Ancient noncoding elements conserved in the human genome

Cartilaginous fishes represent the living group of jawed vertebrates that diverged from the common ancestor of human and teleost fish lineages about 530 million years ago. We generated approximately 1.4x genome sequence coverage for a cartilaginous fish, the elephant shark (Callorhinchus milii), and compared this genome with the human genome to identify conserved noncoding elements (CNEs). The elephant shark sequence revealed twice as many CNEs as were identified by whole-genome comparisons between teleost fishes and human. The ancient vertebrate-specific CNEs in the elephant shark and human genomes are likely to play key regulatory roles in vertebrate gene expression.     

脊椎动物TYR基因的序列特征与正选择位点鉴定

酪氨酸酶是一种含铜金属酶,它广泛存在于各种生物中,是黑色素生物合成的关键酶.利用生物信息学手段详细剖析了脊椎动物TYR基因的序列和进化特性,并模拟了其蛋白的三位结构.系统发生研究显示,脊椎动物TYR基因与物种进化关系之间具有较高的一致性.基因结构分析表明,绝大多数脊椎动物TYR基因有5个外显子,但DrTYR和OlTYR有6个外显子,而Ss TYR有9个外显子.蛋白序列特征分析显示,脊椎动物TYR蛋白均具有典型的TYROSINASE结构域,但不同物种具有特异的保守基序组织模式,其中保守基序13是哺乳类动物TYR蛋白所特有的.位点模型没有检测出正选择位点,但分支位点模型已经检测出马与猪的祖先支(26个正选择位点)、猪进化分支(27个正选择位点)以及斑胸草雀与鸡的祖先支(1个正选择位点)均经历了适应性进化.这些正选择位点虽然被定位于不同二级结构内,但在三维结构中它们分布在相对集中的区域内,很可能与特定功能密切相关.     

Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster

Comparison of the genomes and proteomes of the two diptera Anopheles gambiae and Drosophila melanogaster, which diverged about 250 million years ago, reveals considerable similarities. However, numerous differences are also observed; some of these must reflect the selection and subsequent adaptation associated with different ecologies and life strategies. Almost half of the genes in both genomes are interpreted as orthologs and show an average sequence identity of about 56%, which is slightly lower than that observed between the orthologs of the pufferfish and human (diverged about 450 million years ago). This indicates that these two insects diverged considerably faster than vertebrates. Aligned sequences reveal that orthologous genes have retained only half of their intron/exon structure, indicating that intron gains or losses have occurred at a rate of about one per gene per 125 million years. Chromosomal arms exhibit significant remnants of homology between the two species, although only 34% of the genes colocalize in small "microsyntenic" clusters, and major interarm transfers as well as intra-arm shuffling of gene order are detected.     

The Release 5.1 annotation of Drosophila melanogaster heterochromatin

The repetitive DNA that constitutes most of the heterochromatic regions of metazoan genomes has hindered the comprehensive analysis of gene content and other functions. We have generated a detailed computational and manual annotation of 24 megabases of heterochromatic sequence in the Release 5 Drosophila melanogaster genome sequence. The heterochromatin contains a minimum of 230 to 254 protein-coding genes, which are conserved in other Drosophilids and more diverged species, as well as 32 pseudogenes and 13 noncoding RNAs. Improved methods revealed that more than 77% of this heterochromatin sequence, including introns and intergenic regions, is composed of fragmented and nested transposable elements and other repeated DNAs. Drosophila heterochromatin contains "islands" of highly conserved genes embedded in these "oceans" of complex repeats, which may require special expression and splicing mechanisms.     

