Searching the Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
Our study searched all available sequences of Paphiopedilum from NCBI (National Center for Biotechnology Information) and tested for their species resolution capability in single as well as in combination forms. A total of 28 loci were applied for analyses in the study. From the nuclear genome, the highest resolution was of LFY, followed by ACO, DEF4, and RAD51. These 4 loci were found to be even better than the popular region ITS for Paphiopedilum identification. Among the chloroplast regions, the intergenic spacer atpB-rbcL gave the highest species resolution (76.7%), followed by matK, trnL, rpoC2, and ycf1. The divergence of CHS, XDH, 18S, Nad1, ccsA, rbcL, and ycf2 was very low and should not be used as identifying markers for Paphiopedilum. In addition, 2-locus combinations could improve significantly the resolving capability for the genus, in which 14/36 data sets could be resolved completely (100%) with interspecies relationships. The indel information was also effective supporting data for molecular discrimination of species.
Pubmed ID: 29899659
Publication data is provided by the National Library of Medicine ® and PubMed ®. Data is retrieved from PubMed ® on a weekly schedule. For terms and conditions see the National Library of Medicine Terms and Conditions.
NIH genetic sequence database that provides annotated collection of all publicly available DNA sequences for almost 280 000 formally described species (Jan 2014) .These sequences are obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole-genome shotgun (WGS) and environmental sampling projects. Most submissions are made using web-based BankIt or standalone Sequin programs, and GenBank staff assigns accession numbers upon data receipt. It is part of International Nucleotide Sequence Database Collaboration and daily data exchange with European Nucleotide Archive (ENA) and DNA Data Bank of Japan (DDBJ) ensures worldwide coverage. GenBank is accessible through NCBI Entrez retrieval system, which integrates data from major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of GenBank database are available by FTP.
View all literature mentionsGraphical user interface for multiple sequence alignment and molecular phylogeny. SeaView also generates phylogenetic trees.
View all literature mentions