黄唇鱼(Bahaba flavolabiata)的全基因组测序和基因组特征研究

黄唇鱼(Bahaba flavolabiata)为国家二级重点保护野生动物、IUCN(世界自然保护联盟)红色名录的极度濒危物种(CR)。基于其样本数量极其有限,全基因组研究可以提供大量与重要性状相关的功能基因和分子标记,从而揭示其重要生命现象的遗传机制。采用二代测序技术于2018年5月完成了黄唇鱼基因组精细图的测序,分析结果表明,测序得到约202 Gb的高质量数据,总测序深度约为317×;组装得到的基因组大小为637.43 Mb,Contig N50约为88 Kb,Scaffold N50约为4.65 Mb;重复序列约142.72 Mb,占比22.39%,预测得到23743个基因、920个t RNA、85个rRNA、176个假基因;98.46%的基因可以注释到NR、GO等数据库中;有67个基因家族是黄唇鱼所特有的。本研究从单碱基错误率、核心基因完整性及二代Reads比对分析3个方面对黄唇鱼基因组精细图的组装结果进行了评估,结果显示所组装的基因区的完整性较好。黄唇鱼基因组序列图谱的绘制完成,对于黄唇鱼自然资源的保护和种质资源挖掘具有极其重要的科学意义。     

一株保存的波瓦生病毒全基因组序列测定及分析

目的：对保存的WJBC株波瓦生病毒进行全基因组序列测定和分析,阐明其与已报道毒株之间的关系。方法：将波瓦生病毒基因组编码区分11段进行RT－PCR扩增,扩增产物直接进行测序,非编码区采用RACE法进行扩增,扩增产物纯化并连接pGEM－Teasy载体后转化大肠杆菌DH5ct感受态细胞,挑取阳性克隆鉴定后进行测序,用DNAstar软件将测序结果拼接得到全基因组序列。下载波瓦生病毒全基因组核苷酸序列,利用MEGA5．0软件构建系统进化发生树。结果与结论：WJBC株波瓦生病毒全基因组共11839nt,编码3415个氨基酸残基,病毒基因组5’端和3’端分别有111、483nt的非编码区;进化树结果显示,WJBC株波瓦生病毒与LB株波瓦生病毒的亲缘性最高,可能为同一病毒株．．     

Complete Genome Sequencing of Mosquito and Human Isolates of Ngari Virus

Ngari virus (NRIV) is a recently described, naturally occurring reassortant between two other orthobunyaviruses, Bunyamwera virus (BUNV) and Batai virus (BATV). Intriguingly, this reassortment was associated with the acquisition of heightened virulence, although the molecular basis for this is not understood. Here we report the first complete genome sequences of Ngari virus. We include five isolates from various geographical locations, as well as samples isolated from both mosquitos and human cases. Based on an analysis of these sequence data, NRIVs are clearly genetically distinct from all known BUNV and BATV strains but are very closely related to one another regardless of their source.     

Sequencing Degraded DNA from Non-Destructively Sampled Museum Specimens for RAD-Tagging and Low-Coverage Shotgun Phylogenetics

Ancient and archival DNA samples are valuable resources for the study of diverse historical processes. In particular, museum specimens provide access to biotas distant in time and space, and can provide insights into ecological and evolutionary changes over time. However, archival specimens are difficult to handle; they are often fragile and irreplaceable, and typically contain only short segments of denatured DNA. Here we present a set of tools for processing such samples for state-of-the-art genetic analysis. First, we report a protocol for minimally destructive DNA extraction of insect museum specimens, which produced sequenceable DNA from all of the samples assayed. The 11 specimens analyzed had fragmented DNA, rarely exceeding 100 bp in length, and could not be amplified by conventional PCR targeting the mitochondrial cytochrome oxidase I gene. Our approach made these samples amenable to analysis with commonly used next-generation sequencing-based molecular analytic tools, including RAD-tagging and shotgun genome re-sequencing. First, we used museum ant specimens from three species, each with its own reference genome, for RAD-tag mapping. Were able to use the degraded DNA sequences, which were sequenced in full, to identify duplicate reads and filter them prior to base calling. Second, we re-sequenced six Hawaiian Drosophila species, with millions of years of divergence, but with only a single available reference genome. Despite a shallow coverage of 0.37±0.42 per base, we could recover a sufficient number of overlapping SNPs to fully resolve the species tree, which was consistent with earlier karyotypic studies, and previous molecular studies, at least in the regions of the tree that these studies could resolve. Although developed for use with degraded DNA, all of these techniques are readily applicable to more recent tissue, and are suitable for liquid handling automation.     

