GhEXPA2 , GhEXPA8g , GhEXPA8a , and GhEXPA4n ) had high expression during the fast elongation stage, while GhEXLA1c and GhEXLA1f were preferentially expressed in the transition stage of fibre development. Conclusions: Our results provide a solid basis for further elucidation of biological functions of expansin genes in cotton fibre development and valuable genetic resources used for crop improvement in the future.

scholarly journals Genome-wide identification of the expansin gene family reveals that expansin genes are involved in fibre cell growth in cotton

2020 ◽  
Author(s):  
Limin Lv ◽  
Dongyun Zuo ◽  
Xingfen Wang ◽  
Hailiang Cheng ◽  
Youping Zhang ◽  
...  
Keyword(s):  
Cell Growth ◽  
Gene Family ◽  
Expression Patterns ◽  
Crop Improvement ◽  
Cotton Fibre ◽  
Plant Cell Walls ◽  
Biological Functions ◽  
Genome Wide ◽  
Fibre Development ◽  
Initiation Stage

Abstract Background : Expansins ( EXPs ), a group of proteins that loosen plant cell walls and cellulosic materials, are involved in regulating cell growth and diverse developmental processes in plants. However, the biological functions of this gene family in cotton are still unknown. Results: In this paper, we identified a total of 93 expansin genes in Gossypium hirsutum . These genes were classified into four subfamilies, including 67 GhEXPAs , 8 GhEXPBs , 6 GhEXLAs , and 12 GhEXLBs , and divided into 15 subgroups. The 93 expansin genes are distributed over 24 chromosomes, excluding Ghir_A02 and Ghir_D06. All GhEXP genes contain multiple exons, and each GhEXP protein has multiple conserved motifs. Transcript profiling and qPCR analysis revealed that the expansin genes have distinct expression patterns among different stages of cotton fibre development. Among them, 3 genes ( GhEXPA4o , GhEXPA1A , and GhEXPA8h ) were highly expressed in the initiation stage, 9 genes ( GhEXPA4a , GhEXPA13a , GhEXPA4f , GhEXPA4q , GhEXPA8f , GhEXPA2 , GhEXPA8g , GhEXPA8a , and GhEXPA4n ) had high expression during the fast elongation stage, and GhEXLA1c and GhEXLA1f were preferentially expressed in the transition stage of fibre development. Conclusions: Our results provide a solid basis for further elucidation of the biological functions of expansin genes in relation to cotton fibre development and valuable genetic resources for future crop improvement.

scholarly journals Genome-wide identification of expansin gene family reveals expansin genes are involved in fibre cells growth in cotton

2019 ◽  
Author(s):  
Limin Lv ◽  
Dongyun Zuo ◽  
Xingfen Wang ◽  
Hailiang Cheng ◽  
Youping Zhang ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Patterns ◽  
Crop Improvement ◽  
Cotton Fibre ◽  
Plant Cell Walls ◽  
Biological Functions ◽  
Qpcr Analysis ◽  
Genome Wide ◽  
Fibre Development ◽  
Initiation Stage

Abstract Background : Expansins ( EXPs ), a group of proteins that loosen plant cell walls and cellulosic materials, are involved in regulating cell growth and diverse developmental processes in plants. However, the biological functions of this gene family are still unknown in cotton. Results: In this paper, we identified a total of 93 expansin genes in Gossypium hirsutum . These genes were classified into four subfamilies, including 67 GhEXPAs , 8 GhEXPBs , 6 GhEXLAs , and 12 GhEXLBs , and divided into 15 subgroups. All 93 expansin genes are distributed over 24 chromosomes excluding Ghir_A02 and Ghir_D06. All GhEXP genes contain multiple exons and each GhEXP protein has multiple conserved motifs. Transcript profiling and qPCR analysis revealed that the expansin genes have distinct expression patterns in different stages of cotton fibre development. Among them, 3 genes ( GhEXPA4o , GhEXPA1A , and GhEXPA8h ) were highly expressed in the initiation stage, 9 genes ( GhEXPA4a , GhEXPA13a , GhEXPA4f , GhEXPA4q , GhEXPA8f , GhEXPA2 , GhEXPA8g , GhEXPA8a , and GhEXPA4n ) had high expression during the fast elongation stage, while GhEXLA1c and GhEXLA1f were preferentially expressed in the transition stage of fibre development. Conclusions: Our results provide a solid basis for further elucidation of biological functions of expansin genes in cotton fibre development and valuable genetic resources used for crop improvement in the future.

