DOI: 10.5061/dryad.63xsj3v6w
title: Data from: genetic resources of macroalgae: development of an efficient method using microsatellite markers in non-model organisms

description: 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.
description: Two individuals of each of the
 6 species of algae were used to construct 2 genomics libraries (Lib1 and
 Lib2) according to the methods described by Peterson et al.,
 2012. Sage Science Pippin-Prep (sagescience.com) method was
 used to make the size selection to obtain fragments of interest between
 350 and 550 bp (between 480 and 680 bp with the full library construction
 fragments). Size selection and quality of both libraries were checked
 using Bioanalyzer and High Sensitivity DNA Chips (Agilent Technologies),
 and the final concentrations were estimated through quantitative PCR
 (qPCR) using KAPA Library Quantification Kit (Roche Molecular Systems,
 Inc) and LightCycler® 480 System (Roche Molecular Systems, Inc).
 Sequencing was performed in two runs on a MiSeq sequencer (Illumina, San
 Diego, CA, USA) using the Miseq Reagent Kit v3 600 cycles (2 x 300
 paired-end reads) and libraries at 15pM mixed with 5% of Phix control v3
 (Illumina, San Diego, CA, USA).
description: STACKS software version 2.52
 (Catchen et al., 2013); https://catchenlab.life.illinois.edu/stacks/
description: ###Stéphane Mauger, Aurélien Baud, Gildas Le Corguillé, Gwenn Tanguy,
 Erwan Legeay, Emeline Creis, Myriam Valero, Philippe Potin and Christophe
 Destombe. Genetic resources of macroalgae: development of an efficient
 method using microsatellite markers in non-model organisms. *Algal
 Research*. ###Data S1 ###ddRAD-seq raw reads used to development and
 characterize new microsatellite markers in non-model organisms of
 macroalgae. **Author(s)** Stéphane Mauger IRL EBEA 3614, Evolutionary
 Biology and Ecology of Algae, CNRS, Sorbonne Universit, UC, UACH, Station
 Biologique de Roscoff, CS 90074, Place Georges Teissier, 29688 Roscoff
 cedex [mauger@sb-roscoff.fr](mailto:mauger@sb-roscoff.fr) ###File list
 (files found within DataS1.zip) mauger_et_al_2023_barcodes_Lib1.txt
 mauger_et_al_2023_barcodes_Lib2.txt mauger_et_al_2023_Lib1_R1_fastq.gz
 mauger_et_al_2023_Lib1_R2_fastq.gz mauger_et_al_2023_Lib2_R1_fastq.gz
 mauger_et_al_2023_Lib2_R2_fastq.gz ###File descriptions
 **mauger\_et\_al\_2023\_barcodes\_Lib1.txt** \- The text file with the
 list of barcodes used during the demultiplexing process \(STACKS software
 version 2\.52\) for the library Lib1\. This file containing the barcodes
 list of A\. esculenta\, P\. littoralis and C\. jubata species\.
 **mauger\_et\_al\_2023\_barcodes\_Lib2.txt** \- The text file with the
 list of barcodes used during the demultiplexing process \(STACKS software
 version 2\.52\) for the library Lib2\. This file containing the barcodes
 list of G\. dura\, P\. palmata and G\. gracilis species\.
 **mauger\_et\_al\_2023\_Lib1\_R1\_fastq.gz** \- The \.gz file with the raw
 reads R1 from the library Lib1 obtained by Miseq 2 x 300 paired\-end reads
 sequencing \(Illumina\, San Diego\, CA\, USA\)\. This file containing raw
 reads R1 of A\. esculenta\, P\. littoralis and C\. jubata used to develop
 new microsatellite markers\. **mauger\_et\_al\_2023\_Lib1\_R2\_fastq.gz**
 \- The \.gz file with the raw reads R2 from the library Lib1 obtained by
 Miseq 2 x 300 paired\-end reads sequencing \(Illumina\, San Diego\, CA\,
 USA\)\. This file containing raw reads R1 of A\. esculenta\, P\.
 littoralis and C\. jubata used to develop new microsatellite markers\.
 **mauger\_et\_al\_2023\_Lib2\_R1\_fastq.gz** \- The \.gz file with the raw
 reads R1 from the library Lib2 obtained by Miseq 2 x 300 paired\-end reads
 sequencing \(Illumina\, San Diego\, CA\, USA\)\. This file containing raw
 reads R1 of G\. dura\, P\. palmata and G\. gracilis used to develop new
 microsatellite markers\. **mauger\_et\_al\_2023\_Lib2\_R2\_fastq.gz** \-
 The \.gz file with the raw reads R2 from the library Lib2 obtained by
 Miseq 2 x 300 paired\-end reads sequencing \(Illumina\, San Diego\, CA\,
 USA\)\. This file containing raw reads R1 of G\. dura\, P\. palmata and
 G\. gracilis used to develop new microsatellite markers\.