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| 1 | Analyses of the NAC Transcription Factor Gene Family in Gossypium raimondii Ulbr.:Chromosomal Location,Structure,Phylogeny,and Expression Patterns显示文摘NAC 域蛋白质是知道在各种各样的植物起多样的作用的植物特定的抄写因素发展进程。在现在的学习,我们在 Gossypium raimondii Ulbr 执行了 NAC 基因家庭的第一全面研究,合并种系发生,介绍的 chromosomal 地点,基因结构,保存主题,和表示分析。我们识别了种系发生地被聚类进 18 个不同亚科的 145 NAC 抄写因素(NAC-TF ) 基因。这些, 127 NAC-TF 基因越过 13 个染色体被散布,(55%) 80 优先地被保留位于两个的副本复制了区域,六位于 triplicated chromosomal 区域。NAC-TF 基因的多数出现了时间 -- ,空间 -- ,并且织物特定的表示模式基于 transcriptomic 和 qRT-PCR 分析。然而,几副本基因的表示模式部分是冗余的,建议在他们的进化期间的 sub-functionalization 的出现。基于他们的 genomic 组织,我们结束了复制在 G 显著地贡献了到 NAC-TF 基因家庭的扩大的那 genomic。raimondii。他们的表示侧面的全面分析能在 G 在 NAC 基因家庭的成员之中提供新奇卓见进功能的分叉。raimondii。 | Haihong Shang Wei Li Changsong Zou Youlu Yuan | 2013 | Journal of Integrative Plant Biology2013，55，7： | 25 |
| 2 | A high-quality genome assembly of quinoa provides insights into the molecular basis of salt bladder-based salinity tolerance and the exceptional nutritional value显示文摘 | Changsong Zou Aojun Chen Lihong Xiao Heike M Muller Peter Ache Georg Haberer Meiling Zhang Wei Jia Ping Deng Ru Huang Daniel Lang Feng Li Dongliang Zhan Xiangyun Wu Hui Zhang Jennifer Bohm Renyi Liu Sergey Shabala Rainer Hedrich Jian-Kang Zhu Heng Zhang | 2017 | Cell Research2017，27，11： | 22 |
| 3 | Comprehensive analysis of NAC transcription factors in diploid Gossypium: sequence conservation and expression analysis uncover their roles during fiber development显示文摘Determining how function evolves following gene duplication is necessary for understanding gene expansion.Transcription factors(TFs)are a class of proteins that regulate gene expression by binding to specific cis-acting elements in the promoters of target genes,subsequently activating or repressing their transcription.In the present study,we systematically examined the functional diversification of the NAC transcription factor(NAC-TFs)family by analyzing their chromosomal location,structure,phylogeny,and expression pattern in Gossypium raimondii(Gr)and G.arboreum(Ga).The 145 and 141 NAC genes identified in the Gr and Ga genomes,respectively,were annotated and divided into 18 subfamilies,which showed distinct divergence in gene structure and expression patterns during fiber development.In addition,when the functional parameters were examined,clear divergence was observed within tandem clusters,which suggested that subfunctionalization had occurred among duplicate genes.The expression patterns of homologous gene pairs also changed,suggestive of the diversification of gene function during the evolution of diploid cotton.These findings provide insights into the mechanisms underlying the functional differentiation of duplicated NAC-TFs genes in two diploid cotton species. | Haihong Shang Zhongna Wang Changsong Zou Zhen Zhang Weijie Li Junwen Li Yuzhen Shi Wankui Gong Tingting Chen Aiying Liu Juwu Gong Qun Ge Youlu Yuan | 2016 | Science China(Life Sciences)2016，59，2： | 12 |
| 4 | Genome-Wide Analysis of the Sus Gene Family in Cotton显示文摘蔗糖 synthase (怀疑) 是在植物蔗糖新陈代谢的关键酶。在棉花,怀疑(EC 2.4.1.13 ) 是降级的主要的酶从种子上衣的韧皮部进口进棉花纤维的蔗糖。这研究示威了 Gossypium arboreum L. 的染色体, G。raimondii Ulbr,和 G。hirsutum L. ,包含了 8, 8,和 15 分别地怀疑基因。他们的结构的组织,种系发生的关系,和表示侧面被描绘。genomic 和编码序列的比较识别了哪个高度被保存在之间的多重 introns,数字和位置双并且 allotetraploid 棉花种类。大多数种系发生的 clades 从所有三种包含了序列,建议 tetraploid G 的 Sus 基因。hirsutum 它的双祖先源于那些。一个人怀疑组(怀疑我) 在棉花期间经历了扩大进化。表示分析显示大多数怀疑基因差别在各种各样的纸巾被表示并且在棉花纤维房间有发展依赖者表示侧面。一样的 orthologous 组的成员在所有三种有很类似的表示模式。这些结果提供新卓见进棉花的进化在纤维生长和开发期间怀疑基因家庭,和卓见进它的成员的生理的功能。 | Changsong Zou Cairui Lu Haihong Shang Xinrui Jing Hailiang Cheng Youping Zhang Guoli Song | 2013 | Journal of Integrative Plant Biology2013，55，7： | 10 |
