Complete Mitochondrial Genome of Eruca sativa Mill. (Garden Rocket)

Wang, Yankun; Chu, Pu; Yang, Qing; Chang, Shengxin; Chen, Jianmei; Hu, Meijiao; Guan, Rongzhan

doi:10.1371/journal.pone.0105748

Cited by 16 publications

(10 citation statements)

References 41 publications

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“…Only one complete mitochondrial genome of a gymnosperm has been published so far ( Cycas taitungensis [ Chaw et al 2008 ]), whereas complete mitochondrial genome sequences of the angiosperms Brassica maritima ( Grewe et al 2014 ), Brassica oleracea ( Grewe et al 2014 ), Capsicum annuum ( Jo et al 2014 ), Eruca sativa ( Wang et al 2014 ), Helianthus tuberosus ( Bock et al 2014 ), Raphanus sativus ( Jeong et al 2014 ), Rhazya stricta ( Park et al 2014 ) and Vaccinium macrocarpon ( Fajardo et al 2014 ) have been deposited in NCBI GenBank. Six of these projects gave details of the sample preparation, sequencing, assembly, and annotation strategy.…”

Section: Introductionmentioning

confidence: 99%

Organellar Genomes of White Spruce (Picea glauca): Assembly and Annotation

et al. 2015

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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.

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Section: Introductionmentioning

confidence: 99%

Organellar Genomes of White Spruce (Picea glauca): Assembly and Annotation

et al. 2015

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“…Common translocation Proto-Calepineae Karyotype (tPCK)-like ancestors were deduced to be the likely common ancestor of all current Brassiceae species that had undergone WGT and repetitive chromosomal rearrangements. Phylogenetic analysis based on 32 mitochondrial protein-coding genes suggested that Eruca sativa is closer to the Brassica species and Raphanussativus than to Arabidopsis thaliana [43]. The U's Triangle theory were accordingly revisited and extended into a multi-vertex model [42], which should include not only Raphanus, but also Eruca, Moricandia and Sinapis species as basic diploid species as suggested herein by our studies (Figure 6).…”

Section: Strong Parallel Evolution Among Brassica and Several Relativmentioning

confidence: 84%

Comparison of the cytoplastic genomes by resequencing: insights into the genetic diversity and the phylogeny of the agriculturally important genus Brassica

Qiao

Zhang

Huang³

et al. 2020

Preprint

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Background: The genus Brassica mainly comprises three diploid and three recently derived allotetraploid species, most of which are highly important vegetable, oil or ornamental crops cultivated worldwide. Despite being extensively studied, the origination of B. napus and certain detailed interspecific relationships within Brassica genus remains undetermined and somewhere confused. In the current high-throughput sequencing era, a systemic comparative genomic study based on a large population is necessary and would be crucial to resolve these questions. Results: The chloroplast DNA and mitochondrial DNA were synchronously resequenced in a selected set of Brassica materials, which contain 72 accessions and maximally integrated the known Brassica species. The Brassica genomewide cpDNA and mtDNA variations have been identified. Detailed phylogenetic relationships inside and around Brassica genus have been delineated by the cpDNA- and mtDNA- variation derived phylogenies. Different from B. juncea and B. carinata, the natural B. napus contains three major cytoplasmic haplotypes: the cam-type which directly inherited from B. rapa, polima-type which is close to cam-type as a sister, and the mysterious but predominant nap-type. Certain sparse C-genome wild species might have primarily contributed the nap-type cytoplasm and the corresponding C subgenome to B. napus, implied by their con-clustering in both phylogenies. The strictly concurrent inheritance of mtDNA and cpDNA were dramatically disturbed in the B. napus cytoplasmic male sterile lines (e.g., mori and nsa). The genera Raphanus, Sinapis, Eruca, Moricandia show a strong parallel evolutional relationships with Brassica. Conclusions: The overall variation data and elaborated phylogenetic relationships provide further insights into genetic understanding of Brassica, which can substantially facilitate the development of novel Brassica germplasms.

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“…Since the first mitochondrial genome was sequenced in Arabidopsis (Unseld et al, 1997), a huge number of mitochondrial genomes have been sequenced in angiosperms, such as beetroot (Kubo et al, 2000), rice (Notsu et al, 2002), rapeseed (Handa, 2003), corn (Clifton et al, 2004), wheat (Ogihara et al, 2005), Indian mustard (Heng et al, 2014) and arugula (Wang et al, 2014).…”

Section: Discussionmentioning

confidence: 99%