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Jonathan F. Wendel - One of the best experts on this subject based on the ideXlab platform.
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Comparative analysis of codon usage between Gossypium hirsutum and G. barbadense mitochondrial genomes
Mitochondrial DNA Part B, 2020Co-Authors: Zhiwen Chen, Zhao Jianguo, Jun Qiao, Hai-yan Wang, Zehui Liu, Baoyan Xing, Jonathan F. WendelAbstract:Gossypium hirsutum and G. barbadense mitochondrial genomes were analyzed to understand the factors shaping codon usage. While most analyses of codon usage suggest minimal to no bias, nucleotide com...
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The history and disposition of transposable elements in polyploid Gossypium
2016Co-Authors: Jennifer S. Hawkins, Corrinne E. Grover, Jonathan F. WendelAbstract:Abstract: Transposable elements (TEs) are a major component of plant genomes. It is of particular interest to explore the potential activation of TE proliferation, especially in hybrids and polyploids, which often are associated with rapid ge-nomic and epigenetic restructuring. Here we explore the consequences of genomic merger and doubling on copia and gypsy-like Gorge3 long terminal repeat (LTR) retrotransposons as well as on non-LTR long interspersed nuclear elements (LINEs) in allotetraploid cotton, Gossypium hirsutum. Using phylogenetic and quantitative methods, we describe the com-position and genomic origin of TEs in polyploid Gossypium. In addition, we present information on ancient and recent transposition activities of the three TE types and demonstrate the absence of an impressive proliferation of TEs following polyploidization in Gossypium. Further, we provide evidence for present-day transcription of LINEs, a relatively minor component of Gossypium genomes, whereas the more abundant LTR retrotransposons display limited expression and only under stressed conditions. Key words: copia, gypsy, LINE, genome evolution, repetitive DNA. Résume ́ : Les éléments transposables (ET) constituent une part importante des génomes des plantes. L’activation poten-tielle de la prolifération des ET présente un intérêt particulier, spécialement dans le contexte des hybrides et des polyploı̈-des chez lesquels se produisent fréquemment des changements génomiques et épigénétiques rapides. Ici, les auteurs explorent les conséquences de la fusion et du doublement des génomes sur les rétrotransposons a ̀ LTR copia et Gorge
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1 Taxonomy and Evolution of the Cotton Genus
2016Co-Authors: Jonathan F. Wendel, Corrinne E. GroverAbstract:We present an overview of the taxonomy of Gossypium L. (the cotton genus) and its evolutionary history. Gossypium contains more than 50 recognized species, including several recently described, distributed in arid to semiarid regions of the tropics and subtropics. Diversity in Gossypium has been promoted by two seemingly unlikely pro-cesses: transoceanic, long-distance dispersal and wide hybridization among lineages that presently are widely separated geographically. Included are four species that were independently domesticated for their seed fiber—two diploids from Africa–Asia and two allopolyploids from the Americas. This repeated domestication of different wild progenitors represents a remarkable case of human-driven parallel evolution. Mor-phological variation in Gossypium is extensive; growth forms in the genus range from sprawling herbaceous perennials to?15-m-tall trees, representing a notable array of reproductive and vegetative characteristics. Equally impressive is the striking cyto-genetic and genomic diversity that emerged as Gossypium diversified and spread worldwide, ultimately spawning eight groups of closely related diploid (n = 13) species (i.e., genome groups A through G, and K). DNA sequence data place the origin of Gossy-pium at about 5 to 10 million years ago (mya), which rapidly diversified into these major genome groups shortly thereafter. Allopolyploid cottons appeared within the last 1 to 2 million years, a consequence of the improbable transoceanic dispersal of an A genome taxon to the New World and subsequent hybridization with an indigenous D genome diploid. Diversification of the nascent allopolyploid gave rise to three modern lineages containing seven species, including the agronomically important G. hirsutum L. and G. barbadense L. Because of its economic importance, the cotton genus (Gossypium L.) has been of interest to agricultural scientists, taxonomists, and many other kinds of biologists. Accordingly, a considerable amount is understood regarding the ori-gin and diversification of the genus, its basic plant biology, and its properties a
