High-throughput sequencing of the chloroplast and mitochondrion of Chlamydomonas reinhardtii to generate improved de novo assemblies, analyze expression patterns and transcript speciation, and evaluate diversity among laboratory strains and wild isolates.
High-throughput sequencing of the chloroplast and mitochondrion of Chlamydomonas reinhardtii to generate improved de novo assemblies, analyze expression patterns and transcript speciation, and evaluate diversity among laboratory strains and wild isolates.
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叶绿体和线粒体的高通量测序reinhardtii生成改进的从头组装，分析表达模式和转录物种形成，并评估实验室菌株和野生分离株之间的多样性。
DOI：
10.1111/tpj.13788
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发表时间：
2018-03
期刊：
影响因子：
--
通讯作者：
Merchant SS
中科院分区：
文献类型：
--
作者：
Gallaher SD;Fitz-Gibbon ST;Strenkert D;Purvine SO;Pellegrini M;Merchant SS
莱茵衣藻是一种单细胞的绿藻，作为了解光合作用、感觉和运动纤毛以及开发用于生产生物燃料和生物产品的基于藻类的平台的参考生物被广泛研究。在高通量测序技术出现之前，其高度重复的~205 kbp环状叶绿体基因组和~15.8 kbp线性线粒体基因组被测序。在这里，高覆盖率鸟枪测序用于从头组装两个细胞器基因组。这些新的基因组纠正了先前基因组序列和注释中的数十个错误。基因组测序覆盖率表明每个细胞平均含有83个叶绿体基因组拷贝和130个线粒体基因组拷贝。使用针对细胞器转录物优化的方案和分析，RNA-Seq用于量化它们在12种不同生长条件下的相对丰度。细胞总mRNA的46%归因于几十个叶绿体基因的高表达。RNA-Seq数据用于指导基因注释，以证明多顺反子基因表达，并定量psaA和psbA内含子的剪接。与最近一项研究的结论相反，我们发现叶绿体转录本没有被编辑。出乎意料的是，在所有线粒体转录物的3′端观察到富含胞嘧啶的多核苷酸尾。对8株实验室分离株和11株野生分离株进行了比较基因组学分析。reinhardtii在细胞器基因组中鉴定了2658个变异体，这是细胞核中发现的遗传多样性的十分之一。
Chlamydomonas reinhardtii is a unicellular chlorophyte alga that is widely-studied as a reference organism for understanding photosynthesis, sensory and motile cilia, and for development of an algal-based platform for producing biofuels and bio-products. Its highly repetitive, ~205 kbp circular chloroplast genome and ~15.8 kbp linear mitochondrial genome were sequenced prior to the advent of high-throughput sequencing technologies. Here, high coverage shotgun sequencing was used to assemble both organellar genomes de novo. These new genomes correct dozens of errors in the prior genome sequences and annotations. Genome sequencing coverage indicates that each cell contains on average 83 copies of the chloroplast genome and 130 copies of the mitochondrial genome. Using protocols and analyses optimized for organellar transcripts, RNA-Seq was used to quantify their relative abundances across 12 different growth conditions. 46% of total cellular mRNA is attributable to high expression from a few dozen chloroplast genes. RNA-Seq data were used to guide gene annotation, to demonstrate polycistronic gene expression, and to quantify splicing of psaA and psbA introns. In contrast to a conclusion from a recent study, we found that chloroplast transcripts are not edited. Unexpectedly, cytosine-rich polynucleotide tails were observed at the 3′ end of all mitochondrial transcripts. A comparative genomics analysis of 8 laboratory strains and 11 wild isolates of C. reinhardtii identified 2658 variants in the organellar genomes, which is one tenth as much genetic diversity as is found in the nucleus.
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核苷酸分辨率上杂合性丧失和单相表达的全基因组丧失的综合分析揭示了三阴性乳腺癌的途径中断。
影响因子：
7
作者：
Ha G;Roth A;Lai D;Bashashati A;Ding J;Goya R;Giuliany R;Rosner J;Oloumi A;Shumansky K;Chin SF;Turashvili G;Hirst M;Caldas C;Marra MA;Aparicio S;Shah SP
通讯作者：
Shah SP
影响因子：
11.6
作者：
Cerutti, H;Johnson, AM;Boynton, JE
通讯作者：
Boynton, JE
影响因子：
1.2
作者：
Cingolani, Pablo;Platts, Adrian;Ruden, Douglas M.
通讯作者：
Ruden, Douglas M.
影响因子：
3.3
作者：
Chen, Chun-Long;Chen, Chong-Jian;Qu, Liang-Hu
通讯作者：
Qu, Liang-Hu
DOI：
10.1007/s004380050368
发表时间：
1997-02-20
期刊：
MOLECULAR AND GENERAL GENETICS
影响因子：
--
作者：
Boudreau, E;Turmel, M;Leu, S
通讯作者：
Leu, S