Complete Genome Sequencing of Four Geographically Diverse Strains of Batai Virus

Batai virus (BATV) is a widely distributed but poorly studied member of the Orthobunyavirus genus in the family Bunyaviridae and is of particular interest as a known participant in natural reassortment events. Both research and surveillance efforts on this and other related viruses have been hampered by the lack of available full-length sequence data covering all three genomic segments. Here, we report the complete genome sequence of four BATV strains (MM2222, Chittoor/IG-20217, UgMP-6830, and MS50) isolated from various geographical locations. Based on these data, we have determined that strain MS50 is in fact unrelated to BATV and likely represents as a novel genotype in the genus Orthobunyavirus.     

猪瘟弱毒C81株全基因组测序及分子结构预测

参照已发表的猪瘟病毒弱毒株的序列,设计7对覆盖全长基因组的引物,通过RT-PCR从感染猪瘟病毒弱毒株的PK-15细胞中扩增得到7个cDNA片段,分别克隆到pMD18-T载体并测序,利用DNASIS软件获得猪瘟病毒C81株全基因组序列(GenBank:AY663656)。C81株基因组全长12310nt,只有一个大的开放阅读框,编码3898个氨基酸的聚蛋白。序列分析表明,C81株开放阅读框与其它各毒株核苷酸和氨基酸序列的同源性变化较大,分别为84.4%~99.6%和91.6%~99.4%。同时,我们绘制了26株CSFVORF的进化树,比较了CSFV5'非翻译区核苷酸序列并推测其二级结构,发现不同毒株之间存在较大的差异,另外对C81株聚蛋白的功能域和三维结构进行了预测。     

猪瘟弱毒C81株全基因组测序及分子结构预测

参照已发表的猪瘟病毒弱毒株的序列,设计7对覆盖全长基因组的引物,通过RT-PCR从感染猪瘟病毒弱毒株的PK-15细胞中扩增得到7个cDNA片段,分别克隆到pMD18-T载体并测序,利用DNASIS软件获得猪瘟病毒C81株全基因组序列(GenBankAY663656).C81株基因组全长12310nt,只有一个大的开放阅读框,编码3898个氨基酸的聚蛋白.序列分析表明,C81株开放阅读框与其它各毒株核苷酸和氨基酸序列的同源性变化较大,分别为84.4%～99.6%和91.6%～99.4%.同时,我们绘制了26株CSFV ORF的进化树,比较了CSFV 5'非翻译区核苷酸序列并推测其二级结构,发现不同毒株之间存在较大的差异,另外对C81株聚蛋白的功能域和三维结构进行了预测.     

Application of Glycol Methacrylate Embedding to Herbarium Specimens of Fruits

Aldehyde fixation and glycol methacrylate embedding were applied to herbarium specimens of fruits of the Compositae. Sections 1-2 μm thick were cut with glass knives. Softening was unnecessary and the hydrophilic properties of the resin permitted staining with a number of dyes. Specimens were examined with bright field and polarized light microscopy. The technique gives good structural preservation and resolution even with 81-year-old herbarium material.     

Fixing Formalin: A Method to Recover Genomic-Scale DNA Sequence Data from Formalin-Fixed Museum Specimens Using High-Throughput Sequencing

For 150 years or more, specimens were routinely collected and deposited in natural history collections without preserving fresh tissue samples for genetic analysis. In the case of most herpetological specimens (i.e. amphibians and reptiles), attempts to extract and sequence DNA from formalin-fixed, ethanol-preserved specimens—particularly for use in phylogenetic analyses—has been laborious and largely ineffective due to the highly fragmented nature of the DNA. As a result, tens of thousands of specimens in herpetological collections have not been available for sequence-based phylogenetic studies. Massively parallel High-Throughput Sequencing methods and the associated bioinformatics, however, are particularly suited to recovering meaningful genetic markers from severely degraded/fragmented DNA sequences such as DNA damaged by formalin-fixation. In this study, we compared previously published DNA extraction methods on three tissue types subsampled from formalin-fixed specimens of Anolis carolinensis, followed by sequencing. Sufficient quality DNA was recovered from liver tissue, making this technique minimally destructive to museum specimens. Sequencing was only successful for the more recently collected specimen (collected ~30 ybp). We suspect this could be due either to the conditions of preservation and/or the amount of tissue used for extraction purposes. For the successfully sequenced sample, we found a high rate of base misincorporation. After rigorous trimming, we successfully mapped 27.93% of the cleaned reads to the reference genome, were able to reconstruct the complete mitochondrial genome, and recovered an accurate phylogenetic placement for our specimen. We conclude that the amount of DNA available, which can vary depending on specimen age and preservation conditions, will determine if sequencing will be successful. The technique described here will greatly improve the value of museum collections by making many formalin-fixed specimens available for genetic analysis.     

