Potential use of DNA barcoding for the identification of Salvia based on cpDNA and nrDNA sequences

Wang, Meng; Zhao, Hongxia; Wang, Long; Wang, Tao; Yang, Ruiwu; Wang, Xiaoli; Zhou, Yong‐Hong; Ding, Chunbang; Zhang, Li

doi:10.1016/j.gene.2013.07.009

Cited by 33 publications

(24 citation statements)

References 45 publications

(55 reference statements)

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“…Salvia L. (sages, Lamiaceae), with a nearly worldwide distribution (Fig. ), multiple diversity hotspots, extraordinary evolutionary success in terms of both numbers of species and ecological amplitude, diverse vegetative and floral forms, and a unique staminal architecture to promote outcrossing provides an excellent model to address these questions (Claßen‐Bockhoff et al., , ; Walker et al., , ; Walker and Sytsma, ; Wester and Claßen‐Bockhoff, ; Takano and Okada, ; Jenks et al., ; Li et al., ; Wang et al., ; Celep et al., ; Drew et al., ; Will and Claßen‐Bockhoff, ). Salvia (sensu Drew et al., ), defined in part by only two stamens with at least some elongation in the anther connective, is sister to a relatively depauperate four‐stamen lineage comprising Lepechinia Willd.…”

Section: Subgeneric Classification Of Salvia Sl Used In This Studymentioning

confidence: 99%

Tracking temporal shifts in area, biomes, and pollinators in the radiation of Salvia (sages) across continents: leveraging anchored hybrid enrichment and targeted sequence data

Kriebel

Drew

Drummond

et al. 2019

American J of Botany

113

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Premise of the StudyA key question in evolutionary biology is why some clades are more successful by being widespread geographically, biome diverse, or species‐rich. To extend understanding of how shifts in area, biomes, and pollinators impact diversification in plants, we examined the relationships of these shifts to diversification across the mega‐genus Salvia.MethodsA chronogram was developed from a supermatrix of anchored hybrid enrichment genomic data and targeted sequence data for over 500 of the nearly 1000 Salvia species. Ancestral areas and biomes were reconstructed using BioGeoBEARS. Pollinator guilds were scored, ancestral pollinators determined, shifts in pollinator guilds identified, and rates of pollinator switches compared.Key ResultsA well‐resolved phylogenetic backbone of Salvia and updated subgeneric designations are presented. Salvia originated in Southwest Asia in the Oligocene and subsequently dispersed worldwide. Biome shifts are frequent from a likely ancestral lineage utilizing broadleaf and/or coniferous forests and/or arid shrublands. None of the four species diversification shifts are correlated to shifts in biomes. Shifts in pollination system are not correlated to species diversification shifts, except for one hummingbird shift that precedes a major shift in diversification near the crown of New World subgen. Calosphace. Multiple reversals back to bee pollination occurred within this hummingbird clade.Conclusions Salvia diversified extensively in different continents, biomes, and with both bee and bird pollinators. The lack of tight correlation of area, biome, and most pollinator shifts to the four documented species diversification shifts points to other important drivers of speciation in Salvia.

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Section: Subgeneric Classification Of Salvia Sl Used In This Studymentioning

confidence: 99%

Tracking temporal shifts in area, biomes, and pollinators in the radiation of Salvia (sages) across continents: leveraging anchored hybrid enrichment and targeted sequence data

Kriebel

Drew

Drummond

et al. 2019

American J of Botany

113

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“…By contrast, the ITS1 region has been rarely reported in DNA barcode evaluation or employed as a DNA barcode for species identification except in specific groups of plants (Wang et al . ), fungi (Osmundson et al . ) and animals (Smith et al .…”

Section: Introductionmentioning

confidence: 99%

ITS1: a DNA barcode better than ITS2 in eukaryotes?

Wang

Liu

Huang

et al. 2014

Molecular Ecology Resources

147

107

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A DNA barcode is a short piece of DNA sequence used for species determination and discovery. The internal transcribed spacer (ITS/ITS2) region has been proposed as the standard DNA barcode for fungi and seed plants and has been widely used in DNA barcoding analyses for other biological groups, for example algae, protists and animals. The ITS region consists of both ITS1 and ITS2 regions. Here, a large-scale meta-analysis was carried out to compare ITS1 and ITS2 from three aspects: PCR amplification, DNA sequencing and species discrimination, in terms of the presence of DNA barcoding gaps, species discrimination efficiency, sequence length distribution, GC content distribution and primer universality. In total, 85 345 sequence pairs in 10 major groups of eukaryotes, including ascomycetes, basidiomycetes, liverworts, mosses, ferns, gymnosperms, monocotyledons, eudicotyledons, insects and fishes, covering 611 families, 3694 genera, and 19 060 species, were analysed. Using similarity-based methods, we calculated species discrimination efficiencies for ITS1 and ITS2 in all major groups, families and genera. Using Fisher's exact test, we found that ITS1 has significantly higher efficiencies than ITS2 in 17 of the 47 families and 20 of the 49 genera, which are sample-rich. By in silico PCR amplification evaluation, primer universality of the extensively applied ITS1 primers was found superior to that of ITS2 primers. Additionally, shorter length of amplification product and lower GC content was discovered to be two other advantages of ITS1 for sequencing. In summary, ITS1 represents a better DNA barcode than ITS2 for eukaryotic species.

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“…between Salvia species, with an accuracy of 81.48% (Wang et al, 2013). The three combinations did not increase species discrimination.…”

Section: Phylogenymentioning

confidence: 84%

Phytochemical and biological research of Salvia medicinal resources

Hao¹

2015

Medicinal Plants

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Potential use of DNA barcoding for the identification of Salvia based on cpDNA and nrDNA sequences

Cited by 33 publications

References 45 publications

Tracking temporal shifts in area, biomes, and pollinators in the radiation of Salvia (sages) across continents: leveraging anchored hybrid enrichment and targeted sequence data

Tracking temporal shifts in area, biomes, and pollinators in the radiation of Salvia (sages) across continents: leveraging anchored hybrid enrichment and targeted sequence data

ITS1: a DNA barcode better than ITS2 in eukaryotes?

Phytochemical and biological research of Salvia medicinal resources

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