scholarly journals Genome-wide identification of expansin gene family reveals expansin genes are involved in fibre cells growth in cotton

2020 ◽  
Author(s):  
Limin Lv ◽  
Dongyun Zuo ◽  
Xingfen Wang ◽  
Hailiang Cheng ◽  
Youping Zhang ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Patterns ◽  
Crop Improvement ◽  
Cotton Fibre ◽  
Plant Cell Walls ◽  
Biological Functions ◽  
Qpcr Analysis ◽  
Genome Wide ◽  
Fibre Development ◽  
Initiation Stage

Abstract Background : Expansins ( EXPs ), a group of proteins that loosen plant cell walls and cellulosic materials, are involved in regulating cell growth and diverse developmental processes in plants. However, the biological functions of this gene family are still unknown in cotton. Results: In this paper, we identified a total of 93 expansin genes in Gossypium hirsutum . These genes were classified into four subfamilies, including 67 GhEXPAs , 8 GhEXPBs , 6 GhEXLAs , and 12 GhEXLBs , and divided into 15 subgroups. All 93 expansin genes are distributed over 24 chromosomes excluding Ghir_A02 and Ghir_D06. All GhEXP genes contain multiple exons and each GhEXP protein has multiple conserved motifs. Transcript profiling and qPCR analysis revealed that the expansin genes have distinct expression patterns in different stages of cotton fibre development. Among them, 3 genes ( GhEXPA4o , GhEXPA1A , and GhEXPA8h ) were highly expressed in the initiation stage, 9 genes ( GhEXPA4a , GhEXPA13a , GhEXPA4f , GhEXPA4q , GhEXPA8f , GhEXPA2 , GhEXPA8g , GhEXPA8a , and GhEXPA4n ) had high expression during the fast elongation stage, while GhEXLA1c and GhEXLA1f were preferentially expressed in the transition stage of fibre development. Conclusions: Our results provide a solid basis for further elucidation of biological functions of expansin genes in cotton fibre development and valuable genetic resources used for crop improvement in the future.

scholarly journals Genome-wide investigation of malate dehydrogenase gene family in poplar (Populus trichocarpa) and their expression analysis under salt stress

2019 ◽  
Author(s):  
Xinghao Chen ◽  
Jun Zhang ◽  
Chao Zhang ◽  
Shijie Wang ◽  
Minsheng Yang
Keyword(s):  
Salt Stress ◽  
Gene Family ◽  
Malate Dehydrogenase ◽  
Molecular Mechanisms ◽  
Populus Trichocarpa ◽  
Expression Patterns ◽  
Subcellular Location ◽  
Genome Wide ◽  
Duplication Events ◽  
Gene Structures

Malate dehydrogenase (MDH) is widely distributed in plants and animals, and plays an important role in many metabolic processes. However, there have been few studies on MDH genes in poplar. In this study, 16 MDH gene sequences were identified from the Populus trichocarpa genome and renamed according to their chromosomal locations. Based on phylogenetic analysis, the PtMDH genes were divided into five groups, and genes that grouped together all shared the same subcellular location and had similar sequence lengths, gene structures, and conserved motifs. Two pairs of tandem duplication events and three segmental duplication events involving five genes were identified from the 15 PtMDH genes located on the chromosomes. Each pair of genes had a Ka/Ks ratios <1, indicating that the MDH gene family of P. trichocarpa was purified during evolution. Based on the transcriptome data of P. trichocarpa under salt stress and qRT-PCR verification, the expression patterns of PtMDH genes under salt stress were analyzed. The results showed that most of the genes were upregulated under salt stress, indicating that they play a role in the response of poplar to salt stress. The PtmMDH1 gene can be used as an important salt-tolerant candidate gene for further investigations of molecular mechanisms. This study lays the foundation for functional analysis of MDH genes and genetic improvement in poplar.

