Finding stories in noise: Mitochondrial portraits from RAD data

Stobie, Connor Seamus; Cunningham, Michael J.; Oosthuizen, Carel J.; Bloomer, Paulette

doi:10.1111/1755-0998.12953

Cited by 14 publications

(22 citation statements)

References 66 publications

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“…Our pipeline could be applied well to the Labeobarbus dataset, and our results agreed with those presented by Stobie et al (2019). Despite the presumed higher mutation rate, the polymorphism can be considered relatively low (2.62% of the alignment).…”

Section: Labeobarbusdatasetsupporting

confidence: 83%

“…Despite the presumed higher mutation rate, the polymorphism can be considered relatively low (2.62% of the alignment). Still, we identified the same three clades as the original authors, and the general structure within the main clades was concordant with the results of Stobie et al (2019). Moreover, the number of individuals that bore the haplotype of the sister species was the same; thus, we identified the same number of hybrid individuals as the original authors.…”

Section: Labeobarbusdatasetsupporting

confidence: 82%

“…Moreover, the number of individuals that bore the haplotype of the sister species was the same; thus, we identified the same number of hybrid individuals as the original authors. Given the low error rate of technical replicates, using this dataset, we consider our pipeline to be at least as accurate as the method presented by Stobie et al (2019). Single SNP differences between the technical replicates were observed in our results, which did not otherwise influence phylogenetic results.…”

Section: Labeobarbusdatasetmentioning

confidence: 86%

“…In addition, given the ever growing number of available organellar genomes in public repositories (Tonti-Filippini, Nevill, Dixon, & Small, 2017), the mined organellar loci can help to put the focal taxa into a wider phylogenetic context, if the orthologus organellar regions can be identified by sequence matching against related sequences. Reduced genomic complexity sequencing is a valuable tool for SNP discovery, and, as already pointed by Stobie et al (2019), the complementary analysis of the nuclear and the organellar genome sampled by RRLs can provide important information about cytonuclear discordance, the frequency, and directionality of hybridization, and phylogeography.…”

Section: The Utility Of Organellar Loci Mined From Radseq Datasetsmentioning

confidence: 97%

“…In these studies, however, the RADseq dataset was regarded as a 'representative' of the nuclear genome and the organellar dataset was obtained by Sanger-sequencing mitochondrial or plastid candidate-genes. Nevertheless, RRL approaches may also sample the organellar genome, and can potentially be used to sort out organellar reads from nuclear ones (Stobie, Cunningham, Oosthuizen, & Bloomer, 2019). This approach is different from assembling the organellar genome to achieve increased phylogenetic resolution using capture-based HTS (Mariac et al, 2014) or genome skimming (Cronn et al, 2008;Parks, Cronn, & Liston, 2009;Straub et al, 2012).…”

Section: Introductionmentioning

confidence: 99%

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A magnet to draw a bright needle out from the haystack -- RADOrgMiner, an automated pipeline to genotype organellar reads from RADseq data

Laczkó

Jordán

Sramkó

2021

Preprint

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Different versions of Restriction-site Associated DNA sequencing (RADseq) have become powerful and popular tools in molecular ecology. Although RADseq datasets are regarded as representative of the nuclear genome, reduced representation genomic libraries may also sample the organellar (mitochondrial and, in case of plants, plastid) DNA. Extraction of organellar loci from RADseq data can provide additional insights into the phylogenetics of the study group which comes at no additional sequencing effort. Cytoplasmic genetic variance can help better understand the evolutionary history by uncovering past hybridization and identifying the maternal (or, rarely, the paternal) lineage due to rapid lineage sorting. We developed a pipeline in bash that is based on existing bioinformatic tools to automatically mine and genotype organellar loci contained RADseq libraries. The utility of our pipeline is tested on eight, publicly available datasets spanning different phylogenetic levels (i.e. from family-level phylogenies to phylogeography) and RADseq methods (sdRAD, ddRAD, ezRAD, GBS) for genotyping both mitochondrial and plastid loci, which were subject to phylogenetic tree reconstruction. In all cases, organellar phylogenies adequately supplemented the original studies either by corroborating the large-scale picture based on RADseq or by bringing additional evidence on past or contemporary hybridization. RADseq methods designed to achieve a larger horizontal coverage (i.e. ddRAD, ezRAD) evidently yielded longer organellar alignments, but sdRAD and GBS still provided useful polymorphic loci found in the cytoplasmic DNA. Our newly developed pipeline for the above purpose can be run under a Unix-line operating system and is freely accessible at https://github.com/laczkol/RADOrgMiner

