毛果杨NLP基因家族生物信息学分析与鉴定

NLP基因家族是一类特殊的转录因子,豆科植物根瘤的形成依赖于该基因家族的存在,在非豆科植物中具有调节植物硝酸盐吸收以及同化的功能。通过对毛果杨(Populus trichocarpa)基因组的生物信息学分析,共鉴定出14个毛果杨NLP基因家族成员,这些成员具有低亲水性的特点,基因结构保守,都含有RWP-RK以及PB1两个保守结构域。通过细胞定位预测,所有成员都定位在细胞核中。直系同源与旁系同源进化分析显示,NLP基因家族成员在漫长的进化过程中经历了严格的选择。染色体定位分析表明,毛果杨NLP基因家族成员坐落在毛果杨9条染色体之上,成员数量的扩增来自于杨柳科染色体自身的扩增事件。芯片数据分析结果显示,NLP基因家族成员在嫩叶,根和雄花中表达,部分基因在木质部以及种子萌发过程之中表达,但所有成员均不在成熟叶片中表达。     

水稻全基因组编码抗病基因同源序列分析

利用模糊搜索的方法,在TIGR水稻日本晴基因组数据库(TIGR Rice Genome Annotation-Release5)中识别出565个编码抗病蛋白质的同源序列;利用识别出565个编码抗病蛋白质序列分别与籼稻基因组数据库进行BLASTP联配,共确定320个对应的等位基因。通过在线生物信息学软件,识别了这565个抗病基因的保守结构域、保守模体和DNA序列内转座子元件,其中有14个抗病基因同源序列注释错误。同时绘出了这些基因的基因组分布,并基于这些基因的同源树分析和基因组物理分布,认为基因的原位和远程复制事件产生了抗病基因的现存分布和多样性,其中转座子在复制过程中扮演了重要角色。这些对抗病机制研究和抗病基因进化研究以及抗病基因的转育具有重要意义。     

被子植物DNA去甲基化酶基因的进化分析

DNA甲基化模式和水平取决于DNA甲基转移酶和去甲基化酶的作用,而DNA去甲基化酶在DNA主动去甲基化过程中起到关键作用。文章以已知的10个DNA去甲基化酶基因为参照,鉴定出两种单子叶植物(水稻和高粱)、两种双子叶植物(拟南芥和毛果杨)中所有的DNA去甲基化酶同源基因,其中新鉴定出两类DNA去甲基化酶类似基因DML4和DML5。基于保守的糖苷酶结构域序列的系统进化分析以及基因在染色体上的位置分析表明,植物中DNA去甲基化酶基因存在串联复制、染色体区段复制和全基因组复制而导致基因的新功能化和亚功能化。文章还进一步分析了DNA去甲基化酶基因在不同组织中的表达情况,旨在理解DNA去甲基化酶基因的功能与进化的关系,以期为DNA去甲基化酶基因在植物中的利用提供参考。     

小果野蕉(Musa acuminata)全基因组NBS抗病基因的鉴定与分析

为探讨小果野蕉(Musa acuminata)中NBS基因的功能,基于新近发表的小果野蕉全基因组序列,对NBS基因家族进行鉴定、分类和染色体定位,解析基因的复制特征、系统发育关系及上游启动子调控元件类别,推测这些基因在小果野蕉中可能的功能。结果表明,在小果野蕉全基因组中鉴定出125个NBS基因,包括78个标准和47个非标准NBS基因。多数NBS基因在染色体上以基因簇形式存在,串联复制是NBS基因家族扩张的主要动力。系统发育分析表明标准NBS基因形成两大分支,77个标准NBS基因有EST表达支持。这为群体水平的抗病基因型筛选提供了本底信息,促进栽培香蕉分子抗病育种进程。     

真骨鱼类DMRT基因家族的连锁结构及其系统发生

利用已经报道的多个物种基因组序列资源,我们通过比较真骨鱼类（Teleost fish）共有的DMRT1-5基因所在染色体位置的基因组结构特征,从基因组水平证明了真骨鱼类和四足动物的相应DMRT基因的直系同源关系,揭示了DMRT4和DMRT5是因为真骨鱼类和四足动物的共同祖先发生了染色体重复事件而由同一基因分歧演变形成的。同时通过基因连锁分析,探测到包括SNF2和elavL家族基因在内的多个可能与DMRT基因功能密切相关的基因,为进一步研究DMRT基因和它们之间可能存在的调控机制提供了新的线索。     

