Assessment of genetic diversity among four orchids based on ddRAD sequencing data for conservation purposes

• Published in: Physiology and molecular biology of plants 2017-01, Vol.23 (1), p.169-183
• Main Authors: Roy, Subhas Chandra, Moitra, Kaushik, De Sarker, Dilip
• Format: Article
• Language: English
• Subjects: Archives & records; Biological and Medical Physics; Biological evolution; Biomedical and Life Sciences; Biophysics; Cell Biology; Conservation; Gene sequencing; Genetic diversity; Life Sciences; Nucleotides; Plant Physiology; Plant Sciences; Research Article; Statistical tests
• ISSN: 0971-5894; 0974-0430
• DOI: 10.1007/s12298-016-0401-z

Genetic diversity was assessed in the four orchid species using NGS based ddRAD sequencing data. The assembled nucleotide sequences (fastq) were deposited in the SRA archive of NCBI Database with accession number (SRP063543 for Dendrobium , SRP065790 for Geodorum, SRP072201 for Cymbidium and SRP072378 for Rhynchostylis ). Total base pair read was 1.1 Mbp in case of Dendrobium sp., 553.3 Kbp for Geodorum sp., 1.6 Gbp for Cymbidium , and 1.4 Gbp for Rhynchostylis . Average GC% was 43.9 in Geodorum , 43.7% in Dendrobium , 41.2% in Cymbidium and 42.3% in Rhynchostylis . Four partial gene sequences were used in DnaSP5 program for nucleotide diversity and phylogenetic relationship determination ( Ycf2 gene of Dendrobium, matK gene of Geodorum , psbD gene of Cymbidium and Ycf2 gene of Ryhnchostylis ). Nucleotide diversity (per site) Pi (π) was 0.10560 in Dendrobium, 0.03586 in Geodorum, 0.01364 in Cymbidium and 0.011344 in Rhynchostylis . Neutrality test statistics showed the negative value in all the four orchid species (Tajima’s D value −2.17959 in Dendrobium , −2.01655 in Geodorum, −2.12362 in Rhynchostylis and −1.54222 in Cymbidium ) indicating the purifying selection. Result for these gene sequences ( mat K and Ycf 2 and psb D) indicate that they were not evolved neutrally, but signifying that selection might have played a role in evolution of these genes in these four groups of orchids. Phylogenetic relationship was analyzed by reconstructing dendrogram based on the matK, psbD and Ycf2 gene sequences using maximum likelihood method in MEGA6 program.