Testing and using complete plastomes and ribosomal DNA sequences as the next generation DNA barcodes in <i>Panax</i> (Araliaceae)

Ji, Yunheng; Liu, Changkun; Yang, Zhao; Yang, Lifang; He, Zheng-Shan; Wang, Hengchang; Yang, Jun‐Bo; Yi, Ting‐Shuang

doi:10.1111/1755-0998.13050

Cited by 64 publications

(72 citation statements)

References 63 publications

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“…Although the four specific barcodes had the highest discriminatory power, it was necessary to develop additional markers for Quercus because of its complex evolutionary history. With the advent of the next-generation DNA sequencing technologies, genomic data have extended the concept of DNA barcoding for species identification [6,8,36,37,38]. The DNA barcode has extended from gene or genes to the entire genome, and the extended DNA barcoding approach has been referred to as “ultra-barcoding” [39], “super-barcoding” [7], or “plant barcoding 2.0” [40].…”

Section: Discussionmentioning

confidence: 99%

“…The DNA barcode has extended from gene or genes to the entire genome, and the extended DNA barcoding approach has been referred to as “ultra-barcoding” [39], “super-barcoding” [7], or “plant barcoding 2.0” [40]. Compared to the nuclear and mitochondrial genomes, the chloroplast genome is easily sequenced and may be the best-suited genome for plant species super-barcoding [36,41].…”

Section: Discussionmentioning

confidence: 99%

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Species Identification of Oaks (Quercus L., Fagaceae) from Gene to Genome

Pang

Liu²,

Wu³

et al. 2019

IJMS

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Species identification of oaks (Quercus) is always a challenge because many species exhibit variable phenotypes that overlap with other species. Oaks are notorious for interspecific hybridization and introgression, and complex speciation patterns involving incomplete lineage sorting. Therefore, accurately identifying Quercus species barcodes has been unsuccessful. In this study, we used chloroplast genome sequence data to identify molecular markers for oak species identification. Using next generation sequencing methods, we sequenced 14 chloroplast genomes of Quercus species in this study and added 10 additional chloroplast genome sequences from GenBank to develop a DNA barcode for oaks. Chloroplast genome sequence divergence was low. We identified four mutation hotspots as candidate Quercus DNA barcodes; two intergenic regions (matK-trnK-rps16 and trnR-atpA) were located in the large single copy region, and two coding regions (ndhF and ycf1b) were located in the small single copy region. The standard plant DNA barcode (rbcL and matK) had lower variability than that of the newly identified markers. Our data provide complete chloroplast genome sequences that improve the phylogenetic resolution and species level discrimination of Quercus. This study demonstrates that the complete chloroplast genome can substantially increase species discriminatory power and resolve phylogenetic relationships in plants.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Species Identification of Oaks (Quercus L., Fagaceae) from Gene to Genome

Pang

Liu²,

Wu³

et al. 2019

IJMS

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“…Previous studies have used entire plastome sequences to identify various seed plant species, and argued that plastomes are effective super-barcodes 20,23,24,38,39 . Our analysis further confirms that entire plastomes are effective super-barcodes for identifying both cypress species and varieties (Fig.…”

Section: Discussionmentioning

confidence: 99%

“…With high-throughput NGS data and advances in genomic assembly and analytical tools, utilization of the entire plastome or 35S rDNA sequence as a super-barcode was previously proposed to be a cost-effective way to discriminate species and evaluate phylogenies [18][19][20] . This super-barcoding approach is also encouraged to avoid problems of primer specificity, PCR amplification rate, and loss or duplication of the corresponding loci 21 .…”