毛果杨 NLP 基因家族生物信息学分析与鉴定简

NLP基因家族是一类特殊的转录因子,豆科植物根瘤的形成依赖于该基因家族的存在,在非豆科植物中具有调节植物硝酸盐吸收以及同化的功能。通过对毛果杨（Populus trichocarpa）基因组的生物信息学分析,共鉴定出14个毛果杨NLP基因家族成员,这些成员具有低亲水性的特点,基因结构保守,都含有RWP-RK以及PB1两个保守结构域。通过细胞定位预测,所有成员都定位在细胞核中。直系同源与旁系同源进化分析显示,NLP基因家族成员在漫长的进化过程中经历了严格的选择。染色体定位分析表明,毛果杨NLP基因家族成员坐落在毛果杨9条染色体之上,成员数量的扩增来自于杨柳科染色体自身的扩增事件。芯片数据分析结果显示,NLP基因家族成员在嫩叶,根和雄花中表达,部分基因在木质部以及种子萌发过程之中表达,但所有成员均不在成熟叶片中表达。     

落叶松-杨栅锈菌基因复制事件及共线性分析

落叶松-杨栅锈菌是一种分布广且危害严重的林木病原真菌。了解基因组内发生的基因复制事件及基因组间的共线性关系,能为最终理解落叶松-杨栅锈菌适应性进化等生物学问题提供帮助。落叶松-杨栅锈菌全基因组水平上基因复制相关研究未见报道,共线性研究报道也较少。本研究利用落叶松-杨栅锈菌全基因组序列分析其基因复制模式。结果表明,落叶松-杨栅锈菌转座复制基因的数目远高于片段复制基因、串联复制基因及相邻复制基因。落叶松-杨栅锈菌基因组内不存在大规模的片段复制,且基因年龄法显示节点同义替换率分布图上没有峰形出现,推断该锈菌未发生全基因组复制。富集分析显示不同类型复制基因富集于不同的功能条目,如串联复制基因富集于碳水化合物的转运和代谢而转座复制基因富集于次生代谢物合成、代谢与分解。共线性分析显示落叶松-杨栅锈菌与松栎柱锈菌及小麦条锈菌的共线性程度均较低,3种锈菌间存在1个共同的共线性区域,该保守区域包含6个基因,其中1个可能编码小分泌蛋白的基因值得关注。     

拟南芥和水稻金属蛋白酶ftsH基因家族的基因组比较分析

FtsH(Filamentation temperature-sensitive H)是一种广泛存在于原核生物和真核生物中的ATP依赖型金属蛋白酶。同源性分析表明,在拟南芥和水稻基因组中分别有12个和9个ftsH基因。ftsH基因在染色体上的分布有明显的偏爱性,如拟南芥的1、2、5号染色体和水稻的1、5号染色体。亚细胞定位分析表明,所有FtsH蛋白均定位于叶绿体或线粒体中。系统进化分析表明,21个FtsH蛋白成员可分为8个类群,其中AtFtsH12在水稻中没有发现种间同源物。每个类群成员的蛋白序列高度保守,种内同源物显示出大于80%的相似性,而种间同源物的相似性也大于70%。类群内的同源基因并非平行进化产生的,拟南芥基因组中进化出AtftsH1/5、AtftsH2/8、AtftsH3/10和AtftsH7/9共4个同源基因对,而水稻基因组中只有OsftsH3/8和OsftsH4/5两个同源基因对。每一类群中的成员在基因外显子-内含子边界分布上表现出高度保守性,在蛋白功能结构域的可变残基上具有偏爱性,而内含子在碱基组成和序列长度上表现出广泛的变异。拟南芥和水稻ftsH基因家族的比较分析为其他物种ftsH基因的特...     

毛果杨HMA基因家族的生物信息学分析

重金属转运ATP酶（heavy metal transporting ATPase,HMA）是一种通过水解ATP跨膜运送重金属阳离子的转运蛋白,属于P-ATPase家族中一个亚类。不同HMA蛋白对重金属离子的转运具有选择性,在植物修复重金属污染土壤方面起着重要作用。依据毛果杨全基因组测序的结果,以及HMA基因蛋白的序列和功能特征,从毛果杨基因组中鉴定了13个HMA基因家族成员,分属于Zn亚类（Zn2＋/Co2＋/Cd2＋/Pb2＋P1B-ATPase）和Cu亚类（Cu＋/Ag＋P1B-ATPase）两个亚家族,主要分布于1、3号染色体上。生物信息学分析表明,毛果杨HMA基因的氨基酸序列一致性介于21.3%~89.3%,且具有保守的基序CPC、HP、DKTGT、TGEx、GDG、PxD和CxxC等。蛋白理化特征分析显示,多数毛果杨HMA蛋白稍偏酸性,结构稳定性较好,蛋白脂溶指数高,稍具疏水性。密码子偏好性分析显示,毛果杨HMA蛋白14个氨基酸中存在16个高频密码子,另有1个终止密码子为高频密码子,显示出毛果杨的种属特征。研究结果展示了毛果杨HMA基因家族的基本信息和特点,为深入研究毛果杨HMA基因的功能搭建了基础平台。     

