Accurate authentication of Dendrobium officinale and its closely related species by comparative analysis of complete plastomes

Zhu, Shuifang; Niu, Zhitao; Xue, Quan; Wang, Hui; Xie, Xuezhu; Ding, Xiaoyu

doi:10.1016/j.apsb.2018.05.009

Cited by 56 publications

(54 citation statements)

References 56 publications

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“…In contrast, here, we found that the length of Bulbophyllum plastid genomes is determined by the contraction and expansion of the SSC due to the independent loss of the seven ndh genes present in this region. The pronounced effect of the gain/loss of ndh genes in the SSC has been previously reported (Chang et al, 2006;Jheng et al, 2012;Kim et al, 2015;Zhu et al, 2018), but only in Zhitao et al (2017) was the influence of LSC, IR, and SSC length on the genome size measured. As a result, they found that variation in LSC length plays an important role in plastid genome-size variation.…”

Section: Discussion Plastid Genome Featuresmentioning

confidence: 56%

“…Only four of the 10 most-variable markers identified for Bulbophyllum are shared with its sister genus, Dendrobium (trnR-atpA, psbB-psbT, rpl32-trnL, and clpP-psbB). Among the other six regions, two (matK-trnK and trnS-trnG) were identified by Niu et al (2017a;2017c) and Zhu et al (2018), whereas four (atpH-atpI, ccsA-ndhD, psbK-psbI, and trnM-aptE) are reported for the first time here as highly variable in Orchidaceae. Previous markers used in Bulbophyllum analyses proved here not to be highly variable; for example, Smidt et al (2011) used psbA-trnH and trnS-trnG for the Neotropical sections of Bulbophyllum.…”

Section: Hypervariable Regionsmentioning

confidence: 72%

“…However, different IR/SSC patterns have been reported in Orchidaceae (Yang et al, 2013;Luo et al, 2014;Niu et al, 2017a;Dong et al, 2018;Zhu et al, 2018). According to Kim et al (2015), the stability of the IR/SSC junctions is highly affected by loss/gain of the ndh genes, especially ndhF, the absence of which could create complicated modifications like shifts in the IR border gene, length reduction of ycf1 (less than 1 kb), and changes in ycf1 position within the IR.…”

Section: Discussion Plastid Genome Featuresmentioning

confidence: 99%

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Comparative Plastid Genomics of Neotropical Bulbophyllum (Orchidaceae; Epidendroideae)

et al. 2020

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Pantropical Bulbophyllum, with ∼2,200 species, is one of the largest genera in Orchidaceae. Although phylogenetics and taxonomy of the ∼60 American species in the genus are generally well understood, some species complexes need more study to clearly delimit their component species and provide information about their evolutionary history. Previous research has suggested that the plastid genome includes phylogenetic markers capable of providing resolution at low taxonomic levels, and thus it could be an effective tool if these divergent regions can be identified. In this study, we sequenced the complete plastid genome of eight Bulbophyllum species, representing five of six Neotropical taxonomic sections. All plastomes conserve the typical quadripartite structure, and, although the general structure of plastid genomes is conserved, differences in ndh-gene composition and total length were detected. Total length was determined by contraction and expansion of the small single-copy region, a result of an independent loss of the seven ndh genes. Selection analyses indicated that protein-coding genes were generally well conserved, but in four genes, we identified 95 putative sites under positive selection. Furthermore, a total of 54 polymorphic simple sequence repeats were identified, for which we developed amplification primers. In addition, we propose 10 regions with potential to improve phylogenetic analyses of Neotropical Bulbophyllum species.

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Section: Discussion Plastid Genome Featuresmentioning

confidence: 56%

Section: Hypervariable Regionsmentioning

confidence: 72%

Section: Discussion Plastid Genome Featuresmentioning

confidence: 99%

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Comparative Plastid Genomics of Neotropical Bulbophyllum (Orchidaceae; Epidendroideae)

et al. 2020

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“…The chloroplast genome could distinguish C. indicum from its closely related species and might become a potential superbarcode for the identification of these species 24 . Zhu et al found that the complete plastome sequence dataset had the highest discriminatory power for D. officinale and its closely related species, indicating that complete plastome sequences can be used to accurately authenticate Dendrobium species 25 . The whole chloroplast genome of S. tonkinensis and its hypervariable region, including the most divergent regions (ycf1, ndhF, accD, and rpoC2), which are also the genes containing the most SNP sites, and the six positively selected genes (matK, psbE, psbF, psbM, psaI, and rpl36) could be selected as potential DNA barcodes for identification of species in future studies.…”

