基于Roche 454 GS FLX高通量测序的叶城沙蜥基因组微卫星特征分析

叶城沙蜥Phrynocephalus axillaris是我国特有的一种小型爬行动物,广泛分布于新疆塔里木盆地、吐鲁番-哈密盆地和甘肃敦煌盆地。本研究利用Roche 454 GS FLX高通量测序技术进行叶城沙蜥微卫星位点筛选,获得了91 190条高质量序列。用Krait搜索微卫星位点,共得到1～6个碱基重复类型的完美型微卫星序列29 890个。不同类型微卫星中,单碱基重复类型数目最多,有14 630个,占总数的48. 95%,其次是二碱基,约占28. 60%,四碱基、三碱基、五碱基和六碱基分别占10. 73%、10. 48%、0. 92%和0. 32%。二碱基微卫星中AC重复类型数量最多,三碱基、四碱基、五碱基和六碱基中分别是ATC、AAAT、AAAAT和AATCCC。叶城沙蜥完美型微卫星中数量最多的11种重复拷贝类型分别为C、A、AC、AG、AAAT、ATC、AT、AAT、ATAG、AGG和AAC。本研究深化了对叶城沙蜥基因组的了解,并为以后开发和筛选大量高质量微卫星标记提供了数据支持,也为利用微卫星标记研究叶城沙蜥种群遗传结构和谱系地理模式奠定了基础。     

基于454 GS FLX高通量测序的南疆沙蜥微卫星特征分析及其候选引物设计

南疆沙蜥Phrynocephalus forsythii是我国特有的一种小型爬行动物,分布于塔里木盆地。利用Roche 454 GS FLX高通量测序对该物种基因组测序,获得了55 909条高质量序列。利用Krait搜索并初步统计和分析基因组微卫星序列,共得到1～6个碱基重复类型的完美型微卫星12 109个。不同类型微卫星中,四碱基重复类型数目最多,有4 037个,约占总数的33.34%,其次是二碱基,约占总数的28.09%,再是三碱基、单碱基、五碱基和六碱基,分别约占总数的18.72%、13.91%、4.48%和1.46%。单碱基微卫星中C最多,二碱基微卫星中AC最多,三碱基、四碱基、五碱基和六碱基中最多的分别是AAC、AAAT、AAAAT和AACCCT。AC、AAAT、C、AG、A、AAC、AAT、AAAC、ACC和ACG是数量最多的10种重复拷贝类别。挑选部分三、四碱基重复类型的微卫星序列设计了100对可用于后续对南疆沙蜥微卫星标记开发的候选引物。本研究开启了对南疆沙蜥基因组微卫星特征的了解,为利用微卫星标记研究南疆沙蜥种群遗传结构奠定了基础。     

基于454 GS FLX高通量测序的团头鲂ESTs中微卫星特征分析

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四川山鹧鸪的分布及生境选择

研究了四川山鹧鸪(Arborophila rufipectus)的分布区域和栖息地的生境,认为四川山鹧鸪的分布范围比已知的要大,但其实际分布区呈明显的岛屿状,显示出生境的破碎化;指出四川山鹧鸪的适宜生境是原始的常绿阔叶林、针阔混交林和具有较大常绿落叶阔叶乔木树种盖度的多年生次生林,亦可选择部分人工林,而对地表灌丛密度大的次生幼林以及人工幼林生境不喜好。由于天然林的禁伐和生态林的管护,四川山鹧鸪的栖息地趋于稳定并有所扩大。但四川山鹧鸪仍然处于濒危状态。     

四川山鹧鸪于攀枝花市发现的意义

四川山鹧鸪Ａｒｂｏｒｏｐｈｉｌａｒｅｆｉｐｅｃｔｕｓ是我国国家一级保护野生动物 ,以往仅知分布于四川省的中部 ,南可抵(长江上游的 )金沙江。因其分布范围极为狭小 (直线距离南北约 10 0ｋｍ ,东西约 150ｋｍ) ,所以被视为是全球极危物种 (ＣｒｉｔｉｃａｌｌｙＥｎｄａｎｇｅｒｅｄ) (Ｃｏｌｌａｒｅｔａｌ.,1994 )。基于对山鹧鸪属Ａｒｂｏｒｏｐｈｉｌａ种类在分布型上不应出现明显间断 ,且金沙江亦不应成为对四川山鹧鸪的天然阻隔这一认识 ,作者据 1997年证实该种在云南省的东北部 (至少是在绥江 ,可能还有永善、盐津等地 )确有分…     