| 5 | Transcriptome analysis reveals long noncoding RNAs involved in fiber development in cotton (Gossypium arboreum)显示文摘Long noncoding RNAs(lnc RNAs)play important roles in various biological regulatory processes in yeast,mammals,and plants.However,no systematic identification of lnc RNAs has been reported in Gossypium arboreum.In this study,the strand-specific RNA sequencing(ss RNA-seq)of samples from cotton fibers and leaves was performed,and lnc RNAs involved in fiber initiation and elongation processes were systematically identified and analyzed.We identified 5,996 lnc RNAs,of which 3,510 and 2,486 can be classified as long intergenic noncoding RNAs(linc RNAs)and natural antisense transcripts(lnc NAT),respectively.Linc RNAs and lnc NATs are similar in many aspects,but have some differences in exon number,exon length,and transcript length.Expression analysis revealed that 51.9%of linc RNAs and 54.5%of lnc NATs transcripts were preferentially expressed at one stage of fiber development,and were significantly highly expressed than protein-coding transcripts(21.7%).During the fiber and rapid elongation stages,rapid and dynamic changes in lnc RNAs may contribute to fiber development in cotton.This work describes a set of lnc RNAs that are involved in fiber development.The characterization and expression analysis of lnc RNAs will facilitate future studies on their roles in fiber development in cotton. | Changsong Zou Qiaolian Wang Cairui Lu Wencui Yang Youping Zhang Hailiang Cheng Xiaoxu Feng Mtawa Andrew Prosper Guoli Song | 2016 | Science China(Life Sciences)2016，59，2： | 9 |
| 6 | The draftgenome of a diploid cotton gossypium raimondii 显示文摘 | Kunbo Wang Zhiwen Wang Fuguang Li Wuwei Ye Junyi Wang Guoli Song Zhen Yue Lin Cong Haihong Shang Shilin Zhu Changsong Zou Qin Li Youlu Yuan Cairui Lu Hengling Wei Caiyun Gou Zequn Zheng Ye Yin Xueyan Zhang Kun Liu Bo Wang Chi Song Nan Shi Russell J Kohel Richard G Percy John Z Yu Yu-xian Zhu Jun Wang Shuxun Yu | 2012 | Nat Genet2012，，44： | 1 |
| 7 | Possible contributions of volatile-producing bacteria to soil fungistasis显示文摘 | Changsong Zou Junpei Zhou Yingqi Gu | 2007 | Soil Biol Bioch2007，39，： | 1 |
| 8 | Phylogenetic analysis on the bacteria producing non-volatile fungistatic substances显示文摘 | ZhiFang Li ChangSong Zou YueQiu He | 2008 | J Microbiol2008，46，3： | 1 |
| 9 | A genome-wide identification of the BLH gene family reveals BLH1 involved in cotton fiber development显示文摘Background:Cotton is the world’s largest and most important source of renewable natural fiber.BEL1-like homeodomain(BLH)genes are ubiquitous in plants and have been reported to contribute to plant development.However,there is no comprehensive characterization of this gene family in cotton.In this study,32,16,and 18 BLH genes were identified from the G.hirsutum,G.arboreum,and G.raimondii genome,respectively.In addition,we also studied the phylogenetic relationships,chromosomal location,gene structure,and gene expression patterns of the BLH genes.Results:The results indicated that these BLH proteins were divided into seven distinct groups by phylogenetic analysis.Among them,25 members were assigned to 15 chromosomes.Furthermore,gene structure,chromosomal location,conserved motifs,and expression level of BLH genes were investigated in G.hirsutum.Expression profiles analysis showed that four genes(GhBLH1_3,GhBLH1_4,GhBLH1_5,and GhBLH1_6)from BLH1 subfamily were highly expressed during the fiber cell elongation period.The expression levels of these genes were significantly induced by gibberellic acid and brassinosteroid,but not auxin.Exogenous application of gibberellic acid significantly enhanced GhBLH1_3,GhBLH1_4,and GhBLH1_5 transcripts.Expression levels of GhBLH1_3 and GhBLH1_4 genes were significantly increased under brassinosteroid treatment.Conclusions:The BLH gene family plays a very important role in many biological processes during plant growth and development.This study deepens our understanding of the role of the GhBLH1 gene involved in fiber development and will help us in breeding better cotton varieties in the future. | LIU Cuixia LI Zhifang DOU Lingling YUAN Yi ZOU Changsong SHANG Haihong CUI Langjun XIAO Guanghui | 2020 | Journal of Cotton Research2020，3，3： | 1 |
| 10 | Patterns of presence-absence variants in Upland cotton显示文摘Dear Editor,Sources of genetic variations in genomes include small-scale sources(such as single-nucleotide polymorphisms(SNPs),insertions/deletions(InDels),and simple sequence repeats and larger-scale structural variations(mainly presence-absence variants(PAVs))and copy number variants).PAVs are sequences that are either inserted or missing in genomes in comparison with a reference sequence or genome.PAVs can have a much longer sequence than SNPs and InDels,as illustrated in the human genome(Conrad et al.,2010).PAVs are important genomic structural variations that can directly affect genomic structure and key functional genes in the genome(Kumar et al.,2007).Moreover,the use of PAVs for studying quantitative traits has been valuable(Lam et al.,2010). | Junfang Liu Xianliang Zhang Lingling Dou Wei Li Xiaojian Zhou Yangai Liu Xiaoyu Pei Zhongying Ren Wensheng Zhang Huaizhu Li Wenbo Wang Changsong Zou Kunlun He Fei Zhang Wenyu Ma Haihong Shang Hongbin Li Daigang Yang Guanghui Xiao Xiongfeng Ma | 2020 | Science China(Life Sciences)2020，63，10： | 0 |