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taxonomy and evolution of the cotton genus Gossypium
Cotton, 2015Co-Authors: Jonathan F. Wendel, Corrinne E. GroverAbstract:We present an overview of the taxonomy of Gossypium L. (the cotton genus) and its evolutionary history. Gossypium contains more than 50 recognized species, including several recently described, distributed in arid to semiarid regions of the tropics and subtropics. Diversity in Gossypium has been promoted by two seemingly unlikely processes: transoceanic, long-distance dispersal and wide hybridization among lineages that presently are widely separated geographically. Included are four species that were independently domesticated for their seed fiber—two diploids from Africa–Asia and two allopolyploids from the Americas. This repeated domestication of different wild progenitors represents a remarkable case of human-driven parallel evolution. Morphological variation in Gossypium is extensive; growth forms in the genus range from sprawling herbaceous perennials to ?15-m-tall trees, representing a notable array of reproductive and vegetative characteristics. Equally impressive is the striking cytogenetic and genomic diversity that emerged as Gossypium diversified and spread worldwide, ultimately spawning eight groups of closely related diploid (n = 13) species (i.e., genome groups A through G, and K). DNA sequence data place the origin of Gossypium at about 5 to 10 million years ago (mya), which rapidly diversified into these major genome groups shortly thereafter. Allopolyploid cottons appeared within the last 1 to 2 million years, a consequence of the improbable transoceanic dispersal of an A genome taxon to the New World and subsequent hybridization with an indigenous D genome diploid. Diversification of the nascent allopolyploid gave rise to three modern lineages containing seven species, including the agronomically important G. hirsutum L. and G. barbadense L.
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Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres.
Nature, 2012Co-Authors: Andrew H Paterson, Jonathan F. Wendel, Heidrun Gundlach, Hui Guo, Jerry Jenkins, Dianchuan Jin, Danny Llewellyn, Kurtis C Showmaker, Shengqiang Shu, Joshua UdallAbstract:Polyploidy often confers emergent properties, such as the higher fibre productivity and quality of tetraploid cottons than diploid cottons bred for the same environments. Here we show that an abrupt five- to sixfold ploidy increase approximately 60 million years (Myr) ago, and allopolyploidy reuniting divergent Gossypium genomes approximately 1-2 Myr ago, conferred about 30-36-fold duplication of ancestral angiosperm (flowering plant) genes in elite cottons (Gossypium hirsutum and Gossypium barbadense), genetic complexity equalled only by Brassica among sequenced angiosperms. Nascent fibre evolution, before allopolyploidy, is elucidated by comparison of spinnable-fibred Gossypium herbaceum A and non-spinnable Gossypium longicalyx F genomes to one another and the outgroup D genome of non-spinnable Gossypium raimondii. The sequence of a G. hirsutum A(t)D(t) (in which 't' indicates tetraploid) cultivar reveals many non-reciprocal DNA exchanges between subgenomes that may have contributed to phenotypic innovation and/or other emergent properties such as ecological adaptation by polyploids. Most DNA-level novelty in G. hirsutum recombines alleles from the D-genome progenitor native to its New World habitat and the Old World A-genome progenitor in which spinnable fibre evolved. Coordinated expression changes in proximal groups of functionally distinct genes, including a nuclear mitochondrial DNA block, may account for clusters of cotton-fibre quantitative trait loci affecting diverse traits. Opportunities abound for dissecting emergent properties of other polyploids, particularly angiosperms, by comparison to diploid progenitors and outgroups.
Haihong Shang - One of the best experts on this subject based on the ideXlab platform.
