Data from: genetic resources of macroalgae: development of an efficient method using microsatellite markers in non-model organisms

Red and brown seaweeds are species with high ecological and economic
importance. Here we report the feasibility of cost-effective molecular
marker development in 6 species from different clades. Microsatellites
markers of two brown seaweed species Alaria
esculenta, Pylaiella littoralis, and of four red seaweed
species Calliblepharis jubata, Gracilaria
gracilis, Gracilaria dura and Palmaria
palmata were identified and characterized using genomic sequences
of Double-Digest Restriction site Associated DNA (ddRAD). A total of
64,623,186 reads were generated from two runs of multiplexed Illumina
Miseq sequencing for which 30,636 reads containing microsatellites and
15,443 microsatellite loci with primers pairs were found. Five hundred
seventy-six primers pairs were selected for amplification trials and
levels of polymorphism. From the 338 that gave a positive amplification,
142 primers pairs were polymorphic. For genetic analyses two or three
populations per species from 13 different geographic locations were used.
A total of 28 usable polymorphic markers for A. esculenta, 18
for P. littoralis, 11 for C. jubata, 14 for G.
gracilis, 21 for G. dura and 13 for P.
palmata were developed. The overall number of alleles per locus
ranged from 2 to 22. These 105 new microsatellite markers will be useful
for further studies of population genetics, breeding programs and
conservation genetics of these species. Compared with traditional
approaches, our study yielded thousands of microsatellite loci in a short
time with affordable costs in six different species. This study based on
ddRAD-sequencing for the development of microsatellite markers provides
preliminary data using a few individuals from two distinct populations on
the genetic structure and reproduction mode of a non-model species as
shown with the detection of clonality for the two red
algae, C. jubata and G. dura and the
detection of highly genetically divergent populations corresponding
probably to different cryptic species under the name of P.
littoralis.

红藻与褐藻是具有极高生态及经济价值的物种。本文报道了为6个不同分支物种开发高性价比分子标记的可行性。利用双酶切限制性位点相关DNA（ddRAD）的基因组序列，我们对两种褐藻（Alaria esculenta、Pylaiella littoralis）及四种红藻（Calliblepharis jubata、Gracilaria gracilis、Gracilaria dura、Palmaria palmata）的微卫星标记进行了鉴定与表征。通过两轮Illumina Miseq多重测序，共获得64,623,186条读段；从中鉴定出含微卫星的读段30,636条，以及带引物对的微卫星位点15,443个。我们选取了576对引物进行扩增试验及多态性水平检测；在338对扩增阳性的引物中，142对具有多态性。遗传分析中，每个物种使用了来自13个不同地理区域的2至3个种群。最终开发出可用于A. esculenta的28个多态性标记、P. littoralis的18个、C. jubata的11个、G. gracilis的14个、G. dura的21个及P. palmata的13个。每个位点的等位基因总数范围为2至22。这105个新型微卫星标记将为这些物种的种群遗传学、育种计划及保护遗传学后续研究提供助力。与传统方法相比，本研究能在短时间内以经济成本为6个不同物种获得数千个微卫星位点。本研究基于ddRAD测序开发微卫星标记，通过对来自两个不同种群的少量个体进行分析，为非模式物种的遗传结构及繁殖方式提供了初步数据——例如，在两种红藻（C. jubata与G. dura）中检测到克隆性，且在P. littoralis名下发现遗传差异显著的种群，这些种群可能对应不同的隐存种。