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52 results for “RAD-seq”
Data from: Strengths and potential pitfalls of hay-transfer for ecological restoration revealed by RAD-seq analysis in floodplain Arabis species
Achieving high intraspecific genetic diversity is a critical goal in ecological restoration as it increases the adaptive potential and long-term resilience of populations. Thus, we investigated genetic diversity within and between pristine sites in a fossil floodplain and compared it to sites restored by hay-transfer between 1997 and 2014. RAD-seq genotyping revealed that the stenoecious flood-plain species Arabis nemorensis is co-occurring with individuals that, based on ploidy, ITS-sequencing and morphology, probably belong to the close relative Arabis sagittata, which has a documented preference for dry calcareous grasslands but has not been reported in floodplain meadows. We show that hay-transfer maintains genetic diversity for both species. Additionally, in A. sagittata, transfer from multiple genetically isolated pristine sites resulted in restored sites with increased diversity and admixed local genotypes. In A. nemorensis, transfer did not create novel admixture dynamics because genetic diversity between pristine sites was less differentiated. Thus, the effects of hay-transfer on genetic diversity also depend on the genetic makeup of the donor communities of each species, especially when local material is mixed. Our results demonstrate the efficiency of hay-transfer for habitat restoration and emphasize the importance of pre-restoration characterization of micro-geographic patterns of intraspecific diversity of the community to guarantee that restoration practices reach their goal, i.e. maximize the adaptive potential of the entire restored plant community. Overlooking these patterns may alter the balance between species in the community. Additionally, our comparison of summary statistics obtained from de novo and reference-based RAD-seq pipelines shows that the genomic impact of restoration can be reliably monitored in species lacking prior genomic knowledge.
Data from: Restriction site-associated DNA sequencing (RAD-seq) reveals an extraordinary number of transitions among gecko sex-determining systems
Sex chromosomes have evolved many times in animals and studying these replicate evolutionary "experiments" can help broaden our understanding of the general forces driving the origin and evolution of sex chromosomes. However this plan of study has been hindered by the inability to identify the sex chromosome systems in the large number of species with cryptic, homomorphic sex chromosomes. Restriction site-associated DNA sequencing (RAD-seq) is a critical enabling technology that can identify the sex chromosome systems in many species where traditional cytogenetic methods have failed. Using newly generated RAD-seq data from twelve gecko species, along with data from the literature, we reinterpret the evolution of sex-determining systems in lizards and snakes and test the hypothesis that sex chromosomes can routinely act as evolutionary traps. We uncovered between 17 and 25 transitions among gecko sex-determining systems. This is approximately ½ to ⅔ of the total number of transitions observed among all lizards and snakes. We find support for the hypothesis that sex chromosome systems can readily become trap-like and show that adding even a small number of species from understudied clades can greatly enhance hypothesis testing in a model-based phylogenetic framework. RAD-seq will undoubtedly prove useful in evaluating other species for male or female heterogamety, particularly the majority of fish, amphibian, and reptile species that lack visibly heteromorphic sex chromosomes, and will significantly accelerate the pace of biological discovery.
Plastome and RAD-seq of Polygonatum odoratum
<p><span><i>Polygonatum odoratum</i> (Mill.) Druce (Asparagaceae, Asparagales) is a widely cultivated medicinal herb in China. However, this useful herb is understudied despite being known as a medicinal resource with top grade medical and edible properties since long. In this study, <i>P. odoratum</i> and four cultivars were investigated. The variations in morphological characteristics and vegetative phases of each cultivars were observed. For genetic aspect, the plastid genome of <i>P. odoratum</i> varies in length from 154,569 bp to 155,491 bp, containing a large single-copy region of 83,486—84,459 bp, a small single-copy region of 18,292—18,471 bp, and two inverted repeats of 26,302—26,370 bp. A total of 131 genes were predicted, including 85 protein-coding, 38 tRNA, and eight rRNA genes. Genome comparisons revealed a slight variation in the sequence across the five accessions, but two highly variable regions (<i>trn</i>C-<i>pet</i>N and <i>rpl</i>32-<i>trn</i>L) were detected when comparing the four different cultivars. For the RAD-seq markers, a total of 33.64 Gb of clean data, with an average value of 1.08 Gb per sample, were analyzed for presence of single nucleotide polymorphisms (SNPs). Well-resolved phylogenies of the <i>P. odoratum</i> cultivars are constructed; the non-monophyletic relationship in the plastome-based phylogenetic trees, yet monophyletic form in the RAD-based linkage map suggested possibility of hybrid cultivar for <i>P. odoratum</i> "Dazhu" (GDDZ), which was further supported by morphological observations. Quality assessment based on the standards of the Chinese Pharmacopoeia on Polygonati Odorati Rhizoma (POR) on the four cultivars used in this study recorded that PORs from <i>P. odoratum</i> 'Zhongzhu' (GDZZ) met the minimum criteria for the acceptance as raw material for medicinal drug production. This study has provided insights on the morphological variations, genetic background, and medicinal qualities of <i>P. odoratum</i> cultivars that could be explored for future genetic improvement as well as breeding programs of <i>P. odoratum</i> for POR production.</span></p>