Section: Discussionmentioning

confidence: 99%

The complete chloroplast genome sequence of the medicinal plant Sophora tonkinensis

Fan

Tang

Wei

et al. 2020

Sci Rep

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Sophora tonkinensis belongs to genus Sophora of the fabaceae family. it is mainly distributed in the ridge and peak regions of limestone areas in western china and has high medicinal value and important ecological functions. Wild populations of S. tonkinensis are in danger and need urgent conservation. furthermore, wild S. tonkinensis resources are very limited relative to the needs of the market, and many adulterants are present on the market. therefore, a method for authenticating S. tonkinensis and its adulterants at the molecular level is needed. chloroplast genomes are valuable sources of genetic markers for phylogenetic analyses, genetic diversity evaluation, and plant molecular identification. In this study, we report the complete chloroplast genome of S. tonkinensis. The circular complete chloroplast genome was 154,644 bp in length, containing an 85,810 bp long single-copy (LSC) region, an 18,321 bp short single-copy (SSC) region and two inverted repeat (IR) regions of 50,513 bp. The S. tonkinensis chloroplast genome comprised 129 genes, including 83 protein-coding genes, 38 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. The structure, gene order and guanine and cytosine (Gc) content of the S. tonkinensis chloroplast genome were similar to those of the Sophora alopecuroides and Sophora flavescens chloroplast genomes. A total of 1,760 simple sequence repeats (SSRs) were identified in the chloroplast genome of S. tonkinensis, and most of them (93.1%) were mononucleotides. Moreover, the identified SSRs were mainly distributed in the LSC region, accounting for 60% of the total number of SSRs, while 316 (18%) and 383 (22%) were located in the SSC and IR regions, respectively. Only one complete copy of the rpl2 gene was present at the LSc/iRB boundary, while another copy was absent from the iRA region because of the incomplete structure caused by iR region expansion and contraction. the phylogenetic analysis placed S. tonkinensis in papilionoideae, sister to S. flavescens, and the genera Sophora and Ammopiptanthus were closely related. the complete genome sequencing and chloroplast genome comparative analysis of S. tonkinensis and its closely related species presented in this paper will help formulate effective conservation and management strategies as well as molecular identification approaches for this important medicinal plant.

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“…The clean reads were aligned to Dendrobium officinale (GenBank accession No. LC348521) (Zhu et al 2018) and assembled by GetOrganelle pipe-line (Jin et al 2018). The assembled chloroplast genome was annotated using DOGMA (Wyman et al 2004), and corrected by Geneious 11.1.15 (Kearse et al 2012).…”

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confidence: 99%

The complete chloroplast genome sequence of Liparis vivipara (Orchidaceae)

Zhang

Liu

Yang

et al. 2019

Mitochondrial DNA Part B

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Liparis vivipara is a terrestrial orchid distributes in southwestern China. In this study, we reported the first complete chloroplast genome of L. vivipara. The whole genome was 158,329 bp, consisting of a pair of inverted repeats (IR 27,043 bp), a large single-copy region (LSC 85,950 bp), and a small singlecopy region (SSC 18,293 bp). The complete genome contained 132 genes, including 77 protein-coding genes, 38 tRNA, and 8 rRNA genes. The overall GC content of the whole genome was 36.9%. A maximum-likelihood phylogenetic analysis demonstrated a close relationship between L. vivipara and L. loeselii.

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Accurate authentication of Dendrobium officinale and its closely related species by comparative analysis of complete plastomes

Cited by 56 publications

References 56 publications

Comparative Plastid Genomics of Neotropical Bulbophyllum (Orchidaceae; Epidendroideae)

Comparative Plastid Genomics of Neotropical Bulbophyllum (Orchidaceae; Epidendroideae)

The complete chloroplast genome sequence of the medicinal plant Sophora tonkinensis

The complete chloroplast genome sequence of Liparis vivipara (Orchidaceae)

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