利用 218 个保守的exon-primed、intron-spanning 核基因座估算紫羊茅（牛舌草科）的核苷酸多样性。

Estimating the nucleotide diversity in Ceratodon purpureus (Ditrichaceae) from 218 conserved exon-primed, intron-spanning nuclear loci.

机构信息

Biology Department, University of Florida, Gainesville, Florida 32611 USA ; Biology Department, Washington University in St. Louis, St. Louis, Missouri 63130 USA.

Center for Genome Sciences, Washington University in St. Louis, St. Louis, Missouri 63130 USA.

出版信息

Appl Plant Sci. 2013 Mar 28;1(4). doi: 10.3732/apps.1200387. eCollection 2013 Apr.

DOI:10.3732/apps.1200387

PMID:25202534

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC4105291/

Abstract

PREMISE OF THE STUDY

We developed and tested primers for 218 nuclear loci for studying population genetics, phylogeography, and genome evolution in bryophytes. •

METHODS AND RESULTS

We aligned expressed sequence tags (ESTs) from Ceratodon purpureus to the Physcomitrella patens genome sequence, and designed primers that are homologous to conserved exons but span introns in the P. patens genome. We tested these primers on four isolates from New York, USA; Otavalo, Ecuador; and two laboratory isolates from Austria (WT4 and GG1). The median genome-wide nucleotide diversity was 0.008 substitutions/site, but the range was large (0-0.14), illustrating the among-locus heterogeneity in the species. •

CONCLUSIONS

These loci provide a valuable resource for finely resolved, genome-wide population genetic and species-level phylogenetic analyses of C. purpureus and its relatives.

摘要

研究前提

我们开发并测试了 218 个核基因座的引物，用于研究苔藓植物的种群遗传学、系统地理学和基因组进化。

方法和结果

我们将 Ceratodon purpureus 的表达序列标签（EST）与 Physcomitrella patens 基因组序列进行比对，并设计了与 Physcomitrella patens 基因组中的保守外显子同源但跨越内含子的引物。我们在来自美国纽约、厄瓜多尔奥塔瓦洛和奥地利的两个实验室分离株（WT4 和 GG1）的四个分离株上测试了这些引物。中值全基因组核苷酸多样性为 0.008 个替换/位点，但范围很大（0-0.14），说明该物种的基因座间异质性很大。