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constructing a high density linkage map for Gossypium hirsutum Gossypium barbadense and identifying qtls for lint percentage
Journal of Integrative Plant Biology, 2015Co-Authors: Yuzhen Shi, Baocai Zhang, Guangping Liu, Aiying Liu, Haihong Shang, Juwu Gong, Wankui Gong, Zemao Yang, Feiyu Tang, Zhi LiuAbstract:To introgress the good fiber quality and yield from Gossypium barbadense into a commercial Upland cotton variety, a high-density simple sequence repeat(SSR) genetic linkage map was developed from a BC1F1 population of Gossypium hirsutum×Gossypium barbadense. The map comprised 2,292 loci and covered 5115.16 centi Morgan(c M) of the cotton AD genome, with an average marker interval of 2.23 c M. Of the marker order for 1,577 common loci on this new map, 90.36% agrees well with the marker order on the D genome sequence genetic map. Compared with five published high-density SSR genetic maps, 53.14% of marker loci were newly discovered in this map. Twenty-six quantitative trait loci(QTLs) for lint percentage(LP) were identified on nine chromosomes. Nine stable or common QTLs could be used for marker-assisted selection. Fifty percent of the QTLs were from G. barbadense and increased LP by 1.07%–2.41%. These results indicated that the map could be used for screening chromosome substitution segments from G. barbadense in the Upland cotton background, identifying QTLs or genes from G. barbadense, and further developing the gene pyramiding effect for improving fiber yield and quality.
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genome sequence of cultivated upland cotton Gossypium hirsutum tm 1 provides insights into genome evolution
Nature Biotechnology, 2015Co-Authors: Guangyi Fan, Haihong Shang, Gai Huang, Russell J. Kohel, Richard G Percy, Changsong Zou, Xinming Liang, Guanghui Xiao, Kun Liu, Weihua YangAbstract:Gossypium hirsutum has proven difficult to sequence owing to its complex allotetraploid (AtDt) genome. Here we produce a draft genome using 181-fold paired-end sequences assisted by fivefold BAC-to-BAC sequences and a high-resolution genetic map. In our assembly 88.5% of the 2,173-Mb scaffolds, which cover 89.6%∼96.7% of the AtDt genome, are anchored and oriented to 26 pseudochromosomes. Comparison of this G. hirsutum AtDt genome with the already sequenced diploid Gossypium arboreum (AA) and Gossypium raimondii (DD) genomes revealed conserved gene order. Repeated sequences account for 67.2% of the AtDt genome, and transposable elements (TEs) originating from Dt seem more active than from At. Reduction in the AtDt genome size occurred after allopolyploidization. The A or At genome may have undergone positive selection for fiber traits. Concerted evolution of different regulatory mechanisms for Cellulose synthase (CesA) and 1-Aminocyclopropane-1-carboxylic acid oxidase1 and 3 (ACO1,3) may be important for enhanced fiber production in G. hirsutum.
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genome sequence of the cultivated cotton Gossypium arboreum
Nature Genetics, 2014Co-Authors: Guangyi Fan, Haihong Shang, Youlu Yuan, Kunbo Wang, Guoli Song, Changsong Zou, Fengming Sun, Wenbin Chen, Xinming Liang, Weiqing LiuAbstract:Yu-Xian Zhu, Jun Wang, Shuxun Yu and colleagues report sequencing and assembly of the genome of cultivated cotton, Gossypium arboreum. Comparison with the Gossypium raimondii genome sequence provides insights into genome evolution and speciation, and identifies two shared whole-genome duplication events occurring before the speciation event around 2–13 million years ago.
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the draft genome of a diploid cotton Gossypium raimondii
Nature Genetics, 2012Co-Authors: Kunbo Wang, Haihong Shang, Zhiwen Wang, Junyi Wang, Guoli Song, Zhen Yue, Lin Cong, Shilin Zhu, Changsong Zou, Youlu YuanAbstract:Yuxian Zhu and colleagues report the draft genome of a diploid cotton Gossypium raimondii. This species is a wild South American cotton, whose progenitor is thought to have been the contributor of the D subgenome of the allotetraploid commercial species Gossypium hirsutum and Gossypium barbadense, which account for ~95% of the worldwide cotton crop.