2株WU多瘤病毒全基因组序列测定和分析

WU多瘤病毒(WUPyV)是多瘤病毒科多瘤病毒属的新成员,近来发现与人呼吸道感染等有关。本研究对2株WUPyV进行全基因组序列测定和拼接,获得这2株病毒全基因组序列,并与已上传到GenBank的国内外几株WUPyV的全基因组序列和氨基酸序列进行比对和系统进化分析。这2株WUPyV是环状、双链DNA病毒,基因组全长5 228bp,比GenBank已知WUPyV全序列少1bp。缺失的一对碱基位于位点4 536处,属于大T抗原的非编码区。病毒全基因组编码5个蛋白,分别是3个衣壳蛋白VP2、VP3、VP1与大T抗原和小T抗原。系统进化分析显示相对中国福建福州的FZ18株,另一株FZTF株与参考株-澳大利亚的B0株关系较近。     

绵羊肺腺瘤病毒NM株前病毒基因组的克隆与全序列分析

本研究参照GenBank中已发表的绵羊肺腺瘤病毒的基因组全序列,设计合成8对引物,从内蒙古某羊场自然感染绵羊肺腺瘤病的病肺肿瘤组织中提取总DNA为模板,对JSRV-NM株基因组分8段进行PCR扩增,产物分别为8个(531bp,888bp,949bp,944bp,1428bp,947bp,1836bp,538bp)基因片段,将其分别克隆入pMD-18T载体中进行双向测序并拼接序列,获得完整的JSRV-NM株前病毒基因组全序列。结果表明,JSRV-NM株前病毒基因组全长7430bp,有相互重叠的4个较长的开放阅读框(ORF),分别代表gag、pro、pol和env基因。与绵羊肺腺瘤病毒Ⅰ型即南非代表株(NC-001494)和绵羊肺腺瘤病毒Ⅱ型即美国代表株(AF105220)的核苷酸同源性比较分别为90.4%和90%,推导出的氨基酸同源性分别为90%和89.1%。分析JSRV-NM株基因组结构,发现在LTR的上游和下游都具有外源性exJSRV特有的ScaⅠ酶切位点,在gag基因编码的NC区发现有2个较典型的“胱氨酸—组氨酸序列”,可形成锌指结构。在env基因编码的TM区有特异性的“YXXM”基序。用地高辛标记外源性exJSRV特异的JSRV-2片段制成探针,原位杂交法检测自然感染绵羊肺腺瘤病(OPA)的病肺组织中JSRV-NM的RNA及前病毒DNA,结果表明OPA患羊肺肿瘤细胞的胞浆和核内都有JSRV-2基因mRNA的表达,说明JSRV-NM株是具有致瘤作用的外源性反转录病毒。这是我国首次报道的绵羊肺腺瘤病毒的基因组全序列。     

1株梅花鹿源狂犬病街毒株全基因组测序与分析

对1株梅花鹿源性狂犬病街毒株(DRV)进行全基因组克隆,对全长cDNA进行测序分析.RT-PCR扩增克隆覆盖全基因组9个重叠基因片段,基因组3'和5'末端采取3,-RACE和5'-RACE方法,9个重叠基因片段序列拼接得到DRV全基因组cDNA序列,共11 863个核苷酸.DRV毒株全基因组构成与其他狂犬病毒基因组构成相似,由5个编码区组成,基因起始位点和终止位点高度保守,在核蛋白和糖蛋白的重要抗原位点有个别氨基酸发生变异,对已完成全基因组测序的几个基因1型毒株分别进行了N、P、M、G、L基因核苷酸及氨基酸的同源性比较.与其他具有代表性的毒株进行N基因序列比较建立的系统进化树表明,DRV毒株属于基因1型,与中国人用疫苗株3aG同源性最高为94%,与分类位置未确定的北高加索毒株(WCBV)的同源性最低为71%.本研究结果可为狂犬病毒各项分子生物学研究提供理论参考.     

