Rapid Sequencing of the Bamboo Mitochondrial Genome Using Illumina Technology and Parallel Episodic Evolution of Organelle Genomes in Grasses 英文参考文献.docVIP

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Rapid Sequencing of the Bamboo Mitochondrial Genome Using Illumina Technology and Parallel Episodic Evolution of Organelle Genomes in Grasses 英文参考文献.doc

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Rapid Sequencing of the Bamboo Mitochondrial Genome Using Illumina Technology and Parallel Episodic Evolution of Organelle Genomes in Grasses 英文参考文献

RapidSequencingoftheBambooMitochondrialGenome UsingIlluminaTechnologyandParallelEpisodic EvolutionofOrganelleGenomesinGrasses Peng-FeiMa1,2,3,Zhen-HuaGuo2*,De-ZhuLi1,2* 1KeyLaboratoryofBiodiversityandBiogeography,KunmingInstituteofBotany,ChineseAcademyofSciences,Kunming,Yunnan,People’sRepublicofChina,2Plant GermplasmandGenomicsCenter,GermplasmBankofWildSpecies,KunmingInstituteofBotany,ChineseAcademyofSciences,Kunming,Yunnan,People’sRepublicof China,3GraduateUniversityofChineseAcademyofSciences,Beijing,People’sRepublicofChina Abstract Background:Comparedtotheircounterpartsinanimals,themitochondrial(mt)genomesofangiospermsexhibitanumber of unique features. However, unravelling their evolution is hindered by the few completed genomes, of which are essentially Sanger sequenced. While next-generation sequencing technologies have revolutionized chloroplast genome sequencing,theyarejustbeginningtobeappliedtoangiospermmtgenomes.Chloroplastgenomesofgrasses(Poaceae) haveundergoneepisodicevolutionandtheevolutionaryratewassuggestedtobecorrelatedbetweenchloroplastandmt genomesinPoaceae.Itisinterestingtoinvestigatewhethercorrelatedratechangealsooccurredingrassmtgenomesas expectedunderlineageeffects.Atime-calibratedphylogenetictreeisneededtoexamineratechange. Methodology/Principal Findings: We determined a largely completed mt genome from a bamboo, Ferrocalamus rimosivaginus (Poaceae), through Illumina sequencing of total DNA. With combination of de novo and reference-guided assembly, 39.5-fold coverage Illumina reads were finally assembled into scaffolds totalling 432,839bp. The assembled genomecontainsnearlythesamegenesasthecompletedmtgenomesinPoaceae.Forexaminingevolutionaryrateingrass mt genomes, we reconstructed a phylogenetic tree including 22 taxa based on 31 mt genes. The topology of the well- resolvedtreewasalmostidenticaltothatinferredfromchloroplastgenomewithonlyminordifference.Theinconsistency possiblyderivedfromlongbranchattractioninmtDNAtree.Bycalculatingabsolutesub