葡萄、桃和可可基因组的进化分析

本研究以葡萄、桃和可可为研究对象,基于比较基因组学,利用基因同源共线性方法对基因组内的结构和基因组间同源信息进行比对分析,确定了物种基因组内和基因组间的同源片段。通过统计3个物种基因组间的同源共线基因的保留情况发现,葡萄基因组的保留情况最好,桃次之(为73.4%),可可最差(为68.9%),其丢失均可能是由于双子叶植物共有的三倍化导致基因组稳定性遭到破坏。另外,共线基因间的同义核苷酸替换率的频数分布证实,葡萄、桃和可可仅经历过一次古老的全基因组三倍化,并未经历最近的全基因组加倍,且可可基因组进化最快,葡萄基因组进化最保守;3个物种的分歧时间分别为:葡萄(~110 Mya)、可可(~90 Mya)、桃(~80 Mya)。本研究将为3个物种及双子叶植物基因组的结构、功能和进化等研究提供重要的理论依据。     

LEAFY同源基因研究进展

LEAFY(LFY)同源基因存在于所有的陆生植物中,在植物花发育早期表达,并在花发育过程中抑制茎端分生组织的营养生长,调控花分生组织和花器官的形成,使转LFY基因植株提前开花,LFY同源基因与其上下游基因共同调控花发育过程.LFY同源基因的蛋白质结构在不同物种间保守性很高,但它们的表达部位差异很大.该文总结了近年来国内外已经克隆到的LFY同源基因的表达、功能及其在果树、花卉、粮食作物上的应用,以期为植物花发育的深入研究提供参考.     

猪丙型肝炎病毒核心蛋白结合蛋白6同源基因的克隆化研究

利用不同种属动物之间重要基因序列高度同源的理论,应用分子生物学与生物信息学技术和方法。克隆猪丙型肝炎病毒(HCY)核心蛋白结合蛋白6(HCBP6)的同源基因。首先应用酵母双杂交技术,以表达HCV核心蛋白的表达栽体作为曾饵,对于百万级的肝细胞cDNA文库酵母进行配合、筛选,首先获得人HCBP6的全长鳊码基因。然后应用美国国立生物工程中心(NCBI)建立的核苷酸序列数据库(CenBank)的同源基因的检索,搜索与之同源的来源于猪的表达序列标签(EST)。然后根据基因同泺性的原则,确定猪HCBP6的同源基因。获得了与HCC核心蛋白结合蛋白的36个基因片段,其中之一命名为HCBP6。根据基因同源性搜索,获得了来源于猪的EST基因序列片段。最终确立了猪HCBP6的同源基因。利用不同物种之间基因同泺性的原理、NCBI数据库GenBank同源基因的搜索,获得了猪HCBP6同源基因。生物信息学技术在后基因组时代具有重要地位和作用。     

锌指核酸内切酶:基因操作的有力工具

针对动植物进行基因靶向操作的技术,是解析基因功能、研究疾病,以及农业经济生产中一个有用的工具。至今,基因靶向操作主要是通过在胚胎干细胞(embryonic stem cell,ES cell)中进行同源重组或者是体细胞核转移的方法进行,但同源重组方法由于需要ES细胞而被限制在个别物种,而核转移方法存在核去分化、效率低、成本高的缺陷。近几年,一种基于锌指核酸内切酶(zinc-finger nuclease,ZFN)基因靶向修饰的新技术被应用于包括植物、果蝇、爪蟾、斑马鱼和大鼠等不同物种的基因操作。通过胚胎注射ZFN的质粒或是mRNA可以有效地定靶并迅速地在内源基因上引起可遗传的突变。ZFN介导基因靶向敲除的可行性,使得那些无法获得ES细胞和克隆技术支持的物种的基因靶向修饰成为可能。     

豆科AGAMOUS同源基因结构及功能分析

AGAMOUS(AG)基因是控制高等植物花发育的重要基因,已在20多种植物基因组中发现同源基因。作为MADS-box家族的一员,AG基因结构具有高度的保守性。AG及其同源基因在植物生长发育中的功能已经十分清晰。本文研究AG同源基因在豆科几个代表物种中的分布,对其基因结构和蛋白序列进行分析比对。结果表明,AG同源基因在不同的豆科物种中具有高度的序列同源性及结构保守性。进一步通过蒺藜苜蓿Medicago truncatula的AG同源基因表达模式分析发现,其表达是与功能相互验证的。     

