陆地棉Nudix基因家族的全基因组鉴定及表达分析

[目的]Nudix是一类能够催化各种核苷二磷酸衍生物水解的酶,具有维持遗传物质稳定,响应逆境胁迫等生物学功能.本研究旨在对陆地棉Nudix基因进行全基因组分析,为深入研究Nudix基因家族参与棉纤维生长发育调控机制提供参考.[方法]通过生物信息学方法对陆地棉基因组(ZJU_v2.1)的Nudix基因进行全基因组鉴定,并...     

陆地棉REM基因家族全基因组鉴定及表达分析

[目的]REM(Reproductive meristem)基因家族编码一类转录因子在植物生长发育过程中发挥重要作用,但在棉花中未见报道.[方法]基于陆地棉基因组数据和公共数据库中的转录组数据,运用生物信息学方法对陆地棉REM基因家族成员进行系统鉴定,并对该基因家族的理化性质、基因结构、组织表达特异性以及胁迫条件下的表...     

Genome-Wide Identification and Analysis ofGRGene Family in Cotton

[Objective] Glutathione reductase (GR) gene family is involved in biological processes such as plant growth and abiotic stress response, but its characteristics and functions in cotton have not been known yet. This study aims to explore the role of GR genes in cotton genome evolution and abiotic stress response through the whole genome identification and characterization of GR genes, thus providing a theoretical basis for future studies on the roles of the GR genes in enhancing abiotic stress tolerance in cotton. [Method] The GR genes in Gossypium hirsutum, G. barbadense, G. raimondii and G. arboreum were all identified using bioinformatics software. The physicochemical properties, sequence characteristics, chromosomal location, phylogeny and expression patterns were analyzed. [Result] A total of 18 GR genes were identified. The number of GR genes in G. hirsutum, G. barbadense, G. raimondii and G. arboreum was 6, 6, 3 and 3, respectively. Phylogenetic analysis revealed that GR genes were divided into two sub-groups. The genes in the same subgroup exhibited similar gene structure in relation to exon-intron ratios. The ratios of the non-synonymous mutations (K_a) and homologous mutations (K_s) were all less than 1, indicating that the GR genes underwent strong purification selection during their evolution process. The analysis of the expression patterns of GR genes in upland cotton indicated that all the GR genes responded actively to the stress environment; but under different abiotic stresses, the gene expression patterns were significantly different. [Conclusion] The study explored the evolution and function of the GR gene family in the four cotton genomes, providing a theoretical basis for future studies of cotton GR genes.     

Genome-Wide Selection of MAPKKK Gene Family in Gossypium raimondii and the Expression of Orthologs in Gossypium hirsutum

[Objective] The MAPKKK gene family plays an important regulating role in response to multiple abiotic stresses and the development of plant. This study aims to identify MAPKKK genes of Gossypium raimondii and analyze their functions. [Method] In this study, based on G. raimondii genome database and bioinformatics method, G. raimondii MAPKKK family genes were identified and analyzed. Using the MEGA5, GSDS and Mapchart program, the phylogenetic tree, gene structure and chromosomes location analyses were accomplished. Based on the existing microarray data in cotton and comparative profiles of these MAPKKK genes, different expression of them in multiple abiotic stresses and the expression at different cotton fiber developmental stages were analyzed. [Result] A sum of 114 MAPKKK genes were identified systematically in G. raimondii and classified into 3 subfamilies (Raf, ZIK and MEKK) according to the gene stucture and phylogenetic tree analyses. They were distributed on all the 13 chromosomes of G. raimondii, and segmental duplication and tandem duplication events may have occurred. Compared with the recently released 78 genes of G. raimondii MAPKKK family genes, 47 sequences are exactly the same ones. [Conclusion] The results are helpful to understand the evolution and function of MAPKKK gene family. Our results provide a foundation for future functional characterizations of MAPKKK genes in cotton and probably other Gossypium plants.     

Genome-Wide Identification and Expression Analysis of TLP Genes in Gossypium hirsutum L.