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a conserved rna recognition motif rrm domain of brassica napus fca improves cotton fiber quality and yield by regulating cell size
Molecular Breeding, 2012Co-Authors: Fan Sun, Haihong Shang, Chuanliang Liu, Chaojun Zhang, Xueyan Zhang, Depei Kong, Qianhua Wang, Xiaoyin Qian, Jinshui YangAbstract:Cotton (Gossypium hirsutum L.) is an important crop that is used to produce both natural textile fiber and cottonseed oil. Cotton fiber is a unicellular trichome, whose length is critical to fiber quality and yield but difficult to modify. FCA was originally identified based on flowering time control in Arabidopsis. The function of the second RNA recognition motif (RRM) domain of Oryza sativa FCA in rice cell-size regulation has been previously reported, showing it to be highly conserved across dicotyledonous and monocotyledonous plants. The present study showed that the second RRM domain of Brassica napus FCA functioned in Gossypium hirsutum, leading to enlargement of multiple cell types, such as pollen, cotyledon petiole, and cotton fiber. In the resulting transgenic cotton, fiber length increased by ~10% and fiber yield per plant showed a dramatic increase, ranging from 35 to 66% greater than controls. Thus, this RRM domain may be a cell-size regulator and have great economic value in the cotton industry.
Gai Huang - One of the best experts on this subject based on the ideXlab platform.
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genome sequence of Gossypium herbaceum and genome updates of Gossypium arboreum and Gossypium hirsutum provide insights into cotton a genome evolution
Nature Genetics, 2020Co-Authors: Gai Huang, James Frelichowski, Richard G Percy, Mingzhou Bai, Kun Wang, Yuxian ZhuAbstract:Upon assembling the first Gossypium herbaceum (A1) genome and substantially improving the existing Gossypium arboreum (A2) and Gossypium hirsutum ((AD)1) genomes, we showed that all existing A-genomes may have originated from a common ancestor, referred to here as A0, which was more phylogenetically related to A1 than A2. Further, allotetraploid formation was shown to have preceded the speciation of A1 and A2. Both A-genomes evolved independently, with no ancestor–progeny relationship. Gaussian probability density function analysis indicates that several long-terminal-repeat bursts that occurred from 5.7 million years ago to less than 0.61 million years ago contributed compellingly to A-genome size expansion, speciation and evolution. Abundant species-specific structural variations in genic regions changed the expression of many important genes, which may have led to fiber cell improvement in (AD)1. Our findings resolve existing controversial concepts surrounding A-genome origins and provide valuable genomic resources for cotton genetic improvement. Assembly of the first Gossypium herbaceum genome and improved Gossypium arboreum and Gossypium hirsutum genomes provide insights into the phylogenetic relationships and origin history of cotton A-genomes.
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resequencing of 243 diploid cotton accessions based on an updated a genome identifies the genetic basis of key agronomic traits
Nature Genetics, 2018Co-Authors: Zhaoe Pan, Xueyan Zhang, Gai Huang, Zhaoen Yang, Gaofei Sun, Junling Sun, Min Liu, Yinhua Jia, Wenfang GongAbstract:The ancestors of Gossypium arboreum and Gossypium herbaceum provided the A subgenome for the modern cultivated allotetraploid cotton. Here, we upgraded the G. arboreum genome assembly by integrating different technologies. We resequenced 243 G. arboreum and G. herbaceum accessions to generate a map of genome variations and found that they are equally diverged from Gossypium raimondii. Independent analysis suggested that Chinese G. arboreum originated in South China and was subsequently introduced to the Yangtze and Yellow River regions. Most accessions with domestication-related traits experienced geographic isolation. Genome-wide association study (GWAS) identified 98 significant peak associations for 11 agronomically important traits in G. arboreum. A nonsynonymous substitution (cysteine-to-arginine substitution) of GaKASIII seems to confer substantial fatty acid composition (C16:0 and C16:1) changes in cotton seeds. Resistance to fusarium wilt disease is associated with activation of GaGSTF9 expression. Our work represents a major step toward understanding the evolution of the A genome of cotton.
