DNA barcoding herbaceous and woody plant species at a subalpine forest dynamics plot in Southwest China.

Peter M Hollingsworth,Kun Xu,Ya-Huang Luo,De-Zhu Li,Lian-Ming Gao,Shao-Lin Tan,Kevin S Burgess

doi:10.1002/ece3.4254

Abstract

Although DNA barcoding has been widely used to identify plant species composition in temperate and tropical ecosystems, relatively few studies have used DNA barcodes to document both herbaceous and woody components of forest plot. A total of 201 species (72 woody species and 129 herbaceous species) representing 135 genera distributed across 64 families of seed plants were collected in a 25 ha CForBio subalpine forest dynamics plot. In total, 491 specimens were screened for three DNA regions of the chloroplast genome (rbcL, matK, and trnH‐psbA) as well as the internal transcribed spacers (ITS) of nuclear ribosomal DNA. We quantified species resolution for each barcode separately or in combination using a ML tree‐based method. Amplification and sequencing success were highest for rbcL, followed by trnH‐psbA, which performed better than ITS and matK. The rbcL + ITS barcode had slightly higher species resolution rates (88.60%) compared with rbcL + matK (86.60%) and rbcL + trnH‐psbA (86.01%). The addition of trnH‐psbA or ITS to the rbcL + matK barcode only marginally increased species resolution rates, although in combination the four barcodes had the highest discriminatory power (90.21%). The situations where DNA barcodes did not discriminate among species were typically associated with higher numbers of co‐occurring con‐generic species. In addition, herbaceous species were much better resolved than woody species. Our study represents one of the first applications of DNA barcodes in a subalpine forest dynamics plot and contributes to our understanding of patterns of genetic divergence among woody and herbaceous plant species.

Highlights

Accurate identification of plant species is a key component of biological, ecological, and evolutionary studies
The plastid DNA regions rbcL, matK, trnH-psbA and the internal transcribed spacers (ITS) of nuclear ribosomal DNA have previously been used in systematic studies at various taxonomic levels (Azani et al, 2017; Baldwin et al, 1995; Chase et al, 1993; Harrington, Edwards, Johnson, Chase & Gadek, 2005), as well as for the taxonomy and species identification of specific target families and genera (Liu, Moeller, Gao, Zhang & Li, 2011; Xu et al, 2015; Yan et al, 2015)
Yulong Mountain (26°58′–27°18′ N, 100°04′–100°16′ E) belongs to the Himalaya–Hengduan Mountains Region, which is a part of a global biodiversity hotspot in the Mountains of Southwest China; over 2,800 species of seed plants have been recorded from this mountain (Liu, Li et al, 2015)

Summary

| INTRODUCTION

Accurate identification of plant species is a key component of biological, ecological, and evolutionary studies. One key step in the DNA barcoding process is the establishment of a reliable and comprehensive database (reference library) that includes both high-quality DNA barcode sequences and accurately identified voucher specimens (Taberlet, Coissac, Pompanon, Brochmann & Willerslev, 2012). Once established, such databases can become a valuable toolkit for molecular ecologists to identify plant material such as pollen, seeds, seedlings, roots, and even bark fragments (Liu et al, 2018). DNA barcoding has mainly been used for tree species in forest dynamic plots of tropical, subtropical, and temperate regions (Erickson et al, 2014; Kress et al, 2009; Pei et al, 2015).

| MATERIALS AND METHODS

90 Herbaceous

| DISCUSSION

| CONCLUSION

Findings

CONFLICT OF INTEREST