DNA barcoding of African Podostemaceae (river‐weeds): A test of proposed barcode regions

Abstract

DNA barcoding has the possibility for application in many fields, ranging from biological inventory and species discovery to forensics and quality control. Barcoding could have great utility within the aquatic angiosperm family Podostemaceae, as these plants can be extremely difficult to identify on the basis of morphological characters alone, but are important components of tropical rivers and face threats from increased water pollution. Several potential barcodes for land plants have been suggested, including two 3‐locus combinations proposed by the Plant Working Group of the Consortium for the Barcode of Life. These loci, matK, rpoB, rpoC1, and trnH‐psbA, were tested for their potential utility in African members of the Podostemaceae. Our results show that although the rpoC1 region performs best in terms of universality of amplification and sequencing, the superior resolving power of matK makes it the most promising of the regions for use in barcoding. In the light of these results, we discuss the potential to apply barcoding to Podostemaceae of Africa and make suggestions for the directions of future work to exploit the full potential of this new technology in this group of plants.

The Internal Transcribed Spacer (ITS) Region and trnhH-psbA Are Suitable Candidate Loci for DNA Barcoding of Tropical Tree Species of India

“…Among others, phylogenetic analysis [27], [56], [66], [70], [71], similarity approaches such as BLAST [37], [72], and approaches based on the barcoding gap principle [13], [73] are the most commonly used for DNA barcode data analysis. We employed these three methods to test the efficacy of barcode loci in the identification of tropical tree species.…”

Barcoding diatoms: evaluation of the V4 subregion on the 18S rRNA gene, including new primers and protocols

“…Its potential to identify species is promising and has been demonstrated in many protists, fungi and plant groups (e.g. Gemeinholzer et al 2006;Kelly et al 2010;Litaker et al 2007;Taylor et al 2008). There are, however, some problems, the main one being that ITS is not easy to amplify and sequence with standard laboratory protocols (unpublished data; see also Hamsher et al 2011).…”

Molecular and morphological variation in Terniopsis (Podostemaceae) show contrasting patterns

“…Species of Podostemaceae typically show fragmented local populations in rocky habitats of rivers and they may be distributed in multiple rivers and/or in scattered rocky habitats along a single river. In extreme cases, a species may be endemic to a single river or set of falls (Sharma et al , Kato , Philbrick et al ), while other species have very wide distributions. Tristicha trifaria (Bory ex Willd.)…”

“…Spreng., for example, is distributed throughout Africa and America. However, most species occur in multiple rivers (van Royen , Kita and Kato , Kato , Philbrick et al ). The habitat, i.e.…”

“…the interface between the rock surface and fast currents, is rather uniform. Habitat variation between sites may be due to the nature of the rocks, the velocity of the water current, the seasonal water‐level periodicity, and light and nutrients availiability (Pannier , Noro et al 1994, Quiroz et al , Odinetz‐Collart et al , Philbrick and Novelo , Ghogue et al , Katayama et al 2016).…”