[Objective] Thaumatin-like proteins (TLPs) are important pathogenesis-related proteins that function during disease defense-related responses, participating in the defense reactions triggered by several kinds of pathogen infections. A genome-wide analysis of TLP genes could help increase our understanding of their molecular mechanism in response to Verticillium dahliae infections in cotton (Gossypium hirsutum L.). [Method] The TLP family members in the genomes of the G. hirsutum L. were identified and expression analyses of TLP genes in response to Verticillium dahliae inoculation were conducted using bioinformatics and real-time fluorescent quantitative PCR methods, respectively. [Result] In total, 88 TLP genes were identified in G. hirsutum. These TLPs were classified into 10 groups based on their amino acid sequences and a phylogenetic analysis. A gene structure analysis revealed that the number of exons ranges from 1 to 5, and the number of introns ranges from 0 to 4. TLP genes in the same group shared similar structures. Additionally, most TLP proteins contain five motifs that are arranged in the following order: 5, 4, 2, 3 and 1. In total, 87 TLP genes are distributed on 20 of the 26 chromosomes, and 42 and 45 TLP genes are distributed in the A and D subgroups, respectively. The real-time fluorescent quantitative PCR analysis showed that the expression levels of six candidate TLP genes were induced in both tolerant cotton cultivar GZ-1 and susceptible cotton cultivar 86-1, and showed a higher expression in the former. [Conclusion] These results provide a foundation for future studies of the functions and regulatory mechanisms of TLP family genes.     

Genome-Wide Identification and Functional Prediction of Phytochelatin Synthase Gene in Upland Cotton

[Objective] Heavy metal stress rise advertise effects on growth and development in plant, from which phytochelatin synthase (PCS) plays key roles to protect plant cells. This article will present studies on the gene amount, structure, distribution and features. [Method] PCS gene family in cotton are analyzed based on completely global genome sequence cotton species including Gossypium hirsutum ((AD)1), G. raimondii (D5) and G. arboreum (A2), for further understanding of those genes and protein family features. In this study, we conducted the analysis involving in identification on PCS family members, special protein domain comparison, polygenetic analysis, gene structure prediction and Cysteine survey. [Result] 2, 2 and 4 PCS genes were identified out in G. raimondii (D5), G. arboreum (A2) and G. hirsutum ((AD)1), respectively. All these 8 PCS genes had phytochelatin and phytochelatin_C domains and strictly conserved amino acid residues related to catalytic activity. Cotton PCS protein family members could be divided into 2 sub-group, and these members belongs to sub-group I or sub-group II are close todicotyledon or nematode, respectively. What’s more, there are some difference in both gene structure and Cys distribution between those 2 sub-groups. Less integrity of exons in PCS genes in G. raimondii, comparing to G. hirsutum and G. arboreum. [Conclusion] Comparing to sub-group II, the PCS genes from sub-group I should be higher catalytic activity. G. hirsutum and its donor G. arboreum probably are more heavy metal tolerant than G. raimondii. Based on the results, this research will provide some insights on further functional study.     

大豆PHD家族蛋白的全基因组鉴定及表达特征分析

PHD（Plant Homeodomain Finger）基因家族编码一类锌指转录因子,广泛参与植物的生长发育和逆境应答过程。通过全基因组鉴定获得了95个大豆PHD家族蛋白。通过共线性分析、进化树构建、基因结构和功能结构域鉴定、GO注释分析、不同组织间和非生物胁迫下表达分析等,获得了大豆PHD家族基因复制、家族进化、保守结构域及基因表达等信息。结果表明,大豆PHD基因在家族进化、基因结构和保守结构域上存在较大变异,可能参与Zn ²⁺结合、DNA结合及表观遗传调控等分子过程,参与调控植物生长发育和逆境应答。这些结果为进一步研究大豆PHD家族在生长发育和逆境应答中的生物学功能提供重要线索。     

棉花苯丙氨酸解氨酶基因家族的生物信息学分析

【目的】苯丙氨酸解氨酶是苯丙烷类代谢的关键酶,对调节植物生长和抗逆有重要作用。从全基因组层次了解棉花苯丙氨酸解氨酶基因家族的进化和功能,可为相关研究提供数据支撑。【方法】利用HMMER和BLASTP从棉花基因组筛选苯丙氨酸解氨酶基因家族,利用MEGA-X进行进化分析,利用MCScanX进行共线性分析,并利用NCBI SRA的数据进行表达分析。【结果】本研究分别从陆地棉、海岛棉、亚洲棉和雷蒙德氏棉基因组中筛选到12、13、7、8个苯丙氨酸解氨酶基因,依据进化分析和共线性关系数据,我们推测四种棉花的二倍体祖先起初应有6个苯丙氨酸解氨酶基因。顺式作用元件分析结果表明,苯丙氨酸解氨酶基因家族含有较多的光响应、激素响应、胁迫响应和生长发育相关的元件。苯丙氨酸解氨酶的蛋白序列具有保守的基序。陆地棉的12个苯丙氨酸解氨酶在低温、高温、盐和PEG胁迫下有不同的表达方式。【结论】本研究明确了苯丙氨酸解氨酶在棉花基因组中的数量、理化性质、进化和表达特征,为苯丙氨酸解氨酶的深入研究提供了参考。     