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Section: Labeobarbusdatasetsupporting

confidence: 83%

Section: Labeobarbusdatasetsupporting

confidence: 82%

Section: Labeobarbusdatasetmentioning

confidence: 86%

Section: The Utility Of Organellar Loci Mined From Radseq Datasetsmentioning

confidence: 97%

Section: Introductionmentioning

confidence: 99%

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A magnet to draw a bright needle out from the haystack -- RADOrgMiner, an automated pipeline to genotype organellar reads from RADseq data

Laczkó

Jordán

Sramkó

2021

Preprint

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Mitochondrial Genome of Nonmodel Marine Metazoans by Next-Generation Sequencing (NGS)

Terraneo

Mariappan

Forsman

et al. 2022

Methods in Molecular Biology

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Towards a rigorous species delimitation framework for scleractinian corals based on RAD sequencing: the case study of Leptastrea from the Indo-Pacific

et al. 2020

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Accurate delimitation of species and their relationships is a fundamental issue in evolutionary biology and taxonomy and provides essential implications for conservation management. Scleractinian corals are difficult to identify because of their ecophenotypic and geographic variation and their morphological plasticity. Furthermore, phylogenies based on traditional loci are often unresolved at the species level because of uninformative loci. Here, we attempted to resolve these issues and proposed a consistent species definition method for corals by applying the genome-wide technique Restriction-site Associated DNA sequencing (RADseq) to investigate phylogenetic relationships and species delimitation within the genus Leptastrea. We collected 77 colonies from nine localities of the Indo-Pacific and subjected them to genomic analyses. Based on de novo clustering, we obtained 44,162 SNPs (3701 loci) from the holobiont dataset and 62,728 SNPs (9573 loci) from the reads that map to coral transcriptome to reconstruct a robust phylogenetic hypothesis of the genus. Moreover, nearly complete mitochondrial genomes and ribosomal DNA arrays were retrieved by reference mapping. We combined concatenation-based phylogenetic analyses with coalescent-based species tree and species delimitation methods. Phylogenies suggest the presence of six distinct species, three corresponding to known taxa, namely Leptastrea bottae, Leptastrea inaequalis, Leptastrea transversa, one characterized by a remarkable skeletal variability encompassing the typical morphologies of Leptastrea purpurea and Leptastrea pruinosa, and Please note that this is an author-produced PDF of an article accepted for publication following peer review. The definitive publisher-authenticated version is available on the publisher Web site.two distinct and currently undescribed species. Therefore, based on the combination of genomic, morphological, morphometric, and distributional data, we herein described Leptastrea gibbosa sp. n. from the Pacific Ocean and Leptastrea magaloni sp. n. from the southwestern Indian Ocean and formally considered L. pruinosa as a junior synonym of L. purpurea. Notably, mitogenomes and rDNA yielded a concordant yet less resolved phylogeny reconstruction compared to the ones based on SNPs. This aspect demonstrates the strength and utility of RADseq technology for disentangling species boundaries in closely related species and in a challenging group such as scleractinian corals.

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Finding stories in noise: Mitochondrial portraits from RAD data

Cited by 14 publications

References 66 publications

A magnet to draw a bright needle out from the haystack -- RADOrgMiner, an automated pipeline to genotype organellar reads from RADseq data

A magnet to draw a bright needle out from the haystack -- RADOrgMiner, an automated pipeline to genotype organellar reads from RADseq data

Mitochondrial Genome of Nonmodel Marine Metazoans by Next-Generation Sequencing (NGS)

Towards a rigorous species delimitation framework for scleractinian corals based on RAD sequencing: the case study of Leptastrea from the Indo-Pacific

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