DNA barcoding of invasive plants in China: A resource for identifying invasive plants

Xu, Shufa; Li, Zhenyu; Jin, Xiao‐Hua

doi:10.1111/1755-0998.12715

Cited by 45 publications

(47 citation statements)

References 64 publications

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“…Genetic and genomic data are of critical importance for many applications, including species delimitation [1][2][3], studies on evolution and phylogenies [4][5][6], biodiversity assessments and conservation [7,8], reconstructions of past plant communities [9][10][11], or for more applied tasks such as forensics [12,13], pollination and food web studies [14][15][16] and monitoring of invasive species [17]. While many of these tasks can be undertaken by sequencing plastid or rDNA amplicons [1,2,18,19], increasing emphasis has been given to the potential of using genomic data for DNA barcoding and wider phylogenomic studies [4,[20][21][22][23][24].…”

Section: Introductionmentioning

confidence: 99%

The Treasure Vault Can be Opened: Large-Scale Genome Skimming Works Well Using Herbarium and Silica Gel Dried Material

Alsos

Lavergne

Merkel

et al. 2020

Plants

104

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Genome skimming has the potential for generating large data sets for DNA barcoding and wider biodiversity genomic studies, particularly via the assembly and annotation of full chloroplast (cpDNA) and nuclear ribosomal DNA (nrDNA) sequences. We compare the success of genome skims of 2051 herbarium specimens from Norway/Polar regions with 4604 freshly collected, silica gel dried specimens mainly from the European Alps and the Carpathians. Overall, we were able to assemble the full chloroplast genome for 67% of the samples and the full nrDNA cluster for 86%. Average insert length, cover and full cpDNA and rDNA assembly were considerably higher for silica gel dried than herbarium-preserved material. However, complete plastid genomes were still assembled for 54% of herbarium samples compared to 70% of silica dried samples. Moreover, there was comparable recovery of coding genes from both tissue sources (121 for silica gel dried and 118 for herbarium material) and only minor differences in assembly success of standard barcodes between silica dried (89% ITS2, 96% matK and rbcL) and herbarium material (87% ITS2, 98% matK and rbcL). The success rate was > 90% for all three markers in 1034 of 1036 genera in 160 families, and only Boraginaceae worked poorly, with 7 genera failing. Our study shows that large-scale genome skims are feasible and work well across most of the land plant families and genera we tested, independently of material type. It is therefore an efficient method for increasing the availability of plant biodiversity genomic data to support a multitude of downstream applications.

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Section: Introductionmentioning

confidence: 99%

The Treasure Vault Can be Opened: Large-Scale Genome Skimming Works Well Using Herbarium and Silica Gel Dried Material

Alsos

Lavergne

Merkel

et al. 2020

Plants

104

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“…Since DNA barcoding was formally proposed at a large scale in 2003 [1], it has been widely used in different fields, for example species delimitation [2,3], cryptic diversity discovering [4,5], investigating host-parasitoid interactions [6,7], pest quarantine, and environmental monitoring [8][9][10]. A fragment of the mitochondrial cytochrome oxidase subunit I (COI) gene has been proven to be a standard DNA barcode region for animal species identification and detecting molecular operational taxonomic units (MOTUs) [11,12].…”

Section: Introductionmentioning

confidence: 99%

“…A fragment of the mitochondrial cytochrome oxidase subunit I (COI) gene has been proven to be a standard DNA barcode region for animal species identification and detecting molecular operational taxonomic units (MOTUs) [11,12]. The usability of DNA barcoding has been reported in many groups, for instance Perciformes [13], invasive plants [3], Lepidoptera [2,4], Coleoptera [14,15], and Hymenoptera [16,17]. The power and accuracy of DNA barcoding, as well as unambiguous species identification may depend on sampling scales [18,19].…”