Complete Plastid Genome Sequencing of Four Tilia Species (Malvaceae): A Comparative Analysis and Phylogenetic Implications

Tilia is an ecologically and economically important genus in the family Malvaceae. However, there is no complete plastid genome of Tilia sequenced to date, and the taxonomy of Tilia is difficult owing to frequent hybridization and polyploidization. A well-supported interspecific relationships of this genus is not available due to limited informative sites from the commonly used molecular markers. We report here the complete plastid genome sequences of four Tilia species determined by the Illumina technology. The Tilia plastid genome is 162,653 bp to 162,796 bp in length, encoding 113 unique genes and a total number of 130 genes. The gene order and organization of the Tilia plastid genome exhibits the general structure of angiosperms and is very similar to other published plastid genomes of Malvaceae. As other long-lived tree genera, the sequence divergence among the four Tilia plastid genomes is very low. And we analyzed the nucleotide substitution patterns and the evolution of insertions and deletions in the Tilia plastid genomes. Finally, we build a phylogeny of the four sampled Tilia species with high supports using plastid phylogenomics, suggesting that it is an efficient way to resolve the phylogenetic relationships of this genus.     

貉源阿留申病毒全基因组测序及末端序列分子特征分析

貉源阿留申病毒(Raccoon dog and arctic fox amdoparvovirus,RFAV)是自然感染貉和蓝狐的新种阿留申病毒(Amdoparvovirus),为测序RFAV全基因组序列,预测分析RFAV末端发夹结构序列分子特征。本研究采用分段克隆成功获得3株长4832nt、4827nt、4830nt的RFAV全基因组序列,分别命名为RFAV-Y9J、RFAV-RD15、RFAV-HS-R,利用在线软件预测RFAV末端序列二级结构,并与水貂阿留申病毒(AMDV)末端序列进行同源性比对。结果显示阿留申病毒种间、种内3’末端基因组序列保守性强,均存在116nt的Y型发夹结构;RFAV-Y9J与RFAV-RD15毒株5′末端分别存在310nt、305nt的U型发夹结构,RFAV和AMDV种内5′末端基因组序列保守性强,而种间5′末端基因组序列有较大变异。本研究首次完整测序了RFAV的3′和5′末端序列,为其他种阿留申病毒的末端序列扩增提供一种有效方法,为构建RFAV的全基因组序列感染性克隆奠定了基础。     

Forward Genetics by Genome Sequencing Reveals That Rapid Cyanide Release Deters Insect Herbivory of Sorghum bicolor

Whole genome sequencing has allowed rapid progress in the application of forward genetics in model species. In this study, we demonstrated an application of next-generation sequencing for forward genetics in a complex crop genome. We sequenced an ethyl methanesulfonate-induced mutant of Sorghum bicolor defective in hydrogen cyanide release and identified the causal mutation. A workflow identified the causal polymorphism relative to the reference BTx623 genome by integrating data from single nucleotide polymorphism identification, prior information about candidate gene(s) implicated in cyanogenesis, mutation spectra, and polymorphisms likely to affect phenotypic changes. A point mutation resulting in a premature stop codon in the coding sequence of dhurrinase2, which encodes a protein involved in the dhurrin catabolic pathway, was responsible for the acyanogenic phenotype. Cyanogenic glucosides are not cyanogenic compounds but their cyanohydrins derivatives do release cyanide. The mutant accumulated the glucoside, dhurrin, but failed to efficiently release cyanide upon tissue disruption. Thus, we tested the effects of cyanide release on insect herbivory in a genetic background in which accumulation of cyanogenic glucoside is unchanged. Insect preference choice experiments and herbivory measurements demonstrate a deterrent effect of cyanide release capacity, even in the presence of wild-type levels of cyanogenic glucoside accumulation. Our gene cloning method substantiates the value of (1) a sequenced genome, (2) a strongly penetrant and easily measurable phenotype, and (3) a workflow to pinpoint a causal mutation in crop genomes and accelerate in the discovery of gene function in the postgenomic era.     

地山雀线粒体基因组全序列的测定和分析

基于长距PCR扩增及保守引物步移法测定并注释了地山雀(Pseudopodoces humilis)的线粒体基因组全序列.结果表明,地山雀线粒体基因组全长1.6 809万bp,A+T含量为52.9%,37个基因排列顺序与红原鸡一致.蛋白质基因的起始密码子中,除COI基因为GTG外,其余均为ATG.NDⅠ和ND5基因终止密码子为AGA:COⅡ基凶为AGG:COⅢ和ND4基因为不完全终止密码子T;其余基因均为典型的TAA或TAG.预测了22个tRNA基闪的二级结构,发现tRNAScr(AGN)缺少DHU臂,tRNAPhe的TψC臂存在一单核苷酸插入.预测的地山雀12S和16S rRNA二级结构分别包括3个结构域47个茎环和6个结构域60个茎环. 控制区位于tRNAGlu和tRNAPhe之间,长度1240 bp.控制区结构为高变Ⅰ区、中央保守Ⅱ区和保守序列Ⅲ区3个结构域.