Integrated shotgun sequencing and bioinformatics pipeline allows ultra-fast mitogenome recovery and confirms substantial gene rearrangements in Australian freshwater crayfishes.
Integrated shotgun sequencing and bioinformatics pipeline allows ultra-fast mitogenome recovery and confirms substantial gene rearrangements in Australian freshwater crayfishes.
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DOI：
10.1186/1471-2148-14-19
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发表时间：
2014-02-03
影响因子：
3.4
通讯作者：
Austin CM
中科院分区：
文献类型：
--
作者：
Gan HM;Schultz MB;Austin CM
虽然可以直接从鸟枪测序数据中恢复完整的有丝分裂基因组，但目前报道的方法和管道仍然相对耗时且昂贵。使用澳大利亚淡水小龙虾Engaeus damnana的样品，我们证明了通过整合MiSeq测序平台，Nextera样品制备方案，MITObim组装算法和MITOS注释管道，可以实现从组织样品到NCBI就绪提交文件的三天周转时间（四小时动手时间）。使用Illumina MiSeq台式测序平台，通过适度的鸟枪测序（1.2 giga碱基）回收了寄生酸淡水小龙虾Engaeus damnana的完整线粒体基因组。使用MITObim有丝分裂基因组组装器的基因组组装将线粒体基因组回收为具有97倍平均覆盖率的单个重叠群（最小= 17;最大= 17）。= 138）。有丝分裂基因组由15，934个碱基对组成，包含典型的37个线粒体基因和一个非编码AT富集区。基因组排列类似于唯一其他已发表的来自澳大利亚Cherax属的寄生酸有丝分裂基因组。我们推断，在Cherax destructor中发现的基因顺序排列是常见的澳大利亚小龙虾，可能是南半球家庭Parastacidae的衍生功能。此外，据我们所知，我们报告了使用MiSeq台式测序仪恢复和组装完整线粒体基因组的最简单和最快的协议。
Although it is possible to recover the complete mitogenome directly from shotgun sequencing data, currently reported methods and pipelines are still relatively time consuming and costly. Using a sample of the Australian freshwater crayfish Engaeus lengana, we demonstrate that it is possible to achieve three-day turnaround time (four hours hands-on time) from tissue sample to NCBI-ready submission file through the integration of MiSeq sequencing platform, Nextera sample preparation protocol, MITObim assembly algorithm and MITOS annotation pipeline. The complete mitochondrial genome of the parastacid freshwater crayfish, Engaeus lengana, was recovered by modest shotgun sequencing (1.2 giga bases) using the Illumina MiSeq benchtop sequencing platform. Genome assembly using the MITObim mitogenome assembler recovered the mitochondrial genome as a single contig with a 97-fold mean coverage (min. = 17; max. = 138). The mitogenome consists of 15,934 base pairs and contains the typical 37 mitochondrial genes and a non-coding AT-rich region. The genome arrangement is similar to the only other published parastacid mitogenome from the Australian genus Cherax. We infer that the gene order arrangement found in Cherax destructor is common to Australian crayfish and may be a derived feature of the southern hemisphere family Parastacidae. Further, we report to our knowledge, the simplest and fastest protocol for the recovery and assembly of complete mitochondrial genomes using the MiSeq benchtop sequencer.
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影响因子：
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