绿豆VrWOX基因家族鉴定及表达分析北大核心CSCD

WOX(WUSCHEL-related homebox)基因家族是植物特有的一类转录因子,是同源盒(homeobox,HB)转录因子超家族中的重要成员。WOX基因在植物干细胞调节及生殖发育过程中具有重要作用,其功能已在多个植物物种中鉴定。然而绿豆(Vigna radiate)VrWOX基因家族信息尚不清楚。本研究通过同源比对和聚类分析,在绿豆基因组中鉴定了42个VrWOX基因。VrWOX基因在绿豆染色体中分布不均,其中7号染色体含有的VrWOX数量最多。VrWOX基因分为古老进化支(19个VrWOX)、中等进化支(12个VrWOX)和年轻进化支(WUSCHEL进化支,11个VrWOX)3个亚类。种内和种间共线性分析发现,VrWOX基因共有12个重复事件,与拟南芥(Arabidopsis thaliana)AtWOX有15个同源基因对,与菜豆(Phaseolus vulgaris)PvWOX有22个同源基因对。VrWOX基因在基因结构、保守基序等方面存在很大差异,因而可能存在功能差异。VrWOX基因启动子区域含有不同种类和不同数量的顺式作用元件,导致VrWOX基因在不同组织中表现出不同的基因表达模式。本研究对VrWOX基因家族信息和表达模式进行了分析,为绿豆VrWOX基因功能和调控网络的解析奠定了一定的理论依据。     

三种四膜虫全基因组N6-甲基腺嘌呤比较研究

为了揭示N6-甲基腺嘌呤(6mA)在近缘物种间的分布规律和物种进化过程中的变化, 研究在分离2种四膜虫(Tetrahymena malaccensis和Tetrahymena pyriformi)大核的基础上, 利用三代测序技术绘制了其全基因组单碱基分辨率6mA图谱, 结合公共数据库中已有的模式种Tetrahymena thermophila数据, 开展了3种四膜虫比较6mA甲基化组分析, 发现: (1)3种四膜虫6mA甲基化位点分布特征类似, 包括呈约200 bp周期性分布和具有保守AT基序; (2)6mA主要分布于基因的5′端, 在种间直系同源基因上的分布模式具有区域近似性, 但在单碱基水平不完全保守; (3)在种内近期复制的并系同源基因中, 6mA分布在单碱基水平具有较高的保守性; (4)结合3种四膜虫的分化时间, 估算出了四膜虫中6mA动态变化过程, 6mA位点建立的速度大约为每Mb每百万年69.9—226个位点。     

牦牛与其他物种ZFX/ZFY基因片段间的进化关系

利用PCR扩增、克隆和序列分析法对牦牛ZFX/ZFY基因第11外显子部分片段进行了研究,并同来自于NCBI GenBank中人、猩猩、普通牛等9个物种的ZFX/ZFY基因核苷酸及其氨基酸序列进行了进化分析.结果表明,牦牛ZFX、ZFY基因间核苷酸序列同源性为94.1%,显示同一物种同源基因ZFX/ZFY间存在变异;比较的10个物种间ZFX基因核苷酸序列同源性为87.7%、ZFY基因为81.7%,相应ZFX、ZFY氨基酸同源性分别为96.6%、91.0%,ZFY基因的变异性大于ZFX基因,显示X染色体与Y染色体可能是独立进化.     

小麦黄色素合成途径中Psy基因的克隆及分子特性

对普通小麦(Ttiticum aestivum)黄色素(YP)合成途径中的首要限速酶——八氢番茄红素合成酶(Psy)基因进行克隆和测序,并和玉米Psy基因进行序列比对。结果表明,在高和低YP含量小麦品种中均扩增出一条长1192bp的Psy基因片段,该片段包含一条可编码78个氨基酸的小麦Psy基因的外显子,与玉米Psy基因第4外显子的核苷酸序列同源率为80.74,同源区域内有47个SNPs,但仅11个SNPs导致氨基酸编码序列的改变,二者氨基酸序列的同源率达85.89,推测Psy基因在不同物种中的表达具有较高的保守性。BLAST聚类分析表明,禾谷类植物Psy基因的分类与物种的亲缘关系存在明显的相关性,小麦Psy基因在系统进化中比禾谷类其他植物更为高级。     