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genome sequence of cultivated upland cotton Gossypium hirsutum tm 1 provides insights into genome evolution
Nature Biotechnology, 2015Co-Authors: Guangyi Fan, Haihong Shang, Gai Huang, Russell J. Kohel, Richard G Percy, Changsong Zou, Xinming Liang, Guanghui Xiao, Kun Liu, Weihua YangAbstract:Gossypium hirsutum has proven difficult to sequence owing to its complex allotetraploid (AtDt) genome. Here we produce a draft genome using 181-fold paired-end sequences assisted by fivefold BAC-to-BAC sequences and a high-resolution genetic map. In our assembly 88.5% of the 2,173-Mb scaffolds, which cover 89.6%∼96.7% of the AtDt genome, are anchored and oriented to 26 pseudochromosomes. Comparison of this G. hirsutum AtDt genome with the already sequenced diploid Gossypium arboreum (AA) and Gossypium raimondii (DD) genomes revealed conserved gene order. Repeated sequences account for 67.2% of the AtDt genome, and transposable elements (TEs) originating from Dt seem more active than from At. Reduction in the AtDt genome size occurred after allopolyploidization. The A or At genome may have undergone positive selection for fiber traits. Concerted evolution of different regulatory mechanisms for Cellulose synthase (CesA) and 1-Aminocyclopropane-1-carboxylic acid oxidase1 and 3 (ACO1,3) may be important for enhanced fiber production in G. hirsutum.
Youlu Yuan - One of the best experts on this subject based on the ideXlab platform.
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genome wide identification of the tify gene family in three cultivated Gossypium species and the expression of jaz genes
Scientific Reports, 2017Co-Authors: Quan Sun, Guanghao Wang, Xiao Zhang, Xiangrui Zhang, Peng Qiao, Lu Long, Youlu Yuan, Yingfan CaiAbstract:TIFY proteins are plant-specific proteins containing TIFY, JAZ, PPD and ZML subfamilies. A total of 50, 54 and 28 members of the TIFY gene family in three cultivated cotton species-Gossypium hirsutum, Gossypium barbadense and Gossypium arboretum-were identified, respectively. The results of phylogenetic analysis showed that these TIFY genes were divided into eight clusters. The different clusters of gene family members often have similar gene structures, including the number of exons. The results of quantitative reverse transcription polymerase chain reaction (qRT-PCR) showed that different JAZ genes displayed distinct expression patterns in the leaves of upland cotton under treatment with Gibberellin (GA), methyl jasmonate (MeJA), Jasmonic acid (JA) and abscisic acid (ABA). Different groups of JAZ genes exhibited different expression patterns in cotton leaves infected with Verticillium dahliae. The results of the comparative analysis of TIFY genes in the three cultivated species will be useful for understanding the involvement of these genes in development and stress resistance in cotton.
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genome sequence of the cultivated cotton Gossypium arboreum
Nature Genetics, 2014Co-Authors: Guangyi Fan, Haihong Shang, Youlu Yuan, Kunbo Wang, Guoli Song, Changsong Zou, Fengming Sun, Wenbin Chen, Xinming Liang, Weiqing LiuAbstract:Yu-Xian Zhu, Jun Wang, Shuxun Yu and colleagues report sequencing and assembly of the genome of cultivated cotton, Gossypium arboreum. Comparison with the Gossypium raimondii genome sequence provides insights into genome evolution and speciation, and identifies two shared whole-genome duplication events occurring before the speciation event around 2–13 million years ago.
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the draft genome of a diploid cotton Gossypium raimondii
Nature Genetics, 2012Co-Authors: Kunbo Wang, Haihong Shang, Zhiwen Wang, Junyi Wang, Guoli Song, Zhen Yue, Lin Cong, Shilin Zhu, Changsong Zou, Youlu YuanAbstract:Yuxian Zhu and colleagues report the draft genome of a diploid cotton Gossypium raimondii. This species is a wild South American cotton, whose progenitor is thought to have been the contributor of the D subgenome of the allotetraploid commercial species Gossypium hirsutum and Gossypium barbadense, which account for ~95% of the worldwide cotton crop.
