The complete chloroplast genome of Gleditsia sinensis and Gleditsia japonica: genome organization, comparative analysis, and development of taxon specific DNA mini-barcodes

Tan, Wenfeng; Gao, Han; Jiang, Weiling; Zhang, Huanyu; Yu, Xiaolei; Liu, Erwei; Tian, Xiaoxuan

doi:10.1038/s41598-020-73392-7

Cited by 18 publications

(11 citation statements)

References 79 publications

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“…Codon usage bias is also observed in plastome genes, and it plays a vital role in cp genome evolution as certain codon usage tendencies reshape cp genomes 45 , 46 . Various evolutionary mechanisms have affected the arrangement of codon usage bias 47 .…”

Section: Discussionmentioning

confidence: 99%

Complete chloroplast genome sequence of Lens ervoides and comparison to Lens culinaris

Tayşi

Kaymaz

Ateş

et al. 2022

Sci Rep

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Lens is a member of the Papilionoideae subfamily of Fabaceae and is generally used as a source of vegetable protein as part of human diets in many regions worldwide. Chloroplast (cp) genomes are highly active genetic components of plants and can be utilized as molecular markers for various purposes. As one of the wild lentil species, the Lens ervoides cp genome has been sequenced for the first time in this study using next-generation sequencing. The de novo assembly of the cp genome resulted in a single 122,722 bp sequence as two separate coexisting structural haplotypes with similar lengths. Results indicated that the cp genome of L. ervoides belongs to the inverted repeat lacking clade. Several noteworthy divergences within the coding regions were observed in ndhB, ndhF, rbcL, rpoC2, and ycf2 genes. Analysis of relative synonymous codon usage showed that certain genes, psbN, psaI, psbI, psbE, psbK, petD, and ndhC, preferred using biased codons more often and therefore might have elevated expression and translation efficiencies. Overall, this study exhibited the divergence level between the wild-type and cultured lentil cp genomes and pointed to certain regions that can be utilized as distinction markers for various goals.

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Section: Discussionmentioning

confidence: 99%

Complete chloroplast genome sequence of Lens ervoides and comparison to Lens culinaris

Tayşi

Kaymaz

Ateş

et al. 2022

Sci Rep

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“…The result would be a valuable genetic resource for studying the genetics and evolutionary relationships between the Polygonaceae species. There are about 110–130 genes encoded by chloroplast DNA, which consist of rRNA-coding genes, protein-coding genes, and tRNA-coding genes ( Cheng, Li, Zhang, Cai, Gao, Qiao and Mi 2017 ; Tan et al, 2020 ). In general, gene replication occurs in all rRNA genes, along with some protein-coding and tRNA genes.…”

Section: Introductionmentioning

confidence: 99%

A Comparative Analysis of the Chloroplast Genomes of Four Polygonum Medicinal Plants

et al. 2022

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Polygonum is a generalized genus of the Polygonaceae family that includes various herbaceous plants. In order to provide aid in understanding the evolutionary and phylogenetic relationship in Polygonum at the chloroplast (cp) genome-scale level, we sequenced and annotated the complete chloroplast genomes of four Polygonum species using next-generation sequencing technology and CpGAVAS. Then, repeat sequences, IR contractions, and expansion and transformation sites of chloroplast genomes of four Polygonum species were studied, and a phylogenetic tree was built using the chloroplast genomes of Polygonum. The results indicated that the chloroplast genome construction of Polygonum also displayed characteristic four types of results, comparable to the published chloroplast genome of recorded angiosperms. The chloroplast genomes of the four Polygonum plants are highly consistent in genome size (159,015 bp–163,461 bp), number of genes (112 genes, including 78 protein-coding genes, 30 tRNA genes, and 4 rRNA genes), gene types, gene order, codon usage, and repeat sequence distribution, which identifies the high preservation among the Polygonum chloroplast genomes. The Polygonum phylogenetic tree was recreated by a full sequence of the chloroplast genome, which illustrates that the P. bistorta, P. orientale, and P. perfoliatum are divided into the same branch, and P. aviculare belongs to Fallopia. The precise system site of lots base parts requires further verification, but the study would provide a basis for developing the available genetic resources and evolutionary relationships of Polygonum.

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“…The GC3 contents (29.25–29.47%) were lower than those at the first (44.92–44.97%) and second (37.40–37.48%) positions (Additional file 10 : Table S9). AT preference in the third position in the cp codons also appears in other angiosperms [ 69 ].…”

Section: Resultsmentioning

confidence: 99%

An integrated study of Violae Herba (Viola philippica) and five adulterants by morphology, chemical compositions and chloroplast genomes: insights into its certified plant origin

Qiao

Wang

et al. 2022

Chin Med

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Background Viola philippica Cav. is the only original plant for Violae Herba, as described in the Chinese Pharmacopoeia. The quality of this crude drug is affected by several adulterants from congeneric Viola species, and the authentic plant origin of Violae Herba is still controversial. Genome-based identification offers abundant genetic information and potential molecular markers that can be used for the authentication of closely related species. This study aims to investigate the certified origin of Violae Herba and to develop more effective markers for these easily confused species at the genetic level. Methods We compared the morphology and chemical composition of 18 batches of commercial samples and six widespread medicinal Viola plants used as Violae Herba or its substitutes by TLC and HPLC-Triple-TOF–MS/MS analyses. The complete chloroplast genomes of these species were sequenced and analyzed, including the general features, repeat sequences, mutational hotspots and phylogeny. The complete chloroplast genomes used as superbarcodes and some specific barcodes screened from mutational hotspots were tested for their ability to distinguish Viola species. Results A comparative study showed that Violae Herba is a multi-origin traditional Chinese medicine. Commercial decoction pieces and the standard reference drug were mainly derived from V. prionantha, clashing with the record in the Chinese Pharmacopoeia. Chloroplast genome analyses of V. philippica and five adulterants indicated that sequence divergence was relatively low within Viola species. By tree-based approaches, the complete chloroplast genomes showed a better discrimination ability and phylogenetic resolution for each Viola species. These results indicate that the whole chloroplast genomes can be used as superbarcodes to differentiate Viola medicinal plants. More specific DNA barcodes could be further developed from the Viola chloroplast genomes for more efficient and rapid identification of commercial Violae Herba and its adulterants. Conclusions This study has implications for chloroplast genome-based phylogenetic analysis and the authentication of multiple Viola species used as Violae Herba. The legal origin recorded in the Chinese Pharmacopoeia should be further revised to V. prionantha, in line with the commercial Violae Herba in the TCM markets.

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The complete chloroplast genome of Gleditsia sinensis and Gleditsia japonica: genome organization, comparative analysis, and development of taxon specific DNA mini-barcodes

Cited by 18 publications

References 79 publications

Complete chloroplast genome sequence of Lens ervoides and comparison to Lens culinaris

Complete chloroplast genome sequence of Lens ervoides and comparison to Lens culinaris

A Comparative Analysis of the Chloroplast Genomes of Four Polygonum Medicinal Plants

An integrated study of Violae Herba (Viola philippica) and five adulterants by morphology, chemical compositions and chloroplast genomes: insights into its certified plant origin

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