Parallel patterns of evolution in the genomes and transcriptomes of humans and chimpanzees

The determination of the chimpanzee genome sequence provides a means to study both structural and functional aspects of the evolution of the human genome. Here we compare humans and chimpanzees with respect to differences in expression levels and protein-coding sequences for genes active in brain, heart, liver, kidney, and testis. We find that the patterns of differences in gene expression and gene sequences are markedly similar. In particular, there is a gradation of selective constraints among the tissues so that the brain shows the least differences between the species whereas liver shows the most. Furthermore, expression levels as well as amino acid sequences of genes active in more tissues have diverged less between the species than have genes active in fewer tissues. In general, these patterns are consistent with a model of neutral evolution with negative selection. However, for X-chromosomal genes expressed in testis, patterns suggestive of positive selection on sequence changes as well as expression changes are seen. Furthermore, although genes expressed in the brain have changed less than have genes expressed in other tissues, in agreement with previous work we find that genes active in brain have accumulated more changes on the human than on the chimpanzee lineage.     

Vertebrate-type intron-rich genes in the marine annelid Platynereis dumerilii

Previous genome comparisons have suggested that one important trend in vertebrate evolution has been a sharp rise in intron abundance. By using genomic data and expressed sequence tags from the marine annelid Platynereis dumerilii, we provide direct evidence that about two-thirds of human introns predate the bilaterian radiation but were lost from insect and nematode genomes to a large extent. A comparison of coding exon sequences confirms the ancestral nature of Platynereis and human genes. Thus, the urbilaterian ancestor had complex, intron-rich genes that have been retained in Platynereis and human.     

黄丹木姜子叶绿体基因组特征分析

【目的】分析黄丹木姜子（Litsea elongata）叶绿体基因组特征,为木姜子属物种鉴定、遗传多样性分析和资源保护提供理论参考。【方法】基于Illumina HiSeq 2000高通量测序平台对黄丹木姜子叶绿体基因组进行测序,利用GeSeq在线工具对叶绿体基因组进行注释,并利用REPuter、MISA、CodonW和IQ-TREE等生物信息学软件对其基因组结构、基因数目、序列重复、密码子使用偏性和系统发育进行分析。【结果】黄丹木姜子叶绿体基因组全长为154028 bp,具有典型的四分结构,编码126个基因,其中蛋白编码基因82个,rRNA基因 8个,tRNA基因 36个。叶绿体基因组的注释基因中,有9个基因含1个内含子,有3个基因含有2个内含子,其余基因均不含内含子;44个基因编码蛋白参与光合作用信号途径,21个基因编码蛋白构成了核糖体大小亚基。黄丹木姜子叶绿体基因组含有32对长序列重复和90个SSR位点,其中,正向重复和回文重复最多,均为12对,反向重复和互补重复分别为6和2对;95.56%的SSR位点位于单拷贝区［大单拷贝区（LSC）和小单拷贝区（SSC）］,仅4.44%的SSR位点位于反向重复区（IR）。黄丹木姜子叶绿体蛋白编码基因GC含量为39.14%,GC3s为27.95%,平均有效密码子数（ENC）为49.04,说明其密码子偏性弱;相对同义密码子使用度（RSCU）大于1.00的密码子31个,其中13个以A结尾,16个以U（T）结尾。系统发育进化树分析结果显示,木姜子属的14个物种聚为两组,其中黄丹木姜子和10种木姜子属植物聚在一个组,与日本木姜子的亲缘关系最近。【结论】黄丹木姜子叶绿体基因组结构保守,偏好A或U（T）结尾的密码子,鉴定的SSR位点可用于物种鉴定和群体遗传学研究。     

The Chlamydomonas genome reveals the evolution of key animal and plant functions

Chlamydomonas reinhardtii is a unicellular green alga whose lineage diverged from land plants over 1 billion years ago. It is a model system for studying chloroplast-based photosynthesis, as well as the structure, assembly, and function of eukaryotic flagella (cilia), which were inherited from the common ancestor of plants and animals, but lost in land plants. We sequenced the approximately 120-megabase nuclear genome of Chlamydomonas and performed comparative phylogenomic analyses, identifying genes encoding uncharacterized proteins that are likely associated with the function and biogenesis of chloroplasts or eukaryotic flagella. Analyses of the Chlamydomonas genome advance our understanding of the ancestral eukaryotic cell, reveal previously unknown genes associated with photosynthetic and flagellar functions, and establish links between ciliopathy and the composition and function of flagella.     

