Complete Chloroplast Genome Sequencing and Phylogenetic Analysis of Two <i>Dracocephalum</i> Plants

Yao, Junjun; Zhao, Fangyu; Xu, Yan; Zhao, Kaihui; Hong, Quan; Su, Yanjie; Hao, Peiyu; Liu, Jiang; Yu, Benxia; Yao, Min; Ma, Xiaojing; Liao, Zhihua; Lan, Xiaozhong

doi:10.1155/2020/4374801

Cited by 22 publications

(13 citation statements)

References 39 publications

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“…In this study, SSR and long repeat analyses of plastomes showed variations among Garcinia species and varieties of G. mangostana . This supports that both molecular markers are useful for species identification and taxonomic studies 62–64 .…”

Section: Discussionsupporting

confidence: 77%

Plastomes of Garcinia mangostana L. and comparative analysis with other Garcinia species

Wee

Muhammad

Subbiah

et al. 2022

Preprint

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The two varieties of mangosteen (Garcinia mangostana L.) cultivated in Malaysia are known as Manggis and Mesta. The latter is preferred for its flavor, texture, and seedlessness. Here, we report a complete plastome (156,580 bp) of the Mesta variety which was obtained through a hybrid assembly approach using PacBio and Illumina sequencing reads. It encompasses a large single-copy (LSC) region (85,383 bp) and a small single-copy (SSC) region (17,137 bp) that are separated by 27,230 bp of inverted repeat (IR) regions at both ends. The plastome comprises 128 genes, namely 83 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The plastome of the Manggis variety (156,582 bp) obtained from reference-guided assembly of Illumina reads was found to be nearly identical to Mesta except for two indels and the presence of a single nucleotide polymorphism (SNP). Comparative analyses with other publicly available Garcinia plastomes, including G. anomala, G. gummi-gutta, G. mangostana var. Thailand, G. oblongifolia, G. paucinervis, and G. pedunculata found that the gene content, gene order, and gene orientation were highly conserved among the Garcinia species. Phylogenomic analysis divided the six Garcinia plastomes into three groups with the Mesta and Manggis varieties clustered closer to G. anomala, G. gummi-gutta, and G. oblongifolia, while the Thailand variety clustered with G. pedunculata in another group. These findings serve as future references for the identification of species or varieties and facilitate phylogenomic analysis of lineages from the Garcinia genus to better understand their evolutionary history.

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Section: Discussionsupporting

confidence: 77%

Plastomes of Garcinia mangostana L. and comparative analysis with other Garcinia species

Wee

Muhammad

Subbiah

et al. 2022

Preprint

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“…The DNA samples were then subjected to quality and quantity checks using 1% agarose gel electrophoresis and spectrophotometric methods measured by a Nanodrop ND1000 spectrophotometer [19]. High-quality cp DNA was used to prepare a library with an insert size of 350 bp, which was then sequenced on an Illumina Novaseq platform [20] at Nanjing Genepioneer Biotechnologies Inc. (Nanjing, China).…”

Section: Dna Extraction and Sequencingmentioning

confidence: 99%

Analyses of Chloroplast Genome of Eutrema japonicum Provide New Insights into the Evolution of Eutrema Species

Zhang

et al. 2021

Agronomy

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Wasabi (Eutrema japonicum) is a vegetable of Brassicaceae family, currently cultivated in Southwest Asia. It is rich in nutritional and has a spicy flavour. It is regarded as a rare condiment worldwide. Its genetic profile for yield improvement and the development of E. japonicum germplasm resources remains unknown. Cognizant of this, this study sequenced and assembled the chloroplast (cp) genome of E. japonicum to enrich our genomic information of wasabi and further understand genetic relationships within the Eutrema species. The structural characteristics, phylogeny, and evolutionary relationship of cp genomes among other Brassicaceae plants were analyzed and compared to those of Eutrema species. The cp genome of E. japonicum has 153,851 bp with a typical quadripartite structure, including 37 tRNA genes, 8 rRNA genes, and 87 protein-coding genes. It contains 290 simple sequence repeats and prefers to end their codons with an A or T, which is the same as other Brassicaceae species. Moreover, the cp genomes of the Eutrema species had a high degree of collinearity and conservation during the evolution process. Nucleotide diversity analysis revealed that genes in the IR regions had higher Pi values than those in LSC (Large single copy) and SSC (Small single copy) regions, making them potential molecular markers for wasabi diversity studies. The analysis of genetic distance between Eutrema plants and other Brassicacea plants showed that intraspecies variation was found to be low, while large differences were found between genera and species. Phylogenetic analysis based on 29 cp genomes revealed the existence of a close relationship amongst the Eutrema species. Overall, this study provides baseline information for cp genome-based molecular breeding and genetic transformation studies of Eutrema plants.

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“… 2003 ; Yao et al. 2020 ). The IR sizes of published Phalaenopsis plastid genomes are 24,719 ( P. lobbii ) (Wang et al.…”

Section: Discussionmentioning

confidence: 99%

“…In our present study, the complete plastid genome of P. zhejiangensis is only 143,574 bp in length, which turns out to be the smallest among all known cp genome sequences in genus Phalaenopsis. The cp genomes of most flowering plants range from 120 kb to 160 kb, and the difference in genome size is mainly caused by contraction and expansion of the IR region (Goulding et al 1996;Ingvarsson et al 2003;Yao et al 2020). The IR sizes of published Phalaenopsis plastid genomes are 24,719 (P. lobbii) (Wang et al 2019) to 25,846 bp (P. equestris) (Jheng et al 2012).…”

Section: Discussionmentioning

confidence: 99%

Complete chloroplast genome of a rare and endangered plant species Phalaenopsis zhejiangensis: genomic features and phylogenetic relationship within Orchidaceae

Jiang

Zhu

et al. 2021

Mitochondrial DNA Part B

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Phalaenopsis zhejiangensis is a rare and endangered plant species with extremely small populations. The complete chloroplast (cp) genome of P. zhejiangensis was assembled, its structural organization was described and comparative genomic analyses was carried out. The cp genome of P. zhejiangensis is 143,547 bp in length, with a GC content of 37.2%, which includes a pair of inverted repeats (IRs) of 24,464 bp separated by a small single-copy region of 10,764 bp and a large single-copy region of 83,856 bp. The cp genome contains 126 genes, consisting of 80 protein-coding genes, 38 transfer RNAs, and eight ribosomal RNAs. Six protein-coding genes, including ψndhB (two copies), ψndhD , ψndhG , ψndhK , and ψndhI , are identified as pseudogenes. Another six ndh genes, ndhA , ndhC , ndhE , ndhF , ndhH , and ndhJ , are missing from the plastid genome. A total of 41 cp simple sequence repeats (SSRs) were identified, including 40 mono-nucleotides and one di-nucleotides. Phylogenic analysis revealed P. zhejiangensis was nested inside the Phalaenopsis species and sister to P. wilsonii . The assembly and analysis of P. zhejiangensis cp genome will provide essential data for further study of taxonomy and systematics of Orchidaceae.

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Complete Chloroplast Genome Sequencing and Phylogenetic Analysis of Two Dracocephalum Plants

Cited by 22 publications

References 39 publications

Plastomes of Garcinia mangostana L. and comparative analysis with other Garcinia species

Plastomes of Garcinia mangostana L. and comparative analysis with other Garcinia species

Analyses of Chloroplast Genome of Eutrema japonicum Provide New Insights into the Evolution of Eutrema Species

Complete chloroplast genome of a rare and endangered plant species Phalaenopsis zhejiangensis: genomic features and phylogenetic relationship within Orchidaceae

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