| 11 | Alterations in DNA damage response and repair genes as potential biomarkers for immune checkpoint blockade in gastrointestinal cancer显示文摘Objective:Immune checkpoint inhibitors(ICIs)have achieved remarkable results in cancer treatments.However,there is no effective predictive biomarker for gastrointestinal(GI)cancer.Methods:We conducted integrative analyses of the genomic and survival data of ICI-treated GI cancer patients from the Memorial Sloan Kettering Cancer Center cohort(MSK-GI,n=227),the Janjigian cohort(n=40),and the Peking University Cancer Hospital&Institute cohort(PUCH,n=80)to determine the possible associations between DNA damage response and repair(DDR)gene mutations and clinical outcomes.Data from The Cancer Genome Atlas database were analyzed to determine the possible correlations between DDR gene mutations and the tumor microenvironment.Results:In the MSK cohort,the presence of≥2 DDR gene mutations was correlated with prolonged overall survival(OS).The Janjigian and PUCH cohorts further confirmed that subgroups with≥2 DDR gene mutations displayed a prolonged OS and a higher durable clinical benefit.Furthermore,the DDR gene mutation load could be considered as an independent prognostic factor,and exhibited a potential predictive value for survival in GI cancer patients treated with ICIs.Mechanistically,we showed that the presence of≥2 DDR gene mutations was correlated with higher levels of tumor mutation burden,neoantigen,and T cell infiltration.Conclusions:The DDR gene mutation status was correlated with favorable clinical outcomes in GI cancer patients receiving ICIs,which could serve as a potential biomarker to guide patient selection for immunotherapy. | Yujiao Wang Xi Jiao Shuang Li Huan Chen Xin Wei Chang Liu Jifang Gong Xiaotian Zhang Xicheng Wang Zhi Peng Changsong Qi Zhenghang Wang Yanni Wang Na Zhuo Jianling Zou Henghui Zhang Jian Li Lin Shen Zhihao Lu | 2022 | Cancer Biology & Medicine2022，19，8： | 0 |
| 12 | Genome-wide identification and expression analysis of the GhIQD gene family in upland cotton(Gossypium hirsutum L.)显示文摘Background:Calmodulin(CaM)is one of the most important Ca^(2+)signaling receptors because it regulates diverse physiological and biochemical reactions in plants.CaM functions by interacting with CaM-binding proteins(CaMBPs)to modulate Ca^(2+)signaling.IQ domain(IQD)proteins are plant-specific CaMBPs that bind to CaM by their specific CaM binding sites.Results:In this study,we identified 102 GhIQD genes in the Gossypium hirsutum L.genome.The GhIQD gene family was classified into four clusters(Ⅰ,Ⅱ,Ⅲ,andⅣ),and we then mapped the GhIQD genes to the G.hirsutum L.chromosomes.Moreover,we found that 100 of the 102 GhIQD genes resulted from segmental duplication events,indicating that segmental duplication is the main force driving GhIQD gene expansion.Gene expression pattern analysis showed that a total of 89 GhIQD genes expressed in the elongation stage and second cell wall biosynthesis stage of the fiber cells,suggesting that GhIQD genes may contribute to fiber cell development in cotton.In addition,we found that 20 selected GhIQD genes were highly expressed in various tissues.Exogenous application of MeJA significantly enhanced the expression levels of GhIQD genes.Conclusions:Our study shows that GhIQD genes are involved in fiber cell development in cotton and are also widely induced by MeJA.Thw results provide bases to systematically characterize the evolution and biological functions of GhIQD genes,as well as clues to breed better cotton varieties in the future. | DOU Lingling LV Limin KANG Yangyang TIAN Ruijie HUANG Deqing LI Jiayin LI Siyi LIU Fengping CAO Lingyan JIN Yuhua LIU Yang LI Huaizhu WANG Wenbo PANG Chaoyou SHANG Haihong ZOU Changsong SONG Guoli XIAO Guanghui | 2021 | Journal of Cotton Research2021，4，1： | 0 |
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