Conserved genetic regions across angiosperms as tools to develop single‐copy nuclear markers in gymnosperms: an example using cycads. (5th March 2014)

• Record Type: Journal Article
• Authors: Salas‐Leiva, Dayana E.; Meerow, Alan W.; Francisco‐Ortega, Javier; Calonje, Michael; Griffith, M. Patrick; Stevenson, Dennis W.; Nakamura, Kyoko
• Is Part Of: Molecular ecology resources. Volume 14:Number 4(2014:Jul.)
• Page Start: 831
• Page End: 845
• Publication Date: 2014-03-05
• Subjects: Molecular ecology -- Periodicals; 572.8
• DOI: 10.1111/1755-0998.12228
• Languages: English
• ISSNs: 1755-098X

Abstract

<abstract abstract-type="main" id="men12228-abs-0001"> <title>Abstract</title> <p>Several individuals of the Caribbean <italic>Zamia</italic> clade and other cycad genera were used to identify single‐copy nuclear genes for phylogeographic and phylogenetic studies in Cycadales. Two strategies were employed to select target loci: (i) a tblastX search of <italic>Arabidopsis</italic> conserved ortholog sequence (COS) set and (ii) a tblastX search of <italic>Arabidopsis‐Populus‐Vitis‐Oryza</italic> Shared Single‐Copy genes (APVO SSC) against the EST <italic>Zamia</italic> databases in GenBank. From the first strategy, 30 loci were selected, and from the second, 16 loci. In both cases, the matching GenBank accessions of <italic>Zamia</italic> were used as a query for retrieving highly similar sequences from <italic>Cycas</italic>, <italic> Picea, Pinus</italic> species or <italic>Ginkgo biloba</italic>. After retrieving and aligning all the sequences in each locus, intron predictions were completed to assist in primer design. PCR was carried out in three rounds to detect paralogous loci. A total of 29 loci were successfully amplified as a single band of which 20 were likely single‐copy loci. These loci showed different diversity and divergence levels. A preliminary screening allowed us to select 8 promising loci (40S, ATG2, BG, GroES, GTP, LiSH, PEX4 and TR) for the <italic>Zamia pumila</italic> complex and 4 loci (COS26, GroES, GTP and HTS) for all other cycad genera.</p> </abstract>