陆地棉三个WRKY基因的克隆及表达分析

WRKY转录因子可调控下游抗逆基因的表达,进而在植物生长发育以及对外界环境的反应中起着重要的调控作用,目前对棉花WRKY家族基因的研究比较少。本研究利用电子克隆的方法,从陆地棉品种山农圣杂3号中克隆得到了3个具有完整开放阅读框的棉花WRKY基因,聚类分析表明它们同属于WRKY家族中的第Ⅱ类。利用RT-PCR结果表明:250mmol/LNaCl盐胁迫和20%PEG6000干旱胁迫下同时诱导GhWRKY4的基因表达,GhWRKY5仅受干旱胁迫下的诱导,而GhWRKY6对这两种逆境胁迫都没有变化。     

全基因组鉴定和表达模式分析玉米AP2转录因子

AP2属于AP2/ERF转录因子家族中的一个亚族,其主要特征是具有2个独立的AP2/ERF结构域。本研究利用生物信息学的方法在玉米基因组中鉴定到22个玉米AP2转录因子,并对其理化性质、基因结构、保守基序、系统进化关系和表达模式进行了分析。结果表明,玉米AP2家族成员的理化性质差异较大,且都属于亲水性蛋白。系统进化分析表明玉米AP2家族基因被分为euANT、baselANT、euAP2三个亚组,相同亚组的基因具有相似的基因结构和保守基序。共线性分析发现玉米AP2家族基因中不存在基因串联重复事件,只存在两对片段复制事件,同时结果表明禾本科AP2家族基因之间具有很好的共线性关系。表达模式分析发现ZmAP2基因广泛参与植物的生长发育。转录组数据分析发现,在盐胁迫下一共鉴定到16个ZmAP2基因。本研究为进一步研究玉米AP2转录因子家族的生物学功能提供了科学依据。     

亚洲棉bZIP蛋白家族的鉴定及GaFDs基因的组织表达分析

碱性亮氨酸拉链(basic leucine zipper, bZIP)是真核生物中数量最多并且最具多样性的转录因子之一,参与植物生长发育及响应生物和非生物胁迫。本研究利用亚洲棉(Gossypium arboreum)全基因组数据库,通过生物信息学分析分布在13条染色体上的159个bZIPs家族基因的全序列。系统进化、基因结构和保守基序分析表明这些基因分成13个亚家族。其中,A亚家族有3个GaFD基因GaFD1、GaFD2和GaFD3,通过实时荧光定量PCR分析3个GaFDs基因在不同组织中的表达,结果表明GaFD1和GaFD2在SAM中的表达量最高,GaFD3在茎中表达量最高。研究表明棉花基因组中具有数量众多的bZIP家族成员,不同基因结构及FD基因不同的表达特征表明bZIP基因在棉花生长发育中可能具有不同的功能,这些结果为进一步解析棉花bZIP家族基因的功能和作用机理积累了有价值的资料。     

陆地棉油菜素内酯信号基因GhBES1家族的鉴定及表达分析

BES1基因是植物激素油菜素内酯信号转导过程中的重要转录因子,为了解陆地棉油菜素内酯信号基因Gh BESI家族,通过对陆地棉异源四倍体标准系TM-1基因组数据库的全面分析和鉴定,获得21个GhBES1基因,这些基因分布在不同的亚基因组,有9对基因在A亚组和D亚组上存在对应关系,AD亚组对应基因序列一致性高于95%。根据进化分析,21个GhBES1基因分为4个亚家族,除了亚家族Ⅲ,其他3个亚家族在拟南芥中均有对应基因;除了亚家族Ⅳ基因和亚家族Ⅱ中GhBES1-1基因外,其他GhBES1基因均有2个外显子。亚细胞定位结果表明,21个GhBES1蛋白主要定位到细胞核、细胞质等部位,其中7对基因的蛋白亚细胞定位完全一致。GhBES1基因在根、茎、叶、顶端分生组织中均有表达,但不同亚家族基因在不同组织中的表达水平存在差异。研究结果为棉花GhBES1基因家族功能的深入研究奠定了基础。