攀枝花市发现四川山鹧鸪

四川山鹧鸪 (ＡｒｂｏｒｏｐｈｉｌａｒｕｆｉｐｅｔｕｓＢｏｕｌｔｏｎ)是国家一级重点保护动物。目前仅报道分布于大凉山脉东北端两侧的四川省甘洛县东北部、马边县、雷波县北部、美姑县东部、峨边县以及屏山县和与屏山县隔金沙江相望的云南省绥江县北部 ,分布范围较为狭窄。 1999年 3月 ,笔者在四川省攀枝花市盐边县国胜乡获得一雌性个体 ,量度为 :体重 2 70 ｇ ,全长 2 75 ,嘴峰 18,翅长 148,尾长 70 ,跗 47ｍｍ。形态 :额基及眉纹黑色 ,其上有微杂以黑点的浅黄色纵纹 ;眼先黄白色 ,具矢状黑斑 ,头顶及枕部橄榄褐色 ,羽均具有黑色羽干…     

四川山鹧鸪基因组中内源性逆转录病毒的分析

内源性逆转录病毒(ERV)是插入到宿主基因组中的、可以稳定遗传的病毒基因组,能够在宿主体内表达和复制,调节插入位点附近的基因表达,以及抑制同源病毒的感染。从四川山鹧鸪Arborophila rufipectus基因组中确定了3 962个全长ERV拷贝,其中4个具有完整的结构,72个具有自我复制的能力,554个含有gag、pol或env基因所编码的蛋白质结构域。根据逆转录酶序列的相似性,确定了7个ERV家族,并依据与其他物种的相似性对家族进行了命名。其中,AruERV-L包含122个ERV拷贝,为拷贝数最多的家族。7个ERV家族的年龄分布在0～12百万年,其中AruERV-K1是最年轻的家族,其约86%的拷贝年龄在1百万年以内。     

四川山鹧鸪栖息地分析与预测

四川山鹧鸪Arborophila rufipectus属鸡形目雉科山鹧鸪属,是我国特产珍稀鸟类,国家一级重点保护野生动物,IUCN濒危物种。本文应用卫星遥感影像解译技术对该物种的现实栖息地和潜在栖息地进行了分析和预测。结果表明,现存四川山鹧鸪分布格局自四川中南部向云南东北延伸,跨越金沙江,呈现西北-东南走向,分布区涉及大相岭山系南缘、小相岭山系东缘、凉山山系东北部、乌蒙山山系西部,行政区域涉及2省5市(州)19县(区)。栖息地由10片现实栖息地和36片潜在栖息地组成,总面积约5869 km2。"甘洛-金口河-峨边-马边-美姑"片和"雷波-马边-屏山"片是四川省境内呈南北布局的两大核心分布区,"绥江-永善-水富-盐津-大关"片为云南省境内的核心分布区。     

四川山鹧鸪的冬季生态研究

四川山鹧鸪调查在四川省马力县黄连山林区。冬季单只、成对活动。其数量在原始林为每平方公里２．７５只，人工杉木林和自然更新林为每新林为每平方公里０．７５只。主食草子、根等物，夜栖树上。冬季的主要天敌为猛禽。野外考察还发现沐川县为新的分布。     

再谈四川山鹧鸪的模式产地

四川山鹧鸪 Arborophila rufipectus 系由R.Boulton于1932年依据F.T.Smith'.在原两康省某地"Ta Cho.Fu"采获的单独一号雄性标本而定名.中国鸟类学家以往多认为该种的模式标本产地为今四川甘洛县的大桥乡.通过对大桥乡所在地理坐标的实测,并使用Google Earth对该地区进行查检,作者曾提出"Ta Cho Fu"当在今四川汉源县境内,并指出对该地点具体位置的订正和重新定位,使四川山鹧鸪的总分布区域北推了至少100 km范匍.尽管'"Fraylor(1967)曾对"Ta Cho Fu"这一地点给出过一个差异颇大的地理坐标,作者通过进一步研究和对相关史料的分析,认为F.T.Smith当年采得四川山鹧鸪的地点仍应当是在四川汉源县境内.     