小麦黄色素合成途径中Psy 基因的克隆及分子特性小麦黄色素合成途径中Psy 基因的克隆及分子特性

对普通小麦( Ttiticum aestivum) 黄色素(YP) 合成途径中的首要限速酶———八氢番茄红素合成酶(Psy) 基因进行克隆和测序, 并和玉米Psy 基因进行序列比对。结果表明, 在高和低YP 含量小麦品种中均扩增出一条长1 192 bp 的Psy 基因片段, 该片段包含一条可编码78 个氨基酸的小麦Psy 基因的外显子, 与玉米Psy 基因第4 外显子的核苷酸序列同源率为80 . 74% , 同源区域内有47 个SNPs , 但仅11 个SNPs 导致氨基酸编码序列的改变, 二者氨基酸序列的同源率达85 . 89% , 推测Psy 基因在不同物种中的表达具有较高的保守性。BLAST 聚类分析表明, 禾谷类植物Psy 基因的分类与物种的亲缘关系存在明显的相关性,小麦Psy 基因在系统进化中比禾谷类其他植物更为高级。     

Rates of nuclear and cytoplasmic mitochondrial DNA sequence divergence in mammals

Differential rates of nucleotide substitution among different gene segments and between distinct evolutionary lineages is well documented among mitochondrial genes and is likely a consequence of locus-specific selective constraints that delimit mutational divergence over evolutionary time. We compared sequence variation of 18 homologous loci (15 coding genes and 3 parts of the control region) among 10 mammalian mitochondrial DNA genomes which allowed us to describe different mitochondrial evolutionary patterns and to produce an estimation of the relative order of gene divergence. The relative rates of divergence of mitochondrial DNA genes in the family Felidae were estimated by comparing their divergence from homologous counterpart genes included in nuclear mitochondrial DNA (Numt, pronounced "new might"), a genomic fossil that represents an ancient transfer of 7.9 kb of mitochondrial DNA to the nuclear genome of an ancestral species of the domestic cat (Felis catus). Phylogenetic analyses of mitochondrial (mtDNA) sequences with multiple outgroup species were conducted to date the ancestral node common to the Numt and the cytoplasmic (Cymt) mtDNA genes and to calibrate the rate of sequence divergence of mitochondrial genes relative to nuclear homologous counterparts. By setting the fastest substitution rate as strictly mutational, an empirical "selective retardation index" is computed to quantify the sum of all constraints, selective and otherwise, that limit sequence divergence of mitochondrial gene sequences over time.      

Analysis of the chromocenter DNA composition in polytene chromosomes of Drosophila orena ovarian nurse cells

Chromocenter DNA fragments of polytene chromosomes of Drosophila orena ovarian nurse cells were cloned from a region-specific library (Dore 1) in a plasmid vector to yield 133 clones. A total of 76 clones were selected and sequenced. The total length of the sequenced fragments was 23940 bp. Analysis with several software packages revealed various repetitive sequences among the fragments of the Dore 1 library, including mobile genetic elements (25 fragments homologous to various LTR retrotransposons, five fragments homologous to LINEs, three fragments homologous to Helitrons, one fragment homologous to Polinton, and one fragment homologous to the mini-me non-LTR retrotransposon), four minisatellites, a satellite (SAR_DM), the (TATATG)n simple sequence repeat, and a low-complexity T-rich repeat. Sequences homologous to protein-coding genes were also found in the Dore 1 library. Various repetitive DNA sequences and gene homologs were identified as conserved sequences of pericentric heterochromatin of polytene chromosomes of ovarian nurse cells in nine species of the melanogaster species subgroup.     

nWayComp: a genome-wide sequence comparison tool for multiple strains/species of phylogenetically related microorganisms

The increasing number of whole genomic sequences of microorganisms has led to the complexity of genome-wide annotation and gene sequence comparison among multiple microorganisms. To address this problem, we have developed nWayComp software that compares DNA and protein sequences of phylogenetically-related microorganisms. This package integrates a series of bioinformatics tools such as BLAST, ClustalW, ALIGN, PHYLIP and PRIMER3 for sequence comparison. It searches for homologous sequences among multiple organisms and identifies genes that are unique to a particular organism. The homologous gene sets are then ranked in the descending order of the sequence similarity. For each set of homologous sequences, a table of sequence identity among homologous genes along with sequence variations such as SNPs and INDELS is developed, and a phylogenetic tree is constructed. In addition, a common set of primers that can amplify all the homologous sequences are generated. The nWayComp package provides users with a quick and convenient tool to compare genomic sequences among multiple organisms at the whole-genome level.     

