Jackman Shaun D, Warren René L, Gibb Ewan A, Vandervalk Benjamin P, Mohamadi Hamid, Chu Justin, Raymond Anthony, Pleasance Stephen, Coope Robin, Wildung Mark R, Ritland Carol E, Bousquet Jean, Jones Steven J M, Bohlmann Joerg, Birol Inanç
Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada.
School of Molecular Biosciences, Washington State University.
Genome Biol Evol. 2015 Dec 8;8(1):29-41. doi: 10.1093/gbe/evv244.
The genome sequences of the plastid and mitochondrion of white spruce (Picea glauca) were assembled from whole-genome shotgun sequencing data using ABySS. The sequencing data contained reads from both the nuclear and organellar genomes, and reads of the organellar genomes were abundant in the data as each cell harbors hundreds of mitochondria and plastids. Hence, assembly of the 123-kb plastid and 5.9-Mb mitochondrial genomes were accomplished by analyzing data sets primarily representing low coverage of the nuclear genome. The assembled organellar genomes were annotated for their coding genes, ribosomal RNA, and transfer RNA. Transcript abundances of the mitochondrial genes were quantified in three developmental tissues and five mature tissues using data from RNA-seq experiments. C-to-U RNA editing was observed in the majority of mitochondrial genes, and in four genes, editing events were noted to modify ACG codons to create cryptic AUG start codons. The informatics methodology presented in this study should prove useful to assemble organellar genomes of other plant species using whole-genome shotgun sequencing data.
白云杉（Picea glauca）质体和线粒体的基因组序列是使用ABySS从全基因组鸟枪法测序数据中组装而成的。测序数据包含来自核基因组和细胞器基因组的 reads，并且细胞器基因组的reads在数据中很丰富，因为每个细胞都含有数百个线粒体和质体。因此，通过分析主要代表核基因组低覆盖度的数据集，完成了123 kb质体和5.9 Mb线粒体基因组的组装。对组装好的细胞器基因组的编码基因、核糖体RNA和转运RNA进行了注释。使用RNA-seq实验的数据，对三个发育组织和五个成熟组织中线粒体基因的转录本丰度进行了定量。在大多数线粒体基因中观察到了C到U的RNA编辑，并且在四个基因中，发现编辑事件将ACG密码子修改为隐蔽的AUG起始密码子。本研究中提出的信息学方法应该被证明对于使用全基因组鸟枪法测序数据组装其他植物物种的细胞器基因组是有用的。
