Phylogenomic resolution of paleozoic divergences in harvestmen (Arachnida, Opiliones) via analysis of next-generation transcriptome data.
Phylogenomic resolution of paleozoic divergences in harvestmen (Arachnida, Opiliones) via analysis of next-generation transcriptome data.
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DOI：
10.1371/journal.pone.0042888
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发表时间：
2012
期刊：
影响因子：
3.7
通讯作者：
Shultz JW
中科院分区：
文献类型：
--
作者：
Hedin M;Starrett J;Akhter S;Schönhofer AL;Shultz JW
下一代测序技术正在迅速改变非模式动物分类群的分子系统学研究。蜘蛛目Opiliones（通常称为“收获者”）包括超过6，400个描述的物种，分为四个支持良好的谱系（亚目）。化石加上分子钟的证据表明，这些谱系在志留纪晚期到石炭纪中期开始分化，其中一些化石收割者代表了已知最早的陆地动物。也许是因为这种古老的分歧，系统发育的决议内Opiliones从属的相互关系一直很困难。我们提出了第一个基因组学分析收获，来自比较RNA-Seq数据的8个物种代表所有的亚目。在从头组装中使用了超过30千兆字节的原始Illumina短读数据，每个分类群产生50- 80，000个转录本。将转录本与已发表的蝎子和蜱基因组学数据进行比较，并使用严格的过滤过程来识别超过350个在分类群中共享的pupillin单拷贝、直链蛋白编码基因。系统发育分析使用各种分区策略，数据编码方案，和分析方法压倒性地支持“经典”的假设Opiliones关系，包括更高级别的分支Palpatores和Phalangida。宽松的分子钟分析，使用多种替代化石校准策略证实了古老的分歧内Opiliones可能比记录的化石记录表明更深。组装的数据矩阵，包括保守的，高度表达的，和不同的长度和系统发育信息的基因，代表了一个重要的资源，为未来的分子系统学研究Opiliones和其他蛛形纲动物组。
Next-generation sequencing technologies are rapidly transforming molecular systematic studies of non-model animal taxa. The arachnid order Opiliones (commonly known as “harvestmen”) includes more than 6,400 described species placed into four well-supported lineages (suborders). Fossil plus molecular clock evidence indicates that these lineages were diverging in the late Silurian to mid-Carboniferous, with some fossil harvestmen representing the earliest known land animals. Perhaps because of this ancient divergence, phylogenetic resolution of subordinal interrelationships within Opiliones has been difficult. We present the first phylogenomics analysis for harvestmen, derived from comparative RNA-Seq data for eight species representing all suborders. Over 30 gigabases of original Illumina short-read data were used in de novo assemblies, resulting in 50–80,000 transcripts per taxon. Transcripts were compared to published scorpion and tick genomics data, and a stringent filtering process was used to identify over 350 putatively single-copy, orthologous protein-coding genes shared among taxa. Phylogenetic analyses using various partitioning strategies, data coding schemes, and analytical methods overwhelmingly support the “classical” hypothesis of Opiliones relationships, including the higher-level clades Palpatores and Phalangida. Relaxed molecular clock analyses using multiple alternative fossil calibration strategies corroborate ancient divergences within Opiliones that are possibly deeper than the recorded fossil record indicates. The assembled data matrices, comprising genes that are conserved, highly expressed, and varying in length and phylogenetic informativeness, represent an important resource for future molecular systematic studies of Opiliones and other arachnid groups.
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影响因子：
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作者：
Garwood, Russell J.;Dunlop, Jason A.;Sutton, Mark D.
通讯作者：
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影响因子：
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Crandall KA
DOI：
10.1098/rspb.2005.3063
发表时间：
2005-05-22
影响因子：
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作者：
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通讯作者：
Dunlop, JA
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作者：
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