DOI: 10.5061/dryad.1zcrjdfxp
title: Data from: Signs of local adaptation by genetic selection and isolation promoted by extreme temperature and salinity in the Mediterranean seagrass Posidonia oceanica

description: Adaptation to local conditions is known to occur in seagrasses, however,
 knowledge of the genetic basis underlying this phenomenon remains scarce.
 Here, we analyzed Posidonia oceanica from six sites within and
 around the Stagnone di Marsala, a semi-enclosed coastal lagoon where
 salinity and temperature exceed the generally described tolerance
 thresholds of the species. Sea surface temperatures (SSTs) were measured
 and plant samples were collected for the assessment of morphology,
 flowering rate and for screening genome-wide polymorphisms using double
 digest restriction-site-associated DNA sequencing. Results demonstrated
 more extreme SSTs and salinity levels inside the lagoon than the outer
 lagoon regions. Morphological results showed significantly fewer and
 shorter leaves and reduced rhizome growth of P. oceanica from the inner
 lagoon and past flowering events were recorded only for a meadow farthest
 away from the lagoon. Using an array of 51,329 SNPs, we revealed a clear
 genetic structure among the study sites and confirmed the genetic
 isolation and high clonality of the innermost site. Fourteen outlier loci
 were identified and annotated with several proteins including those relate
 to plant stress response, protein transport, and regulators of
 plant-specific developmental events. Especially, five outlier loci showed
 maximum allele frequency at the innermost site, likely reflecting
 adaptation to the extreme temperature and salinity regimes, possibly due
 to the selection of more resistant genotypes and the progressive
 restriction of gene flow. Overall, this study helps us to disentangle the
 genetic basis of seagrass adaptation to local environmental conditions and
 may support future works on assisted evolution in seagrasses.
description: Ninety-five ddRAD-seq library construction and sequencing were
 conducted at IGATech (Udine, Italy) using an IGATech custom protocol, with
 minor modifications with respect to Peterson’s double digest
 restriction-site associated DNA preparation (Peterson et al., 2012). To
 ensure the quality of sequencing outcomes, for each site, one sample was
 randomly selected and sequenced twice. The final number of biological
 replicates for each site was <em>n </em>= 14 for OpenSea-C and
 <em>n </em>= 15 for the other sites (i.e. North-basin,
 South-basin, OpenSea-A, OpenSea-B, and OpenSea-D), respectively (i.e. 89
 unique samples + 6 technical replicates). In short, gDNA was double
 digested with both <em>Sph</em>I and
 <em>Mbo</em>I<em> </em>endonucleases (New England
 BioLabs). Fragmented DNA was purified with AMPureXP beads (Agencourt) and
 subsequently ligated with T4 DNA ligase (New England BioLabs). Samples
 were pooled on multiplexing batches and bead purified as before and then
 they were size-selected and underwent several purification steps.
 ddRAD-seq libraries were sequenced with 150 cycles in paired-end mode on
 NovaSeq 6000 instrument following the manufacturer’s instructions
 (Illumina, San Diego, CA). Single nucleotide
 polymorphisms (SNPs) calling was performed <em>de novo</em>
 using Stacks software package v2.53 (Catchen, Hohenlohe, Bassham, Amores,
 & Cresko, 2013). First, raw Illumina reads were demultiplexed
 using the <em>process_radtags</em> utility (Catchen et al.,
 2013). The short reads of each sample were assembled into exactly matching
 stacks using the <em>ustacks</em> utility (Catchen et al.,
 2013). The creation of the loci catalog (i.e. a set of consensus loci from
 all the analyzed samples) was done using <em>cstacks</em> and
 matching each sample against the catalog using
 <em>sstacks</em> and <em>tsv2bam </em>utilities
 (Catchen et al., 2013). <em>gstacks</em> ultility (Catchen et
 al., 2013) was used to pull in paired-end reads, assemble the paired-end
 contigs and merge them with the single-end locus, align reads to the locus
 and ultimately call SNPs. Finally, detected loci were filtered using the
 <em>populations</em> program included in Stacks v2.53 (Catchen
 et al., 2013), with option –R=0.75 to retain only loci that were
 represented in at least the 75% of the whole metapopulation and with
 cutoff <em>--max-obs-het</em>=0.8, to process a nucleotide
 site at a locus with observed heterozygosity at a maximum of
 80%.
description: # Raw sequencing data and VCF files --- This dataset contains raw
 sequencing files and vcf files of a field experiment on the seagrass
 *Posidonia oceanic*. Samples were collected from six sites within and
 around the Stagnone di Marsala, a semi-enclosed coastal lagoon
 where salinity and temperature exceed the generally described tolerance
 thresholds of the species. This study aimed at better understanding the
 genetic basis of local adaptation in *P. oceanica* to extreme temperature
 and salinity. The screening of genome-wide polymorphisms using double
 digest restriction-site-associated DNA sequencing revealed a clear genetic
 structure among the study sites and confirmed the genetic isolation and
 high clonality of the innermost site. Fourteen outlier loci were
 identified and annotated with several proteins including those relate to
 plant stress response, protein transport and regulators of plant-specific
 developmental events. Especially, five outlier loci showed maximum allele
 frequency at the innermost site, likely reflecting adaptation to the
 extreme temperature and salinity regimes, possibly due to the selection of
 more resistant genotypes and the progressive restriction of gene flow. ##
 Description of the data and file structure This dataset includes: *
 *.fq.gz: 95 raw paired-end sequences (sequenced on NovaSeq 6000 instrument
 following the manufacturers instructions, Illumina, San Diego, CA) *
 inds2pops_6pop.tab contains sample IDs corresponding to different study
 sites: (+) pop1: North-basin (n = 15) (+) pop2: South-basin (n = 15) (+)
 pop3: Open-sea A (n = 15) (+) pop4: Open-sea B (n = 15) (+) pop5: Open-sea
 C (n = 14) (+) pop6: Open-sea D (n = 15) Technical replicates are with the
 letter 'r' in the names. E.g., 96-F3r-A001 is a technical
 replicate of 83-F3-A001 * Nguyen_et_al_populations_snps.vcf contains data
 for the whole 95 samples * Nguyen_et_al_50distinctMLGs_snps.vcf contains
 data for 50 distinct MLGs after the removal of clones and technical
 replicates ## Sharing/Access information n/a ## Code/Software n/a