Characterization of the whole chloroplast genome of Chikusichloa mutica and its comparison with other rice tribe (Oryzeae) species

Wu, Zhiqiang; Gu, Cuihua; Tembrock, Luke R.; Zhang, Dong; Ge, Song

doi:10.1371/journal.pone.0177553

Cited by 15 publications

(12 citation statements)

References 64 publications

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“…There were more repeat sequences in the expanded portion, meaning that repeat sequences influenced the expansion or contraction of the cpDNA and partially led to the difference in cpDNA sizes. Our results were consistent with Wu’s study in rice, which indicates the main source of cp length variation is coming from mononucleotide SSRs ( Wu et al, 2017 ). The variation in cpDNA size may influence energy generation and ecological strategy ( Zheng et al, 2017 ) and provide more information for phylogenic study.…”

Section: Discussionsupporting

confidence: 93%

Phylogenic study of Lemnoideae (duckweeds) through complete chloroplast genomes for eight accessions

Ding

Fang

Guo

et al. 2017

PeerJ

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BackgroundPhylogenetic relationship within different genera of Lemnoideae, a kind of small aquatic monocotyledonous plants, was not well resolved, using either morphological characters or traditional markers. Given that rich genetic information in chloroplast genome makes them particularly useful for phylogenetic studies, we used chloroplast genomes to clarify the phylogeny within Lemnoideae.MethodsDNAs were sequenced with next-generation sequencing. The duckweeds chloroplast genomes were indirectly filtered from the total DNA data, or directly obtained from chloroplast DNA data. To test the reliability of assembling the chloroplast genome based on the filtration of the total DNA, two methods were used to assemble the chloroplast genome of Landoltia punctata strain ZH0202. A phylogenetic tree was built on the basis of the whole chloroplast genome sequences using MrBayes v.3.2.6 and PhyML 3.0.ResultsEight complete duckweeds chloroplast genomes were assembled, with lengths ranging from 165,775 bp to 171,152 bp, and each contains 80 protein-coding sequences, four rRNAs, 30 tRNAs and two pseudogenes. The identity of L. punctata strain ZH0202 chloroplast genomes assembled through two methods was 100%, and their sequences and lengths were completely identical. The chloroplast genome comparison demonstrated that the differences in chloroplast genome sizes among the Lemnoideae primarily resulted from variation in non-coding regions, especially from repeat sequence variation. The phylogenetic analysis demonstrated that the different genera of Lemnoideae are derived from each other in the following order: Spirodela, Landoltia, Lemna, Wolffiella, and Wolffia.DiscussionThis study demonstrates potential of whole chloroplast genome DNA as an effective option for phylogenetic studies of Lemnoideae. It also showed the possibility of using chloroplast DNA data to elucidate those phylogenies which were not yet solved well by traditional methods even in plants other than duckweeds.

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Section: Discussionsupporting

confidence: 93%

Phylogenic study of Lemnoideae (duckweeds) through complete chloroplast genomes for eight accessions

Ding

Fang

Guo

et al. 2017

PeerJ

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“…DOGMA is the most popular software for cp genome annotation and is used widely 27 – 30 . This software can detect protein-coding genes, rRNA, and tRNA quickly.…”

Section: Discussionmentioning

confidence: 99%

Complete chloroplast genome sequence of Dryopteris fragrans (L.) Schott and the repeat structures against the thermal environment

Gao

Wang

Huang

et al. 2018

Sci Rep

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Dryopteris fragrans (L.) Schott is a fern growing on the surface of hot rocks and lava. It is exposed to sunlight directly and bears local hot environment. We sequenced the complete nucleotide sequence of its chloroplast (cp) genome. The cp genome was 151,978 bp in length, consisting of a large single-copy region (85,332 bp), a small single-copy region (31,947 bp) and a pair of inverted repeats (17,314 bp). The cp genome contained 112 genes and 345 RNA editing sites in protein-coding genes. Simple sequence repeats (SSRs) and long repeat structure pairs (30–55 bp) were identified. The number and percent of repeat structures are extremely high in ferns. Thermal denaturation experiments showed its cp genome to have numerous, dispersed and high GC percent repeat structures, which conferred the strongest thermal stability. This repeat-heavy genome may provide the molecular basis of how D. fragrans cp survives its hot environment.

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“…The progress of high-throughput sequencing technologies and the relatively simple assembling process of cpDNA gave a huge boost to genomic and phylogenetic studies [ 5 , 6 , 7 , 8 ]. As chloroplast genomes are characterized by a high number of potentially informative nucleotide sites, they became an efficient and cost-effective option for evolutionary and comparative genomic research in higher plants [ 9 , 10 , 11 , 12 , 13 , 14 ].…”

Section: Introductionmentioning

confidence: 99%

The Complete Plastome Sequences of Eleven Capsicum Genotypes: Insights into DNA Variation and Molecular Evolution

D’Agostino¹,

Tamburino

Cantarella³

et al. 2018

Genes

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Members of the genus Capsicum are of great economic importance, including both wild forms and cultivars of peppers and chilies. The high number of potentially informative characteristics that can be identified through next-generation sequencing technologies gave a huge boost to evolutionary and comparative genomic research in higher plants. Here, we determined the complete nucleotide sequences of the plastomes of eight Capsicum species (eleven genotypes), representing the three main taxonomic groups in the genus and estimated molecular diversity. Comparative analyses highlighted a wide spectrum of variation, ranging from point mutations to small/medium size insertions/deletions (InDels), with accD, ndhB, rpl20, ycf1, and ycf2 being the most variable genes. The global pattern of sequence variation is consistent with the phylogenetic signal. Maximum-likelihood tree estimation revealed that Capsicum chacoense is sister to the baccatum complex. Divergence and positive selection analyses unveiled that protein-coding genes were generally well conserved, but we identified 25 positive signatures distributed in six genes involved in different essential plastid functions, suggesting positive selection during evolution of Capsicum plastomes. Finally, the identified sequence variation allowed us to develop simple PCR-based markers useful in future work to discriminate species belonging to different Capsicum complexes.

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Characterization of the whole chloroplast genome of Chikusichloa mutica and its comparison with other rice tribe (Oryzeae) species

Cited by 15 publications

References 64 publications

Phylogenic study of Lemnoideae (duckweeds) through complete chloroplast genomes for eight accessions

Phylogenic study of Lemnoideae (duckweeds) through complete chloroplast genomes for eight accessions

Complete chloroplast genome sequence of Dryopteris fragrans (L.) Schott and the repeat structures against the thermal environment

The Complete Plastome Sequences of Eleven Capsicum Genotypes: Insights into DNA Variation and Molecular Evolution

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