毛果杨GATA基因家族全基因组水平鉴定及表达分析

GATA转录因子基因家族在植物生长发育、细胞分化以及响应环境变化中具有重要作用。然而,目前在木本植物中尚无该基因家族全基因组水平的分析报导。本项研究从基因组水平对毛果杨GATA家族成员的数量、基因结构、染色体定位、系统进化、编码蛋白的理化特征和保守基序等信息进行了系统分析,结果表明,毛果杨GATA家族包含39个基因,共分布于15条染色体上,其中5号染色体上含有6个基因,9号、13号和19号染色体含有基因数量为1,其余染色上无基因分布。该家族各基因的结构与编码蛋白的基本特性均存在一定异性,可分成4个亚族。qRT-PCR研究表明,GATA家族各基因在不同发育阶段的茎部表达量存在明显差异,且盐胁迫对各基因的表达特性影响显著。以上结果表明,毛果杨GATA家族基因在复制后,基因的结构与功能产生了明显分化,其中部分基因在毛果杨次生生长与盐胁迫响应中可能具有重要作用。本项研究为全面解析毛果杨GATA家族各成员在其生长发育与盐胁迫响应中的生物学功能奠定了基础。     

The organization of cytoplasmic ribosomal protein genes in the Arabidopsis genome

Eukaryotic ribosomes are made of two components, four ribosomal RNAs, and approximately 80 ribosomal proteins (r-proteins). The exact number of r-proteins and r-protein genes in higher plants is not known. The strong conservation in eukaryotic r-protein primary sequence allowed us to use the well-characterized rat (Rattus norvegicus) r-protein set to identify orthologues on the five haploid chromosomes of Arabidopsis. By use of the numerous expressed sequence tag (EST) accessions and the complete genomic sequence of this species, we identified 249 genes (including some pseudogenes) corresponding to 80 (32 small subunit and 48 large subunit) cytoplasmic r-protein types. None of the r-protein genes are single copy and most are encoded by three or four expressed genes, indicative of the internal duplication of the Arabidopsis genome. The r-proteins are distributed throughout the genome. Inspection of genes in the vicinity of r-protein gene family members confirms extensive duplications of large chromosome fragments and sheds light on the evolutionary history of the Arabidopsis genome. Examination of large duplicated regions indicated that a significant fraction of the r-protein genes have been either lost from one of the duplicated fragments or inserted after the initial duplication event. Only 52 r-protein genes lack a matching EST accession, and 19 of these contain incomplete open reading frames, confirming that most genes are expressed. Assessment of cognate EST numbers suggests that r-protein gene family members are differentially expressed.     

New in silico insight into the synteny between rice (Oryza sativa L.) and maize (Zea mays L.) highlights reshuffling and identifies new duplications in the rice genome

A unigene set of 1411 contigs was constructed from 2629 redundant maize expressed sequence tags (ESTs) mapped on the maizeDB genetic map. Rice orthologous sequences were identified by blast alignment against the rice genomic sequence. A total of 1046 (74%) maize contigs were associated with their corresponding homologues in the rice genome and 656 (47%) defined as potential orthologous relationships. One hundred and seventeen (8%) maize EST contigs mapped to two distinct loci on the maize genetic map, reflecting the tetraploid nature of the maize genome. Among 492 mono-locus contigs, 344 (484 redundant ESTs) identify collinear blocks between maize chromosomes 2 and 4 and a single rice chromosome, defining six new collinear regions. Fine-scale analysis of collinearity between rice chromosomes 1 and 5 with maize chromosomes 3, 6 and 8 shows the presence of internal rearrangements within collinear regions. Mapping of maize contigs to two distinct loci on the rice sequence identifies five new duplication events in rice. Detailed analysis of a duplication between rice chromosomes 1 and 5 shows that 11% of the annotated genes from the chromosome 1 locus are found duplicated on the chromosome 5 paralogous counterpart, indicating a high degree of re-organisations. The implications of these findings for map-based cloning in collinear regions are discussed.     

A 2600-locus chromosome bin map of wheat homoeologous group 2 reveals interstitial gene-rich islands and colinearity with rice

The complex hexaploid wheat genome offers many challenges for genomics research. Expressed sequence tags facilitate the analysis of gene-coding regions and provide a rich source of molecular markers for mapping and comparison with model organisms. The objectives of this study were to construct a high-density EST chromosome bin map of wheat homoeologous group 2 chromosomes to determine the distribution of ESTs, construct a consensus map of group 2 ESTs, investigate synteny, examine patterns of duplication, and assess the colinearity with rice of ESTs assigned to the group 2 consensus bin map. A total of 2600 loci generated from 1110 ESTs were mapped to group 2 chromosomes by Southern hybridization onto wheat aneuploid chromosome and deletion stocks. A consensus map was constructed of 552 ESTs mapping to more than one group 2 chromosome. Regions of high gene density in distal bins and low gene density in proximal bins were found. Two interstitial gene-rich islands flanked by relatively gene-poor regions on both the short and long arms and having good synteny with rice were discovered. The map locations of two ESTs indicated the possible presence of a small pericentric inversion on chromosome 2B. Wheat chromosome group 2 was shown to share syntenous blocks with rice chromosomes 4 and 7.     