Data mining for miRNAs and their targets in the Triticeae.

MicroRNAs (miRNAs) and the mRNA targets of miRNAs were identified by sequence complementarity within a DNA sequence database for species of the Triticeae. Data screening identified 28 miRNA precursor sequences from 15 miRNA families that contained conserved mature miRNA sequences within predicted stem-loop structures. In addition, the identification of 337 target sequences among Triticeae genes provided further evidence of the existence of 26 miRNA families in the cereals. MicroRNA targets included genes that are homologous to known targets in diverse model species as well as novel targets. MicroRNA precursors and targets were identified in 10 related species, though the great majority of them were identified in bread wheat, Triticum aestivum, and barley, Hordeum vulgare, the two species with the largest EST data sets among the Triticeae.     

Molecular phylogeny and evolution of primate mitochondrial DNA

We determined nucleotide sequences of homologous 0.9-kb fragments of mitochondrial DNAs (mtDNAs) derived from four species of old-world monkeys, one species of new-world monkeys, and two species of prosimians. With these nucleotide sequences and homologous sequences for five species of hominoids, we constructed a phylogenetic tree for the four groups of primates. The phylogeny obtained is generally consistent with evolutionary trees constructed in previous studies. Our results also suggest that the rate of nucleotide substitution for mtDNAs in hominines (human, chimpanzee, and gorilla) may have slowed down compared with that for old-world monkeys. This evolutionary feature of mitochondrial genes is similar to one found in nuclear genes.      

Analysis of the chromocenter DNA composition in polytene chromosomes of <Emphasis Type="Italic">Drosophila orena</Emphasis> ovarian nurse cells

Chromocenter DNA fragments of polytene chromosomes of Drosophila orena ovarian nurse cells were cloned from a region-specific library (Dore1) in a plasmid vector to yield 133 clones. A total of 76 clones were selected and sequenced. The total length of the sequenced fragments was 23940 bp. Analysis with several software packages revealed various repetitive sequences among the fragments of the Dore1 library, including mobile genetic elements (25 fragments homologous to various LTR retrotransposons, five fragments homologous to LINEs, three fragments homologous to Helitrons, one fragment homologous to Polinton, and one fragment homologous to the mini-me non-LTR retrotransposon), four minisatellites, a satellite (SAR_DM), the (TATATG)n simple sequence repeat, and a low-complexity T-rich repeat. Sequences homologous to protein-coding genes were also found in the Dore1 library. Various repetitive DNA sequences and gene homologs were identified as conserved sequences of pericentric heterochromatin of polytene chromosomes of ovarian nurse cells in nine species of the melanogaster species subgroup.     

Cloning and characterization of resistance gene analogs from Avena species.

Sequences analogous to plant resistance genes of the NBS-LRR class were cloned from the genomic DNA of 11 Avena species with different genomes and levels of ploidy. Three pairs of degenerate primers were used, based on conserved DNA sequence motifs belonging to the NBS domain, and 33 sequences were identified. These were subdivided into 7 classes depending on nucleotide sequence identity. Despite the high level of degeneracy, the primers behaved in a highly selective way; the majority of sequences from the different species obtained with every primer combination showed strong identity and were considered homologous. For most species, only one sequence of each class was identified in each genome, suggesting that duplicated sequences are fairly divergent. The strong identity among specific NBS sequences precludes any conclusions being made on the evolution of these species. The genomic organization of the RGA sequences was explored using those of A. strigosa as probes in Southern blots involving digested DNA from 15 Avena species. The hybridization patterns showed wide diversity both among sequences within a species and among species for each sequence. However, the dendrogram generated using the RFLPs showed relationships among species to be in good agreement with those previously established using other molecular markers.