Data from: RAD-Seq derived markers flank the shell colour and banding loci of the Cepaea nemoralis supergene
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Data from: Restriction site-associated DNA sequencing (RAD-seq) reveals an extraordinary number of transitions among gecko sex-determining systems
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Plastome and RAD-seq of Polygonatum odoratum
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Data from: Identification of sex-specific molecular markers using restriction site associated DNA sequencing (RAD-seq)
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Data from: Integrating restriction site-associated DNA sequencing (RAD-seq) with morphological cladistic analysis clarifies evolutionary relationships among major species groups of bee orchids
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Data from: Strengths and potential pitfalls of hay-transfer for ecological restoration revealed by RAD-seq analysis in floodplain Arabis species
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Data from: Development and preliminary evaluation of a genome-wide single-nucleotide polymorphisms resource generated by RAD-seq for the small yellow croaker (Larimichthys polyactis)
Recent advances in high-throughput sequencing technologies have offered the possibility to generate genome-wide sequence data to delineate previously unidentified genetic structure, obtain more accurate estimates of demographic parameters, and to evaluate potential adaptive divergence. Here, we identified 27 556 single-nucleotide polymorphisms for the small yellow croaker (Larimichthys polyactis) using restriction-site-associated DNA (RAD) sequencing of 24 individuals from two populations. Significant sources of genetic variation was identified, with an average nucleotide diversity (π) of 0.00105 ± 0.000425 across individuals and long-term effective population size was thus estimated to range between 26 172 and 261 716. According to the results, no differentiation between the two populations was detected based on the SNP dataset of top quality score per contig or neutral loci. However, the two analyzed populations were highly differentiated based on SNP dataset of both top FST value per contig and the outlier SNPs. Moreover, local adaptation was highlighted by an FST-based outlier tests implemented in LOSITAN and a total of 538 potentially locally selected SNPs were identified. BLAST2GO annotation of contigs containing the outlier SNPs yielded hits for 37 (66%) of 56 significant BLASTX matches. Candidate genes for local adaptation constituted a wide array of biological functions, including cellular response to oxidative stress, actin filament binding, ion transmembrane transport and synapse assembly. The generated SNP resources in the present study provided a valuable tool for future population genetics and genomics studies of L. polyactis.
Investigating the genetic basis of vertebrate dispersal combining RNA-seq, RAD-seq and quantitative genetics
<p>Although animal dispersal is known to play key roles in ecological and evolutionary processes such as colonization, population extinction and local adaptation, little is known about its genetic basis, particularly in vertebrates. Untapping the genetic basis of dispersal should deepen our understanding of how dispersal behaviour evolves, the molecular mechanisms that regulate it and link it to other phenotypic aspects in order to form the so-called dispersal syndromes. Here, we comprehensively combined quantitative genetics, genome-wide sequencing and transcriptome sequencing to investigate the genetic basis of natal dispersal in a known ecological and evolutionary model of vertebrate dispersal: the common lizard, <em>Zootoca vivipara.</em> Our study supports the heritability of dispersal in semi-natural populations, with less variation attributable to maternal and natal environment effects. In addition, we found an association between natal dispersal and both variation in the carbonic anhydrase (<em>CA10</em>) gene, and in the expression of several genes (<em>TGFB2</em>, <em>SLC6A4</em>, <em>NOS1</em>) involved in central nervous system functioning. These findings suggest that neurotransmitters (serotonin and nitric oxide) are involved in the regulation of dispersal and shaping dispersal syndromes. Several genes from the circadian clock (<em>CRY2, KCTD21</em>) were also differentially expressed between disperser and resident lizards, supporting that the circadian rhythm, known to be involved in long-distance migration in other taxa, might affect dispersal as well. Since neuronal and circadian pathways are relatively well conserved across vertebrates, our results are likely to be generalisable, and we therefore encourage future studies to further investigate the role of these pathways in shaping dispersal in vertebrates.</p>
Data from: Development and preliminary evaluation of a genome-wide single-nucleotide polymorphisms resource generated by RAD-seq for the small yellow croaker (Larimichthys polyactis)
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.