Complete chloroplast genome sequence of Pedicularis cheilanthifolia, an alpine plant in China

Zhang, Ruiting; Wang, Jiao; Han, Kai; Ren, Tao; Zeng, Shuyun; Biffin, Ed; Liu, Zhan‐Lin

doi:10.1007/s12686-017-0740-2

Cited by 4 publications

(5 citation statements)

References 4 publications

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“…The genome comprises two IR regions of 24,916 bp separated by an LSC region (82,718 bp) and SSC region (15,257 bp), with a total of 117 genes: 72 coding genes, 8 rRNAs, and 37 tRNAs. Almost all ndh genes, except for ndhB, were lost, which contrasts with the previous result (Zhang et al 2017). Additionally, loss of rps16 was found in the chloroplast genome of P. verticillata but not P. cheilanthifolia.…”

contrasting

confidence: 97%

“…Almost all ndh genes are pseudogenized, truncated, or deleted, except ndhB of the IR region. The previously reported P. cheilanthifolia genome was only pseudogenized for ndhF (Zhang et al 2017), in contrast to other Pedicularis (Cho et al 2018;Wu et al 2019). Accordingly, we re-identified the P. cheilanthifolia gene content.…”

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confidence: 87%

“…Pedicularis L. is a core member of Orobanchaceae. The first complete chloroplast genome sequence of Pedicularis genus was reported for P. cheilanthifolia Schrenk in 2017 (Zhang et al 2017). The chloroplast genomes reported for four other Pedicularis species demonstrated drastic changes in genome structure, mainly characterized by the loss of ndh and expansion of inverted repeat (IR) regions (Cho et al 2018;Wu et al 2019).…”

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confidence: 99%

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Complete chloroplast genome sequence of Pedicularis verticillata and chloroplast genome reconstruction of P. cheilanthifolia (Orobanchaceae)

Cho

Han²,

Choi

et al. 2020

Mitochondrial DNA Part B

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We here report the complete chloroplast genome of Pedicularis verticillata and the reconstructed chloroplast genome of Pedicularis cheilanthifolia, the first such genome reported for this genus. The P. verticillata genome is 142,733 bp, including a 24,984-bp inverted repeat (IR) region, 89,723-bp large single-copy (LSC) region, and 12,042-bp small single copy (SSC) region, and the P. cheilanthifolia genome is 147,807 bp (IRs: 24,916 bp; LSC: 82,718 bp; SSC: 15,257 bp). The chloroplast genome of P. verticillata contains 116 genes, including 71 coding genes, 8 rRNAs, and 37 tRNAs. In the genomes of both species, 10 ndh genes are lost and ndhB was identified in the IR region. Additionally, rps16 is also lost in P. verticillata but not in P. cheilanthifolia. The maximum-likelihood phylogenetic tree showed that Pedicularis is a monophyletic and sister group to other hemi-parasitic species in Orobanchaceae.

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confidence: 97%

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confidence: 87%

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confidence: 99%

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Complete chloroplast genome sequence of Pedicularis verticillata and chloroplast genome reconstruction of P. cheilanthifolia (Orobanchaceae)

Cho

Han²,

Choi

et al. 2020

Mitochondrial DNA Part B

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“…Pseudogenization and gene deletions were common and lineage-specific, with the ndh genes involved in electron recycling being particularly often and independently lost [ 29 ]. It is suggested that the ndh pathway is redundant in some species of Uncaria spp., and it may even be selected against [ 36 ]. Further investigation into the nature of cp genome modification should yield a new understanding of which genetic (and thus physiological) functions are lost.…”

Section: Discussionmentioning

confidence: 99%

Characterization and Comparative Analysis of Chloroplast Genomes in Five Uncaria Species Endemic to China

Chen

Zhang

Liang

et al. 2022

IJMS

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Uncaria, a perennial vine from the Rubiaceae family, is a typical Chinese traditional medicine. Currently, uncertainty exists over the Uncaria genus’ evolutionary relationships and germplasm identification. The complete chloroplast genomes of four Uncaria species mentioned in the Chinese Pharmacopoeia and Uncaria scandens (an easily confused counterfeit) were sequenced and annotated. The findings demonstrated that the whole chloroplast genome of Uncaria genus is 153,780–155,138 bp in full length, encoding a total of 128–131 genes, containing 83–86 protein-coding genes, eight rRNAs and 37 tRNAs. These regions, which include eleven highly variable loci and 31–49 SSRs, can be used to create significant molecular markers for the Uncaria genus. The phylogenetic tree was constructed according to protein-coding genes and the whole chloroplast genome sequences of five Uncaria species using four methods. The topology of the two phylogenetic trees showed no difference. The sequences of U. rhynchophylla and U. scandens are clustered in one group, while the U. hirsuta and U. macrophylla are clustered in another group. U. sessilifructus is clustered together with the above two small clades. New insights on the relationship were revealed via phylogenetic research in five Uncaria species. This study will provide a theoretical basis for identifying U. rhynchophylla and its counterfeits, as well as the species of the Uncaria genus. This research provides the initial chloroplast genome report of Uncaria, contributes to elucidating the chloroplast genome evolution of Uncaria in China.

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“…The Elymus nutans belongs to Elymus of Gramineae, which mainly distributes in northwest of China with an average elevation 3000-4000 m, even exists in Himalayan area with altitude over 5200 m (Qiao et al 2006). It has strong stress resistance and adaptation to cold and dry environment in Qinghai-Tibetan Plateau (QTP), which is one of the indispensable forages for yaks (Zhang et al 2017). However, the rapidly increasing population of grazing yak and the destruction of ecological system caused deterioration of natural grassland, so wild E. nutans severely shrunk on the QTP.…”

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The characterization of the complete chloroplast genome of wild Elymus nutans

Yang

Guo

et al. 2019

Mitochondrial DNA Part B

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2019) The characterization of the complete chloroplast genome of wild Elymusnutans, Mitochondrial DNA Part B, 4:1, 925-926, ABSTRACTElymus nutans is an alpine plant, which plays an important role in maintaining ecological system and the development of animal husbandry in the Tibetan region of China. However, the population of wild E. nutans notably decreased in recent years with overgrazing and ecological environment deterioration, and the germplasm resources have been threatened. This study reported a complete circular chloroplast genome of E. nutans, which was 134,147 bp in length, containing a pair of inverted repeats (IRs) of 10,541 bp separated by one small single copy (SSC) region of 14,036 bp and one large single copy (LSC) region of 99,029 bp. A total of 123 genes, including 87 protein-coding genes, 32 transfer RNA genes and four ribosomal RNA genes were predicted from the chloroplast genomes. The overall GC content of the chloroplast genome was 38.34% and the corresponding values of the IR, SSC and LSC were 48.7%, 32.4% and 37.0%, respectively. The results of phylogenetic analysis showed that wild E. nutans was clustered closely with Triticum aestivum. ARTICLE HISTORY

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Complete chloroplast genome sequence of Pedicularis cheilanthifolia, an alpine plant in China

Cited by 4 publications

References 4 publications

Complete chloroplast genome sequence of Pedicularis verticillata and chloroplast genome reconstruction of P. cheilanthifolia (Orobanchaceae)

Complete chloroplast genome sequence of Pedicularis verticillata and chloroplast genome reconstruction of P. cheilanthifolia (Orobanchaceae)

Characterization and Comparative Analysis of Chloroplast Genomes in Five Uncaria Species Endemic to China

The characterization of the complete chloroplast genome of wild Elymus nutans

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