Schistosoma mansoni genome project: an update

A schistosome genome project was initiated by the World Health Organization in 1994 with the notion that the best prospects for identifying new targets for drugs, vaccines, and diagnostic development lie in schistosome gene discovery, development of chromosome maps, whole genome sequencing and genome analysis. Schistosoma mansoni has a haploid genome of 270 Mb contained on 8 pairs of chromosomes. It is estimated that the S. mansoni genome contains between 15000 and 25000 genes. There are approximately 16689 ESTs obtained from diverse libraries representing different developmental stages of S. mansoni, deposited in the NCBI EST database. More than half of the deposited sequences correspond to genes of unknown function. Approximately 40-50% of the sequences form unique clusters, suggesting that approximately 20-25% of the total schistosome genes have been discovered. Efforts to develop low resolution chromosome maps are in progress. There is a genome sequencing program underway that will provide 3X sequence coverage of the S. mansoni genome that will result in approximately 95% gene discovery. The genomics era has provided the resources to usher in the era of functional genomics that will involve microarrays to focus on specific metabolic pathways, proteomics to identify relevant proteins and protein-protein interactions to understand critical parasite pathways. Functional genomics is expected to accelerate the development of control and treatment strategies for schistosomiasis.     

Single-copy genes define a conserved order between rice and wheat for understanding differences caused by duplication, deletion, and transposition of genes

The high-quality rice genome sequence is serving as a reference for comparative genome analysis in crop plants, especially cereals. However, early comparisons with bread wheat showed complex patterns of conserved synteny (gene content) and colinearity (gene order). Here, we show the presence of ancient duplicated segments in the progenitor of wheat, which were first identified in the rice genome. We also show that single-copy (SC) rice genes, those representing unique matches with wheat expressed sequence tag (EST) unigene contigs in the whole rice genome, show more than twice the proportion of genes mapping to syntenic wheat chromosome as compared to the multicopy (MC) or duplicated rice genes. While 58.7% of the 1,244 mapped SC rice genes were located in single syntenic wheat chromosome groups, the remaining 41.3% were distributed randomly to the other six non-syntenic wheat groups. This could only be explained by a background dispersal of genes in the genome through transposition or other unknown mechanism. The breakdown of rice–wheat synteny due to such transpositions was much greater near the wheat centromeres. Furthermore, the SC rice genes revealed a conserved primordial gene order that gives clues to the origin of rice and wheat chromosomes from a common ancestor through polyploidy, aneuploidy, centromeric fusions, and translocations. Apart from the bin-mapped wheat EST contigs, we also compared 56,298 predicted rice genes with 39,813 wheat EST contigs assembled from 409,765 EST sequences and identified 7,241 SC rice gene homologs of wheat. Based on the conserved colinearity of 1,063 mapped SC rice genes across the bins of individual wheat chromosomes, we predicted the wheat bin location of 6,178 unmapped SC rice gene homologs and validated the location of 213 of these in the telomeric bins of 21 wheat chromosomes with 35.4% initial success. This opens up the possibility of directed mapping of a large number of conserved SC rice gene homologs in wheat. Overall, only 46.4% of these SC genes code for proteins with known functional domains; the remaining 53.6% have unknown function, and hence, represent an important, but yet, under explored category of genes. Electronic supplementary material Supplementary material is available for this article at and is accessible for authorized users.     

EST data suggest that poplar is an ancient polyploid

We analysed the publicly available expressed sequence tag (EST) collections for the genus Populus to examine whether evidence can be found for large-scale gene-duplication events in the evolutionary past of this genus. The ESTs were clustered into unigenes for each poplar species examined. Gene families were constructed for all proteins deduced from these unigenes, and K(S) dating was performed on all paralogs within a gene family. The fraction of paralogs was then plotted against the K(S) values, which resulted in a distribution reflecting the age of duplicated genes in poplar. Sufficient EST data were available for seven different poplar species spanning four of the six sections of the genus Populus. For all these species, there was evidence that a large-scale gene-duplication event had occurred. From our analysis it is clear that all poplar species have shared the same large-scale gene-duplication event, suggesting that this event must have occurred in the ancestor of poplar, or at least very early in the evolution of the Populus genus.