Comparison of the Illumina Genome Analyzer and Roche 454 GS FLX for Resequencing of Hypertrophic Cardiomyopathy-Associated Genes

Next-generation sequencing (NGS) is widely used in biomedical research, but its adoption has been limited in molecular diagnostics. One application of NGS is the targeted resequencing of genes whose mutations lead to an overlapping clinical phenotype. This study evaluated the comparative performance of the Illumina Genome Analyzer and Roche 454 GS FLX for the resequencing of 16 genes associated with hypertrophic cardiomyopathy (HCM). Using a single human genomic DNA sample enriched by long-range PCR (LR-PCR), 40 GS FLX and 31 Genome Analyzer exon variants were identified using ≥30-fold read-coverage and ≥20% read-percentage selection criteria. Twenty-seven platform concordant variants were Sanger-confirmed. The discordant variants segregated into two categories: variants with read coverages ≥30 on one platform but <30-fold on the alternate platform and variants with read percentages ≥20% on one platform but <20% on the alternate platform. All variants with <30-fold coverage were Sanger-confirmed, suggesting that the coverage criterion of ≥30-fold is too stringent for variant discovery. The variants with <20% read percentage were identified as reference sequence based on Sanger sequencing. These variants were found in homopolymer tracts and short-read misalignments, specifically in genes with high identity. The results of the current study demonstrate the feasibility of combining LR-PCR with the Genome Analyzer or GS FLX for targeted resequencing of HCM-associated genes.     

四川山鹧鸪的转录组组装和注释

四川山鹧鸪Arborophila rufipectus是中国特有的珍稀濒危鸟类.本研究对1只成年雄性四川山鹧鸪个体的心脏、肝脏和肾脏进行了转录组测序、组装和注释.其原始序列过滤后分别产生了5.70 G、4.60 G和5.16 G数据.286661条转录本经过Trinity组装并去掉冗余后共得到234488个基因.BUS...     

Artificial duplicate reads in sequencing data of 454 Genome Sequencer FLX System

The 454 Genome Sequencer (GS) FLX System is one of the next-generation sequencing systems featured by long reads, high accuracy, and ultra-high throughput. Based on the mechanism of emulsion PCR, a unique DNA template would only generate a unique sequence read after being amplified and sequenced on GS FLX. However, biased amplification of DNA templates might occur in the process of emulsion PCR, which results in production of artificial duplicate reads. Under the condition that each DNA template is unique to another, 3.49%-18.14% of total reads in GS FLX-sequencing data were found to be artificial duplicate reads. These duplicate reads may lead to misunderstanding of sequencing data and special attention should be paid to the potential biases they introduced to the data.     

Near-Complete Genome Sequencing of Swine Vesicular Disease Virus Using the Roche GS FLX Sequencing Platform

Swine vesicular disease virus (SVDV) is an enterovirus that is both genetically and antigenically closely related to human coxsackievirus B5 within the Picornaviridae family. SVDV is the causative agent of a highly contagious (though rarely fatal) vesicular disease in pigs. We report a rapid method that is suitable for sequencing the complete protein-encoding sequences of SVDV isolates in which the RNA is relatively intact. The approach couples a single PCR amplification reaction, using only a single PCR primer set to amplify the near-complete SVDV genome, with deep-sequencing using a small fraction of the capacity of a Roche GS FLX sequencing platform. Sequences were initially verified through one of two criteria; either a match between a de novo assembly and a reference mapping, or a match between all of five different reference mappings performed against a fixed set of starting reference genomes with significant genetic distances within the same species of viruses. All reference mappings used an iterative method to avoid bias. Further verification was achieved through phylogenetic analysis against published SVDV genomes and additional Enterovirus B sequences. This approach allows high confidence in the obtained consensus sequences, as well as provides sufficiently high and evenly dispersed sequence coverage to allow future studies of intra-host variation.