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confidence: 99%

Genome skimming and exploration of DNA barcodes for Taiwan endemic cypresses

Sudianto

Hung

et al. 2020

Sci Rep

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Cypresses are characterized by their longevity and valuable timber. In Taiwan, two endemic cypress species, Chamaecyparis formosensis and C. obtusa var. formosana, are threatened by prevalent illegal logging. A DNA barcode system is urgently needed for reforestation and conservation of these two cypresses. In this study, both plastomes and 35S rDNAs from 16, 10, and 6 individuals of C. formosensis, C. obtusa var. formosana, and C. obtusa var. obtusa were sequenced, respectively. We show that the loss of plastid trnT-GGU readily distinguishes C. formosensis from its congeneric species. We demonstrate that entire sequences of plastomes or 35S rDNAs are capable of correctly identifying cypress species and varieties, suggesting that they are effective super-barcodes. We also discover three short hypervariable loci (i.e., 3′ETS, ITS1, and trnH-psbA) that are promising barcodes for identifying cypress species and varieties. Moreover, nine species-specific indels of > 100 bp were detected in the cypress plastomes. These indels, together with the three aforementioned short barcodes, constitute an alternative and powerful barcode system crucial for identifying specimens that are fragmentary or contain degraded/poor DNA. Our sequenced data and barcode systems not only enrich the genetic reference for cypresses, but also contribute to future reforestation, conservation, and forensic investigations.

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“…Whole chloroplast (cp) genomes have been extensively used in plant phylogeny, biogeography, and species discrimination ( Moore et al., 2010 , Shaw et al., 2014 ). Plastome sequences are maternally inherited, lack recombination, and hold more variable sites, which have the potential to resolve complicated evolutionary relationships ( Huang et al., 2017 ; Ji et al., 2019 ). Notably, the sequences display significant variation in the divergence rate between coding and non-coding regions, which is crucial in resolving the phylogenetic relationships at different taxonomic levels ( Niu et al., 2017 , Zhang et al., 2017 ).…”

Section: Introductionmentioning

confidence: 99%

The complete plastome sequences of five Aponogeton species (Aponogetonaceae): Insights into the structural organization and mutational hotspots

Mwanzia

Gichira

et al. 2020

Plant Diversity

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Members of the aquatic plant genus Aponogeton are widely used commercially in aquariums because of their variable leaf shape and unique inflorescences. However, due to extensive similarity between species in this genus, morphological characters are generally inadequate for taxonomic classification. Currently, molecular makers available for taxonomic and phylogenetic studies of Aponogeton are limited. One approach to clarifying relationships between species in these complex groups is to use divergence hotspot regions within the genome. Here, we sequenced and analyzed the plastomes of five Aponogeton species collected from China, Zambia, and Kenya, and subsequently screened these plastomes for divergent DNA hotspots. The five plastomes are circular structures with sizes ranging from 154,167 bp to 154,860 bp. The Large and the Small Single Copies are separated by two Inverted Repeats. One hundred and thirteen unique genes were identified including 79 protein-coding, 30 tRNA, and four rRNA genes. We found that the most abundant repeats in all but one species were mononucleotide repeats (A/T) and that there were 23 potential RNA ending sites. Interestingly, a ~3 kb inversion, which includes the accD gene, was detected within the Asian species of Aponogeton . The inversion may be related to more frequent exchanges between this region and the nuclear genome. Furthermore, we detected mutational hotspot sites among the five Aponogeton species. Three of these hotspots are intergenic spacer regions ( accD-psaI , rbcL-accD and trnH-GUG-psbA ) that might be suitable for use as barcodes to resolve intra-generic relationships. We also identified four highly variable protein-coding genes ( ccsA , rpl22 , rps16 and ycf1 ) may be used as barcodes to resolve the higher-level phylogenies. Our study will provide valuable molecular resources for the taxonomic and phylogenomic study of the complex genus Aponogeton .

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Testing and using complete plastomes and ribosomal DNA sequences as the next generation DNA barcodes in Panax (Araliaceae)

Cited by 64 publications

References 63 publications

Species Identification of Oaks (Quercus L., Fagaceae) from Gene to Genome

Species Identification of Oaks (Quercus L., Fagaceae) from Gene to Genome

Genome skimming and exploration of DNA barcodes for Taiwan endemic cypresses

The complete plastome sequences of five Aponogeton species (Aponogetonaceae): Insights into the structural organization and mutational hotspots

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