Deep sequencing of mixed total DNA without barcodes allows efficient assembly of highly plastic ascidian mitochondrial genomes.
Deep sequencing of mixed total DNA without barcodes allows efficient assembly of highly plastic ascidian mitochondrial genomes.
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DOI：
10.1093/gbe/evt081
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发表时间：
2013
影响因子：
3.3
通讯作者：
Huchon D
中科院分区：
文献类型：
--
作者：
Rubinstein ND;Feldstein T;Shenkar N;Botero-Castro F;Griggio F;Mastrototaro F;Delsuc F;Douzery EJ;Gissi C;Huchon D
海鞘或海鞘在脊索动物中形成了一个多样化的群体，其中包括数千种海洋无柄滤食动物。它们的线粒体基因组的特点是特别高的进化率和猖獗的基因重排。这种极端的变异性使基于标准聚合酶链反应（PCR）的分子表征研究技术变得复杂，因此只有少数完整的海鞘线粒体基因组序列可用。使用标准的PCR和桑格测序方法，经过一番努力，我们才获得了Ascidiella aspersa的线粒体基因组。相比之下，我们采用一种新颖的策略产生了另外 5 种有丝分裂基因组（Botrylloides aff. leachii、Halocynthia spinosa、Polycarpa mytiligera、Pyura gangelion 和 Rhodosoma turcicum），即使用一个 Illumina HiSeq 2000 流动槽对这 5 个物种的总 DNA 样本进行测序。使用从头转录组组装将每个有丝分裂基因组有效地组装在单个重叠群中，因为从头基因组组装通常在这项任务中表现不佳。新的六个有丝分裂基因组中的每一个都呈现出不同的新颖的基因顺序，表明在序数水平上没有保守的同线性块（在Stolidobranchia和Phlebobranchia中）。系统发育分析支持海鞘纲和海藻纲的并系，其中海藻纲嵌套在海藻纲内部，尽管海藻纲-海藻纲的最深节点尚未得到很好的解析。因此，本文描述的策略提供了一种经济高效的方法来获得完整的有丝分裂基因组，其特征是高度可塑的基因顺序和快速的核苷酸/氨基酸替换率。
Ascidians or sea squirts form a diverse group within chordates, which includes a few thousand members of marine sessile filter-feeding animals. Their mitochondrial genomes are characterized by particularly high evolutionary rates and rampant gene rearrangements. This extreme variability complicates standard polymerase chain reaction (PCR) based techniques for molecular characterization studies, and consequently only a few complete Ascidian mitochondrial genome sequences are available. Using the standard PCR and Sanger sequencing approach, we produced the mitochondrial genome of Ascidiella aspersa only after a great effort. In contrast, we produced five additional mitogenomes (Botrylloides aff. leachii, Halocynthia spinosa, Polycarpa mytiligera, Pyura gangelion, and Rhodosoma turcicum) with a novel strategy, consisting in sequencing the pooled total DNA samples of these five species using one Illumina HiSeq 2000 flow cell lane. Each mitogenome was efficiently assembled in a single contig using de novo transcriptome assembly, as de novo genome assembly generally performed poorly for this task. Each of the new six mitogenomes presents a different and novel gene order, showing that no syntenic block has been conserved at the ordinal level (in Stolidobranchia and in Phlebobranchia). Phylogenetic analyses support the paraphyly of both Ascidiacea and Phlebobranchia, with Thaliacea nested inside Phlebobranchia, although the deepest nodes of the Phlebobranchia–Thaliacea clade are not well resolved. The strategy described here thus provides a cost-effective approach to obtain complete mitogenomes characterized by a highly plastic gene order and a fast nucleotide/amino acid substitution rate.
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影响因子：
3.7
作者：
Dettai A;Gallut C;Brouillet S;Pothier J;Lecointre G;Debruyne R
通讯作者：
Debruyne R
DOI：
10.1093/bioinformatics/btp348
发表时间：
2009-08-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Capella-Gutiérrez S;Silla-Martínez JM;Gabaldón T
通讯作者：
Gabaldón T
影响因子：
4.4
作者：
Groenenberg DS;Pirovano W;Gittenberger E;Schilthuizen M
通讯作者：
Schilthuizen M
影响因子：
64.8
作者：
Delsuc, F;Brinkmann, H;Philippe, H
通讯作者：
Philippe, H
DOI：
10.1126/science.1194167
发表时间：
2010-12-03
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Denoeud F;Henriet S;Mungpakdee S;Aury JM;Da Silva C;Brinkmann H;Mikhaleva J;Olsen LC;Jubin C;Cañestro C;Bouquet JM;Danks G;Poulain J;Campsteijn C;Adamski M;Cross I;Yadetie F;Muffato M;Louis A;Butcher S;Tsagkogeorga G;Konrad A;Singh S;Jensen MF;Huynh Cong E;Eikeseth-Otteraa H;Noel B;Anthouard V;Porcel BM;Kachouri-Lafond R;Nishino A;Ugolini M;Chourrout P;Nishida H;Aasland R;Huzurbazar S;Westhof E;Delsuc F;Lehrach H;Reinhardt R;Weissenbach J;Roy SW;Artiguenave F;Postlethwait JH;Manak JR;Thompson EM;Jaillon O;Du Pasquier L;Boudinot P;Liberles DA;Volff JN;Philippe H;Lenhard B;Roest Crollius H;Wincker P;Chourrout D
通讯作者：
Chourrout D