title: Assessment of genetic diversity among four orchids based on ddRAD sequencing data for conservation purposes.
abstract: 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 forDendrobium, SRP065790 forGeodorum,SRP072201 forCymbidiumand SRP072378 forRhynchostylis). Total base pair read was 1.1 Mbp in case ofDendrobiumsp., 553.3 Kbp forGeodorumsp., 1.6 Gbp forCymbidium, and 1.4 Gbp forRhynchostylis. Average GC% was 43.9 inGeodorum, 43.7% inDendrobium, 41.2% inCymbidiumand 42.3% inRhynchostylis. Four partial gene sequences were used in DnaSP5 program for nucleotide diversity and phylogenetic relationship determination (Ycf2gene ofDendrobium, matKgene ofGeodorum,psbDgene ofCymbidiumandYcf2gene ofRyhnchostylis). Nucleotide diversity (per site) Pi (π) was 0.10560 inDendrobium,0.03586 inGeodorum,0.01364 inCymbidiumand 0.011344 inRhynchostylis. Neutrality test statistics showed the negative value in all the four orchid species (Tajima's D value -2.17959 inDendrobium, -2.01655 inGeodorum,-2.12362 inRhynchostylisand -1.54222 inCymbidium) indicating the purifying selection. Result for these gene sequences (matK andYcf2 andpsbD) 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 thematK, psbDandYcf2gene sequences using maximum likelihood method in MEGA6 program.
authors.affiliation: Plant Genetics and Molecular Breeding Laboratory, Department of Botany, University of North Bengal, PO-NBU, Siliguri, WB 734013 India.
authors.forename: Subhas Chandra
authors.initials: SC
authors.lastname: Roy
authors.affiliation: Plant Genetics and Molecular Breeding Laboratory, Department of Botany, University of North Bengal, PO-NBU, Siliguri, WB 734013 India.
authors.forename: Kaushik
authors.initials: K
authors.lastname: Moitra
authors.affiliation: Department of Botany, Raiganj University, Raiganj, WB 733134 India.
authors.forename: Dilip
authors.initials: D
authors.lastname: De Sarker
keywords:  Orchids; Genetic diversity; Nucleotide diversity and evolution; Phylogenetic analysis; ddRADSeq