Section: Introductionmentioning

confidence: 99%

DNA Barcoding Subtropical Aphids and Implications for Population Differentiation

Deng

Cui

et al. 2019

Insects

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DNA barcoding has proven its worth in species identification, discovering cryptic diversity, and inferring genetic divergence. However, reliable DNA barcode reference libraries that these applications depend on are not available for many taxonomic groups and geographical regions. Aphids are a group of plant sap sucking insects, including many notorious pests in agriculture and forestry. The aphid fauna of the subtropical region has been understudied. In this study, based on extensive sampling effort across main subtropical areas, we sequenced 1581 aphid specimens of 143 morphospecies, representing 75 genera, and 13 subfamilies, to build the first comprehensive DNA barcode library for subtropical aphids. We examined the utility of DNA barcodes in identifying aphid species and population differentiation and evaluated the ability of different species delimitation methods (automatic barcode gap discovery (ABGD), generalized mixed Yule-coalescent (GMYC), and Bayesian Poisson tree processes (bPTP)). We found that most aphid species demonstrated barcode gaps and that a threshold value of 2% genetic distance is suitable for distinguishing most species. Our results indicated that ten morphospecies may have species divergence related to factors such as host plant or geography. By using two pest species Aphis spiraecola and A. gossypii as examples, we also discussed the effect of the sampling scale of host plants on the results and reliability of DNA barcoding of phytophagous insects. This DNA barcode library will be valuable for future studies and applications.

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“…The MEGA software v.7 (Kumar et al, 2016) was used to edit the raw sequence reads and to construct the consensus sequences. To search the phylogenetic position of the study-species, the phylogeny given in Xu et al (2018) was reconstructed with the sequences generated in this study. Initially, the multiple sequence alignments were constructed separately for ITS and rbcL markers individually and then the alignments were concatenated in MEGA v.7.…”

Section: Phylogenetic Analysismentioning

confidence: 99%

Green-Spinach, Red-Spinach, and Tree-Spinach (‘Three-Fold Spinach’ in Sri Lanka): An Insight into Phylogenetics and Consumer Preference

Gayathree¹,

Karunarathne²,

Jayarathne³

et al. 2020

Emir J Food Agric

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Three types of spinach, green spinach (GS), red spinach (RS), and tree spinach (TS) are consumed in Sri Lanka. GS, RS, and TS are referred to as Basella alba, Basella rubra, and Talinum fruticosum respectively. However, some taxonomists categorize GS and RS under B. alba causing an ambiguity. Due to the poor sanitation, consumers prefer to purchase greenhouse-grown spinach over field grown material. However, the taste parameters of field grown and greenhouse-grown spinach have not been assessed. The objectives of the present study were to resolve the taxonomic ambiguity between GS and RS, identify the evolutionary relationship of TS to other two species and to assess the organoleptic preference on the dishes prepared using greenhouse and field-grown shoot-tops of three spinach. The genomic DNA extracted from GS, RS, and TS, PCR amplified and sequenced for the barcoding markers rbcL, ITS, matK-trnT and atpB-rbcL. The sequences obtained along with other reported related sequences were subjected to phylogenetic analysis. A sensory test was carried out using the shoot-tops of three species grown under greenhouse and field conditions. The taste panelists were asked to rank the dishes for preferred levels of color, aroma, texture, bitterness, and overall taste and the data were subjected to the association analysis. The rbcL and ITS markers separate GS and RS into two well -supported clades, B. alba and B. rubra respectively. The polymorphisms of atpB-rbcL and matK-trnT markers support the definition of two species. The monophyly of B. alba and B. rubra with T. fruticosum must be the reason for the same palate in dishes and designation of all three species under “spinach” in Sri Lanka. The taste panel data demonstrated that there is no specific fondness for greenhouse or field grown materials enabling the popularization of greenhouse-grown spinach to answer the safety concerns.

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DNA barcoding of invasive plants in China: A resource for identifying invasive plants

Cited by 45 publications

References 64 publications

The Treasure Vault Can be Opened: Large-Scale Genome Skimming Works Well Using Herbarium and Silica Gel Dried Material

The Treasure Vault Can be Opened: Large-Scale Genome Skimming Works Well Using Herbarium and Silica Gel Dried Material

DNA Barcoding Subtropical Aphids and Implications for Population Differentiation

Green-Spinach, Red-Spinach, and Tree-Spinach (‘Three-Fold Spinach’ in Sri Lanka): An Insight into Phylogenetics and Consumer Preference

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