scholarly journals Genome-wide investigation of malate dehydrogenase gene family in poplar (Populus trichocarpa) and their expression analysis under salt stress

2019 ◽  
Author(s):  
Xinghao Chen ◽  
Jun Zhang ◽  
Chao Zhang ◽  
Shijie Wang ◽  
Minsheng Yang
Keyword(s):  
Salt Stress ◽  
Gene Family ◽  
Malate Dehydrogenase ◽  
Molecular Mechanisms ◽  
Populus Trichocarpa ◽  
Expression Patterns ◽  
Subcellular Location ◽  
Genome Wide ◽  
Duplication Events ◽  
Gene Structures

Malate dehydrogenase (MDH) is widely distributed in plants and animals, and plays an important role in many metabolic processes. However, there have been few studies on MDH genes in poplar. In this study, 16 MDH gene sequences were identified from the Populus trichocarpa genome and renamed according to their chromosomal locations. Based on phylogenetic analysis, the PtMDH genes were divided into five groups, and genes that grouped together all shared the same subcellular location and had similar sequence lengths, gene structures, and conserved motifs. Two pairs of tandem duplication events and three segmental duplication events involving five genes were identified from the 15 PtMDH genes located on the chromosomes. Each pair of genes had a Ka/Ks ratios <1, indicating that the MDH gene family of P. trichocarpa was purified during evolution. Based on the transcriptome data of P. trichocarpa under salt stress and qRT-PCR verification, the expression patterns of PtMDH genes under salt stress were analyzed. The results showed that most of the genes were upregulated under salt stress, indicating that they play a role in the response of poplar to salt stress. The PtmMDH1 gene can be used as an important salt-tolerant candidate gene for further investigations of molecular mechanisms. This study lays the foundation for functional analysis of MDH genes and genetic improvement in poplar.

scholarly journals Roles of the 14-3-3 gene family in cotton flowering

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Na Sang ◽  
Hui Liu ◽  
Bin Ma ◽  
Xianzhong Huang ◽  
Lu Zhuo ◽  
...  
Keyword(s):  
Gene Family ◽  
Protein Interactions ◽  
Leucine Zipper ◽  
Expression Patterns ◽  
Bimolecular Fluorescence Complementation ◽  
Structural Motif ◽  
Virus Induced Gene Silencing ◽  
Protein Protein Interactions ◽  
Basic Leucine Zipper ◽  
Genome Wide

Abstract Background In plants, 14-3-3 proteins, also called GENERAL REGULATORY FACTORs (GRFs), encoded by a large multigene family, are involved in protein–protein interactions and play crucial roles in various physiological processes. No genome-wide analysis of the GRF gene family has been performed in cotton, and their functions in flowering are largely unknown. Results In this study, 17, 17, 31, and 17 GRF genes were identified in Gossypium herbaceum, G. arboreum, G. hirsutum, and G. raimondii, respectively, by genome-wide analyses and were designated as GheGRFs, GaGRFs, GhGRFs, and GrGRFs, respectively. A phylogenetic analysis revealed that these proteins were divided into ε and non-ε groups. Gene structural, motif composition, synteny, and duplicated gene analyses of the identified GRF genes provided insights into the evolution of this family in cotton. GhGRF genes exhibited diverse expression patterns in different tissues. Yeast two-hybrid and bimolecular fluorescence complementation assays showed that the GhGRFs interacted with the cotton FLOWERING LOCUS T homologue GhFT in the cytoplasm and nucleus, while they interacted with the basic leucine zipper transcription factor GhFD only in the nucleus. Virus-induced gene silencing in G. hirsutum and transgenic studies in Arabidopsis demonstrated that GhGRF3/6/9/15 repressed flowering and that GhGRF14 promoted flowering. Conclusions Here, 82 GRF genes were identified in cotton, and their gene and protein features, classification, evolution, and expression patterns were comprehensively and systematically investigated. The GhGRF3/6/9/15 interacted with GhFT and GhFD to form florigen activation complexs that inhibited flowering. However, GhGRF14 interacted with GhFT and GhFD to form florigen activation complex that promoted flowering. The results provide a foundation for further studies on the regulatory mechanisms of flowering.

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