trnL-F is a powerful marker for DNA identification of field vittarioid gametophytes (Pteridaceae)

Chen, Christopher; Huang, Yao; Kuo, Li Chung; Nguyễn, Quốc Đạt; Luu, Hong Truong; Callado, John Rey; Farrar, Donald R.; Chiou, Wen Liang

doi:10.1093/aob/mct004

Cited by 49 publications

(40 citation statements)

References 45 publications

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“…The trnL‐F region showed a high PCR success rate (88.6% %) with only one pair primer and had the longest DNA sequence among the tested loci, which corresponded well with the results of studies carried out on other groups of plants (Chen et al . b; Wong et al . ).…”

Section: Discussionmentioning

confidence: 99%

Testing DNA barcodes in closely related species of Curcuma (Zingiberaceae) from Myanmar and China

Chen

Zhao

Erickson

et al. 2014

Molecular Ecology Resources

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The genus Curcuma L. is commonly used as spices, medicines, dyes and ornamentals. Owing to its economic significance and lack of clear-cut morphological differences between species, this genus is an ideal case for developing DNA barcodes. In this study, four chloroplast DNA regions (matK, rbcL, trnH-psbA and trnL-F) and one nuclear region (ITS2) were generated for 44 Curcuma species and five species from closely related genera, represented by 96 samples. PCR amplification success rate, intra- and inter-specific genetic distance variation and the correct identification percentage were taken into account to assess candidate barcode regions. PCR and sequence success rate were high in matK (89.7%), rbcL (100%), trnH-psbA (100%), trnL-F (95.7%) and ITS2 (82.6%) regions. The results further showed that four candidate chloroplast barcoding regions (matK, rbcL, trnH-psbA and trnL-F) yield no barcode gaps, indicating that the genus Curcuma represents a challenging group for DNA barcoding. The ITS2 region presented large interspecific variation and provided the highest correct identification rates (46.7%) based on BLASTClust method among the five regions. However, the ITS2 only provided 7.9% based on NJ tree method. An increase in discriminatory power needs the development of more variable markers.

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Section: Discussionmentioning

confidence: 99%

Testing DNA barcodes in closely related species of Curcuma (Zingiberaceae) from Myanmar and China

Chen

Zhao

Erickson

et al. 2014

Molecular Ecology Resources

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“…A drawback of the trnL intron is that the most commonly used primer combination (i.e. the c and d primers of Taberlet et al 1991) do not work in at least some ferns (Trewick et al 2002) although alternative primer combinations targeting this region are considered to have potential for exploring fern diversity (Chen et al 2013). Moreover, and perhaps more importantly, Drummond et al (2015) report that when used in soil, the majority of sequences produced by these primers were of prokaryotic origin.…”