The protein kinase complement of the human genome

We have catalogued the protein kinase complement of the human genome (the "kinome") using public and proprietary genomic, complementary DNA, and expressed sequence tag (EST) sequences. This provides a starting point for comprehensive analysis of protein phosphorylation in normal and disease states, as well as a detailed view of the current state of human genome analysis through a focus on one large gene family. We identify 518 putative protein kinase genes, of which 71 have not previously been reported or described as kinases, and we extend or correct the protein sequences of 56 more kinases. New genes include members of well-studied families as well as previously unidentified families, some of which are conserved in model organisms. Classification and comparison with model organism kinomes identified orthologous groups and highlighted expansions specific to human and other lineages. We also identified 106 protein kinase pseudogenes. Chromosomal mapping revealed several small clusters of kinase genes and revealed that 244 kinases map to disease loci or cancer amplicons.     

Two Dobzhansky-Muller genes interact to cause hybrid lethality in Drosophila

The Dobzhansky-Muller model proposes that hybrid incompatibilities are caused by the interaction between genes that have functionally diverged in the respective hybridizing species. Here, we show that Lethal hybrid rescue (Lhr) has functionally diverged in Drosophila simulans and interacts with Hybrid male rescue (Hmr), which has functionally diverged in D. melanogaster, to cause lethality in F1 hybrid males. LHR localizes to heterochromatic regions of the genome and has diverged extensively in sequence between these species in a manner consistent with positive selection. Rapidly evolving heterochromatic DNA sequences may be driving the evolution of this incompatibility gene.     

玉米ZmEXO70s基因家族鉴定及苗期耐热性关联分析

【目的】鉴定玉米EXO70s（ZmEXO70s）基因家族成员,分析其遗传变异与玉米耐热性的关联性,为揭示其在玉米耐热方面的功能和分子机制打下基础。【方法】以拟南芥EXO70s（AtEXO70s）基因家族成员序列为参考,利用MaizeGDB和NCBI数据库从玉米全基因组中鉴定出ZmEXO70s基因家族成员,对其进行基因结构及系统进化分析,根据其在系统发育进化树上的位置对其进行系统命名,并基于转录组测序（RNA-Seq）数据分析ZmEXO70s基因家族成员在不同组织及非生物胁迫下的表达模式。最后,鉴定玉米自交群体AM368中ZmEXO70s基因SNP位点,结合玉米AM368群体苗期耐热存活率进行基因家族关联分析。【结果】从玉米全基因组序列中共鉴定出36个ZmEXO70s基因,分布在10条染色体上,长度为228～3726 bp,编码75～1241个氨基酸残基,蛋白分子量为8.6～136.6 kD,理论等电点（pI）介于4.5～9.9,大部分蛋白pI小于7.0。拟南芥、水稻和玉米的EXO70s蛋白被分为9组（A组～I组）,其中ZmEXO70s蛋白在各组中均有分布。大多数ZmEXO70s基因不含内含子,只有少数基因含有内含子,且内含子数量不同。36个ZmEXO70s蛋白共含8种基序（Motif 1～Motif 8）,主要集中在C端,说明这些蛋白端序列较保守,且Motif 1～Motif 8组成Exo70保守结构域。ZmEXO70s基因在不同组织中的表达水平均存在明显差异,其中ZmEXO70B3基因在雄穗、花药、叶片和花丝中高表达,ZmEXO70C1a基因只在雄穗和花药中高表达,ZmEXO70D2b基因在胚乳和萌发种子中低表达,ZmEXO70G1c基因在花丝和萌发种子中低表达。有23个ZmEXO70s基因至少可响应一种非生物胁迫,说明这些ZmEXO70s基因参与非生物胁迫响应过程。ZmEXO70D2a和ZmEXO70E1基因的遗传变异与玉米苗期耐热性具有显著相关性（P≤0.01）。【结论】ZmEXO70s基因家族成员在系统发育进化上较保守,其基因组复制事件可能发生在禾本科植物分化后,且大多数ZmEXO70s基因被保留,仅部分基因被丢失。ZmEXO70s基因可能在非生物胁迫响应过程中发挥重要作用,ZmEXO70D2a和ZmEXO70E1基因可作为调控玉米苗期耐热性重要候选基因。     