Huiru Sun - One of the best experts on this subject based on the ideXlab platform.
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genome wide identification and expression analyses of the pectate lyase pel gene family in cotton Gossypium hirsutum l
BMC Genomics, 2018Co-Authors: Meng Zhang, Hengling Wei, Huiru Sun, Pengbo Hao, Yuan Qin, Hantao Wang, Nuohan WangAbstract:Pectin is a major component and structural polysaccharide of the primary cell walls and middle lamella of higher plants. Pectate lyase (PEL, EC 4.2.2.2), a cell wall modification enzyme, degrades de-esterified pectin for cell wall loosening, remodeling and rearrangement. Nevertheless, there have been few studies on PEL genes and no comprehensive analysis of the PEL gene family in cotton. We identified 53, 42 and 83 putative PEL genes in Gossypium raimondii (D5), Gossypium arboreum (A2), and Gossypium hirsutum (AD1), respectively. These PEL genes were classified into five subfamilies (I-V). Members from the same subfamilies showed relatively conserved gene structures, motifs and protein domains. An analysis of gene chromosomal locations and gene duplication revealed that segmental duplication likely contributed to the expansion of the GhPELs. The 2000 bp upstream sequences of all the GhPELs contained auxin response elements. A transcriptomic data analysis showed that 62 GhPELs were expressed in various tissues. Notably, most (29/32) GhPELs of subfamily IV were preferentially expressed in the stamen, and five GhPELs of subfamily V were prominently expressed at the fiber elongation stage. In addition, qRT-PCR analysis revealed the expression characteristics of 24 GhPELs in four pollen developmental stages and significantly different expression of some GhPELs between long- and short-fiber cultivars. Moreover, some members were responsive to IAA treatment. The results indicate that GhPELs play significant and functionally diverse roles in the development of different tissues. In this study, we comprehensively analyzed PELs in G. hirsutum, providing a foundation to better understand the functions of GhPELs in different tissues and pathways, especially in pollen, fiber and the auxin signaling pathway.
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Genome-wide identification and expression analyses of the pectate lyase (PEL) gene family in cotton (Gossypium hirsutum L.)
BMC, 2018Co-Authors: Huiru Sun, Meng Zhang, Hengling Wei, Pengbo Hao, Yuan Qin, Hantao Wang, Nuohan WangAbstract:Abstract Background Pectin is a major component and structural polysaccharide of the primary cell walls and middle lamella of higher plants. Pectate lyase (PEL, EC 4.2.2.2), a cell wall modification enzyme, degrades de-esterified pectin for cell wall loosening, remodeling and rearrangement. Nevertheless, there have been few studies on PEL genes and no comprehensive analysis of the PEL gene family in cotton. Results We identified 53, 42 and 83 putative PEL genes in Gossypium raimondii (D5), Gossypium arboreum (A2), and Gossypium hirsutum (AD1), respectively. These PEL genes were classified into five subfamilies (I-V). Members from the same subfamilies showed relatively conserved gene structures, motifs and protein domains. An analysis of gene chromosomal locations and gene duplication revealed that segmental duplication likely contributed to the expansion of the GhPELs. The 2000 bp upstream sequences of all the GhPELs contained auxin response elements. A transcriptomic data analysis showed that 62 GhPELs were expressed in various tissues. Notably, most (29/32) GhPELs of subfamily IV were preferentially expressed in the stamen, and five GhPELs of subfamily V were prominently expressed at the fiber elongation stage. In addition, qRT-PCR analysis revealed the expression characteristics of 24 GhPELs in four pollen developmental stages and significantly different expression of some GhPELs between long- and short-fiber cultivars. Moreover, some members were responsive to IAA treatment. The results indicate that GhPELs play significant and functionally diverse roles in the development of different tissues. Conclusions In this study, we comprehensively analyzed PELs in G. hirsutum, providing a foundation to better understand the functions of GhPELs in different tissues and pathways, especially in pollen, fiber and the auxin signaling pathway