Section: Current Practices For the Analysis Of Plant Communities Withmentioning

confidence: 99%

Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples

Lear¹,

Dickie²,

Banks³

et al. 2018

109

112

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Advances in the sequencing of DNA extracted from media such as soil and water offer huge opportunities for biodiversity monitoring and assessment, particularly where the collection or identification of whole organisms is impractical. However, there are myriad methods for the extraction, storage, amplification and sequencing of DNA from environmental samples. To help overcome potential biases that may impede the effective comparison of biodiversity data collected by different researchers, we propose a standardised set of procedures for use on different taxa and sample media, largely based on recent trends in their use. Our recommendations describe important steps for sample pre-processing and include the use of (a) Qiagen DNeasy PowerSoil ® and PowerMax ® kits for extraction of DNA from soil, sediment, faeces and leaf litter; (b) DNeasy PowerSoil ® for extraction of DNA from plant tissue; (c) DNeasy Blood and Tissue kits for extraction of DNA from animal tissue; (d) DNeasy Blood and Tissue kits for extraction of DNA from macroorganisms in water and ice; and (e) DNeasy PowerWater ® kits for extraction of DNA from microorganisms in water and ice. Based on key parameters, including the specificity and inclusivity of the primers for the target sequence, we recommend the use of the following primer pairs to amplify DNA for analysis by Illumina MiSeq DNA sequencing: (a) 515f and 806RB to target bacterial 16S rRNA genes (including regions V3 and V4); (b) #3 and #5RC to target eukaryote 18S rRNA genes (including regions V7 and V8); (c) #3 and #5RC are also recommended for the routine analysis of protist community DNA; (d) ITS6F and ITS7R to target the chromistan ITS1 internal transcribed spacer region; (e) S2F and S3R to target the ITS2 internal transcribed spacer in terrestrial plants; (f) fITS7 or gITS7, and ITS4 to target the fungal ITS2 region; (g) NS31 and AML2 to target glomeromycota 18S rRNA genes; and (h) mICOIintF and jgHCO2198 to target cytochrome c oxidase subunit I (COI) genes in animals. More research is currently required to confirm primers suitable for the selective amplification of DNA from specific vertebrate taxa such as fish. Combined, these recommendations represent a framework for efficient, comprehensive and robust DNA-based investigations of biodiversity, applicable to most taxa and ecosystems. The adoption of standardised protocols for biodiversity assessment and monitoring using DNA extracted from environmental samples will enable more informative comparisons among datasets, generating significant benefits for ecological science and biosecurity applications.

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“…Recently, DNA barcoding has been increasingly applied to identify field‐collected fern gametophytes, and has revealed that gametophytes do indeed occur outside of the range of sporophytes in some species (e.g., Chen et al. , Ebihara et al. , Kuo et al ).…”

Section: Discussionmentioning

confidence: 99%

“…, Chen et al. ). Furthermore, the DNA sequences generated by such a study can also be used to infer phylogenetic trees, thus enabling a phylogenetically informed study of community ecology (Kress et al.…”

Section: Introductionmentioning

confidence: 99%

Life cycle matters: DNA barcoding reveals contrasting community structure between fern sporophytes and gametophytes

Nitta

Meyer

Taputuarai

et al. 2017

Ecological Monographs

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Ferns are the only major lineage of vascular plants that have nutritionally independent sporophyte (diploid) and gametophyte (haploid) life stages. However, the implications of this unique life cycle for fern community ecology have rarely been considered. To compare patterns of community structure between fern sporophytes and gametophytes, we conducted a survey of the ferns of the islands of Moorea and Tahiti (French Polynesia). We first constructed a DNA barcode library (plastid rbcL and trnH‐psbA) for the two island floras including 145 fern species. We then used these DNA barcodes to identify more than 1300 field‐collected gametophytes from 25 plots spanning an elevational gradient from 200 to 2000 m. We found that species richness of fern sporophytes conforms to the well‐known unimodal (i.e., mid‐elevation peak) pattern, reaching a maximum at ~1000–1200 m. Moreover, we found that fern sporophyte communities become increasingly phylogenetically clustered at high elevations. In contrast, species richness of fern gametophytes was consistent across sites, and gametophytes showed no correlation of phylogenetic community structure with elevation. Turnover of sporophyte and gametophyte communities was closely linked with elevation at shallow phylogenetic levels, but not at deeper nodes in the tree. Finally, we found several species for which gametophytes had broader ranges than sporophytes, including a vittarioid fern with abundant gametophytes but extremely rare sporophytes. Our study highlights the importance of including diverse life history stages in surveys of community structure, and has implications for the possible impacts of climate change on the distribution of fern diversity.

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trnL-F is a powerful marker for DNA identification of field vittarioid gametophytes (Pteridaceae)

Abstract: This study demonstrates that DNA barcoding (i.e. reference databasing, tissue-direct PCR and molecular analysis), especially the trnL-F region, is an efficient tool to identify field gametophytes, and has considerable potential in exploring the ecology of fern gametophytes.

Cited by 49 publications

References 45 publications

Testing DNA barcodes in closely related species of Curcuma (Zingiberaceae) from Myanmar and China

Testing DNA barcodes in closely related species of Curcuma (Zingiberaceae) from Myanmar and China

Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples

Life cycle matters: DNA barcoding reveals contrasting community structure between fern sporophytes and gametophytes

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