陆地棉CRK基因家族的鉴定及其表达分析

【目的】富含半胱氨酸类受体激酶（CRK）是植物中最大的类受体激酶家族之一,在植物生长发育、激素信号传导和抗逆境胁迫中发挥重要作用。从全基因组水平鉴定陆地棉CRK基因家族并进行生物信息学和表达模式分析,为研究和利用陆地棉CRK基因家族奠定基础。【方法】从Pfam数据库下载stress-antifung结构域氨基酸序列,应用BLASTp程序搜索棉花基因组数据库,鉴定棉花CRK基因家族;利用Compute pI/Mw tool、SignalP、TMHMM Server V2.0、WoLF POSRT等在线工具预测陆地棉CRK家族蛋白的分子量、信号肽、跨膜结构域和亚细胞定位等;用ClustalX1.8软件对棉花和拟南芥CRK蛋白质进行氨基酸序列比对,MEGA5.0分析棉花和拟南芥CRK蛋白的系统进化关系;使用TBtools制作陆地棉CRK基因家族的染色体定位、基因结构和蛋白质结构域示意图;应用植物顺式调控元件数据库PlantCARE分析棉花启动子序列;通过植物磷酸化位点数据库PlantPhos预测陆地棉CRK家族蛋白的磷酸化位点;从NCBI数据库下载RNA-Seq数据,利用转录组定量工具Kallisto计算TPM值,通过在线工具Morpheus绘制陆地棉CRK家族基因表达热图。【结果】陆地棉基因组中有70个CRK基因,分布于14条染色体,其中52个基因（74.3%）集中串联成簇分布于A6/D6、A9/D9、A10/D10染色体,且在A/D染色体组之间呈现高度共线性关系。编码302-901个氨基酸,58个蛋白质（82.9%）具有跨膜结构域,主要定位于叶绿体、质膜和胞外。磷酸化位点预测结果表明,陆地棉和拟南芥CRK有5个相同的磷酸化位点基序,包括3种丝氨酸磷酸化位点基序和2种苏氨酸磷酸化位点基序。65个陆地棉CRK基因的启动子区（92.9%）至少含有一种逆境激素响应元件,69个基因启动子区（98.6%）至少含有一种生物或非生物胁迫响应元件。根据RNA-Seq数据分析结果,陆地棉CRK基因可分为3种不同的组织表达特征类型;盐、干旱、冷、热胁迫以及接种大丽轮枝菌均可以导致部分陆地棉CRK基因表达水平的改变。GhCRK25在根、茎、叶和胚珠中优势表达,在纤维中几乎不表达,ABA、GA3、SA、PEG-6000、氯化钠和大丽轮枝菌Vd991处理均能刺激GhCRK25迅速上调表达。应用病毒诱导的基因沉默技术（VIGS）沉默GhCRK25可导致棉花对大丽轮枝菌Vd991更为敏感。【结论】陆地棉CRK基因家族有70个成员,具有保守的基因结构和功能结构域,多样化的组织表达特征,大多数基因受激素和逆境调控。     

大豆SBP基因家族的序列特征、表达及进化分析

SBP基因家族是植物所特有的一类重要转录因子,由多个成员组成,主要参与植物生长、发育以及多种生理生化过程.试验在大豆基因组中鉴定49个SBP基因,被命名为GmSBP1~49.基于生物信息学手段,对大豆该基因家族49个成员的基因结构、染色体定位、蛋白保守序列、亚细胞定位、表达情况及进化关系进行分析.序列分析表明,SBP基因家族成员分散于不同染色体上,不同基因具有不同个数的外显子,其数目变异范围为1~14;该家族蛋白含有5个保守基序,尽管与SBP结构域有所重叠,但它们能形成6种不同的组织模式,这说明该基因家族序列变异较为复杂.表达分析结果显示,除GmSBP2和GmSBP11等6个基因没有相应的EST外,其余基因都有转录活性;在具有转录活性的基因中,只有GmSBP46显示出组成型表达模式,剩余基因表现出不同程度的组织特异性表达模式.拟南芥、水稻和大豆SBP蛋白的进化树揭示该家族具有8个类群,其中E类群只包括大豆SBP基因,其他类群中大豆SBP基因数目也是最多,这充分说明大豆SBP基因家族起源与进化的复杂性.研究为大豆SBP基因功能研究提供线索     

