Annotation of two large contiguous regions from the Haemonchus contortus genome using RNA-seq and comparative analysis with Caenorhabditis elegans.
Annotation of two large contiguous regions from the Haemonchus contortus genome using RNA-seq and comparative analysis with Caenorhabditis elegans.
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DOI：
10.1371/journal.pone.0023216
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发表时间：
2011
期刊：
影响因子：
3.7
通讯作者：
Gilleard JS
中科院分区：
文献类型：
--
作者：
Laing R;Hunt M;Protasio AV;Saunders G;Mungall K;Laing S;Jackson F;Quail M;Beech R;Berriman M;Gilleard JS
目前正在对许多寄生线虫的基因组进行测序，但它们的复杂性和大小，以及高水平的种内序列变异和缺乏参考基因组，使它们的组装和注释成为一项具有挑战性的任务。捻转血矛线虫是一种经济上重要的家畜寄生虫，广泛用于基础研究以及疫苗开发和药物发现。它是圆线虫组中许多医学和经济上重要的寄生虫之一。这组寄生虫与模式生物秀丽隐杆线虫具有最接近的系统发育关系，使比较分析成为基因组注释和功能研究的潜在有力工具。为了研究这一假设，我们对来自H.并与C.优雅成虫H.使用Illumina平台对捻转肌转录组进行测序，并使用RNA-seq来注释与X染色体相关的409 kb重叠BAC平铺路径和与染色体I相关的181 kb BAC插入片段。总共鉴定了40个基因和12个推定的转座因子。97.5%的注释基因在C.其中60%具有推定的直向同源物，显著高于先前基于EST分析的分析。基因密度在H. contortus比C. elegans，带注释的H. contortus基因平均比它们假定的C.由于更大的内含子数量和大小，同线性似乎很高，但基因顺序通常保守性很差，尽管保守的微同线性区域是明显的。C.线虫操纵子在H.扭曲我们的研究结果表明，RNA-seq和C. elegans是圆线虫基因组注释和分析的有力手段。
The genomes of numerous parasitic nematodes are currently being sequenced, but their complexity and size, together with high levels of intra-specific sequence variation and a lack of reference genomes, makes their assembly and annotation a challenging task. Haemonchus contortus is an economically significant parasite of livestock that is widely used for basic research as well as for vaccine development and drug discovery. It is one of many medically and economically important parasites within the strongylid nematode group. This group of parasites has the closest phylogenetic relationship with the model organism Caenorhabditis elegans, making comparative analysis a potentially powerful tool for genome annotation and functional studies. To investigate this hypothesis, we sequenced two contiguous fragments from the H. contortus genome and undertook detailed annotation and comparative analysis with C. elegans. The adult H. contortus transcriptome was sequenced using an Illumina platform and RNA-seq was used to annotate a 409 kb overlapping BAC tiling path relating to the X chromosome and a 181 kb BAC insert relating to chromosome I. In total, 40 genes and 12 putative transposable elements were identified. 97.5% of the annotated genes had detectable homologues in C. elegans of which 60% had putative orthologues, significantly higher than previous analyses based on EST analysis. Gene density appears to be less in H. contortus than in C. elegans, with annotated H. contortus genes being an average of two-to-three times larger than their putative C. elegans orthologues due to a greater intron number and size. Synteny appears high but gene order is generally poorly conserved, although areas of conserved microsynteny are apparent. C. elegans operons appear to be partially conserved in H. contortus. Our findings suggest that a combination of RNA-seq and comparative analysis with C. elegans is a powerful approach for the annotation and analysis of strongylid nematode genomes.
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DOI：
10.1073/pnas.96.8.4482
发表时间：
1999-04-13
影响因子：
11.1
作者：
Duret, L;Mouchiroud, D
通讯作者：
Mouchiroud, D
影响因子：
9.8
作者：
Hillier LW;Miller RD;Baird SE;Chinwalla A;Fulton LA;Koboldt DC;Waterston RH
通讯作者：
Waterston RH
BAMVIEW：在参考序列的上下文中查看映射的读取对齐数据。
影响因子：
5.8
作者：
Carver, Tim;Bohme, Ulrike;Otto, Thomas D.;Parkhill, Julian;Berriman, Matthew
通讯作者：
Berriman, Matthew
影响因子：
5.8
作者：
Abbott, JC;Aanensen, DM;Spratt, BG
通讯作者：
Spratt, BG
影响因子：
14.9
作者：
Deutsch, M;Long, M
通讯作者：
Long, M