DNA barcoding, inter-specific and inter-generic variation studies on South Indian scaly tree ferns (Cyathea sp.pl.) using chloroplast rbcL gene

Abstract

DNA barcoding is an effective identification tool for tree ferns with heteromorphic generations with morphologically simple gametophytic phase. A complete reference dataset which includes coverage of the target local flora is necessary for accurate identification. Three different Cyathea sp.pl. were investigated to test the utility of plastid DNA barcode regions rbcL with the intention of developing an identification system for native pteridophytes. In addition, the inter-specific and inter-generic variations among the Cyathea sp.pl. were also focused. BLAST analysis revealed the similar rbcL sequences related to C. nilgirensis Holttum, C. gigantea (Wallich ex Hook. f.) Holttum and C. crinita (Hook.) Copel and a sum of 143 sequences viz., Cyathea sp.pl. (121), Gymnosphaera sp.pl.(4), Sphaeropteris sp.pl. (1) and Alsophila sp.pl. (17). The sequences of 143 plants were retrieved from GenBank in FASTA format. The sequences were aligned using multiple sequence alignment tool MUSCLE. The inter-specific and inter-generic distance percentage were calculated using Maximum Likelihood, Minimum Evolution, UPGMA (Unweighted Pair Group Method with Arithmetic Mean) and Neighbor-Joining method. The analyses were constructed using MEGA X software. The rbcL gene provided sequence variation with its strong resolving power. This study demonstrates the overall effectiveness of DNA barcodes for species identification of tree fern genus Cyathea in the pteridophyte flora of Southern Western Ghats.

Keywords:

• Scaly tree ferns
• rbcL
• barcoding
• phylogeny
• taxonomy

Disclosure statement

No potential conflict of interest was reported by the author(s).