A draft sequence of the rice genome (Oryza sativa L. ssp. japonica)

The genome of the japonica subspecies of rice, an important cereal and model monocot, was sequenced and assembled by whole-genome shotgun sequencing. The assembled sequence covers 93% of the 420-megabase genome. Gene predictions on the assembled sequence suggest that the genome contains 32,000 to 50,000 genes. Homologs of 98% of the known maize, wheat, and barley proteins are found in rice. Synteny and gene homology between rice and the other cereal genomes are extensive, whereas synteny with Arabidopsis is limited. Assignment of candidate rice orthologs to Arabidopsis genes is possible in many cases. The rice genome sequence provides a foundation for the improvement of cereals, our most important crops.     

核盘菌基因组微卫星序列分析

利用已经公布的核盘菌基因组测序结果,对已有的核盘菌基因组中SSR的类型、大小及分布等数据进行统计分析.在核盘菌基因组内发现1 693个SSR序列,其中出现频率最高的为6碱基和4碱基的SSR序列,分别达到577次和449次,1碱基、3碱基和5碱基的SSR则分别出现97、180、57次.其中有340个SSR序列出现在308个基因内.大多数基因(284个基因)都只含有1个SSR,占含SSR基因总数的92.21％; 17个基因中含有2个SSR,6个基因中含有3个SSR,含4个SSR的基因只有1个.在基因序列内,出现最多的是3碱基与6碱基的SSR,这表明较之基因间区,在选择压力下基因内SSR多趋向于密码子的整数倍,这与其他物种的分析结果一致.为了解含有较多SSR序列与核盘菌基因功能的关系,将含2个以上SSR的基因预测蛋白序列根据NCBI网站CDD软件进行比对发现,24个基因只有6个具有保守的蛋白结构域,且这些结构域多与转录、DNA修复有关.     

Inferring nonneutral evolution from human-chimp-mouse orthologous gene trios

Even though human and chimpanzee gene sequences are nearly 99% identical, sequence comparisons can nevertheless be highly informative in identifying biologically important changes that have occurred since our ancestral lineages diverged. We analyzed alignments of 7645 chimpanzee gene sequences to their human and mouse orthologs. These three-species sequence alignments allowed us to identify genes undergoing natural selection along the human and chimp lineage by fitting models that include parameters specifying rates of synonymous and nonsynonymous nucleotide substitution. This evolutionary approach revealed an informative set of genes with significantly different patterns of substitution on the human lineage compared with the chimpanzee and mouse lineages. Partitions of genes into inferred biological classes identified accelerated evolution in several functional classes, including olfaction and nuclear transport. In addition to suggesting adaptive physiological differences between chimps and humans, human-accelerated genes are significantly more likely to underlie major known Mendelian disorders.     

水稻中富含亮氨酸的重复序列和核苷酸结合位点(LRR-NBS)基因家族的生物信息学分析

 采用HMM(HiddenMarkovModel) ,对源于日本晴的粳稻 (国际水稻测序计划 ,IRGSP)基因组和 9311的籼稻基因组 (北京华大 ,BGI)的蛋白质数据库进行了搜索 ,分别获得了 32 5和 344个富含亮氨酸的重复序列和核苷酸结合位点 (leucinerichrepeat-nucleotidebindingsite ,LRR -NBS)类的抗病基因的蛋白序列 ,并得到了与这些蛋白相应的cDNA序列。对粳稻蛋白功能结构域的分析表明 ,多个蛋白具有与植物防卫反应相关的结构域 ,还发现多个蛋