Skimming genomes for systematics and DNA barcodes of corals

Abstract

1: Numerous genomic methods developed over the past two decades have enabled the discovery and extraction of orthologous loci to help resolve phylogenetic relationships across various taxa and scales. Genome skimming (or low-coverage whole genome sequencing) remains a low-cost, promising method to not only extract high-copy loci, but also 100s to 1000s of phylogenetically informative single-copy nuclear loci (e.g., ultraconserved elements [UCEs] and exons) from contemporary and historical museum samples. The subphylum Anthozoa, which includes important ecosystem engineers (e.g., stony corals, black corals, anemones and octocorals) in the marine environment, is in critical need of phylogenetic resolution and thus might benefit from a genome-skimming approach. 2: Genome skimming was conducted on 242 hexacorals and octocorals collected from 1890 to 2022. Using previously developed target-capture baitsets, we bioinformatically obtained UCEs and exons from the genome-skimming data and incorporated them with data from previously published target-capture studies. We also extracted partial to whole mitogenomes and nuclear rRNA genes from the skim data. 3: The mean number of UCE and exon loci extracted from the genome skimming data was 1,837 ± 662 SD for octocorals and 1,422 ± 720 loci for hexacorals; phylogenetic relationships were well resolved within each class. A mean of 1,422 ± 720 loci were obtained from the historical museum specimens, with 1,253 loci recovered from the oldest specimen collected in 1886 and 1,336 loci recovered from a holotype. The nuclear rRNA genes and the majority of mitochondrial genes were successfully obtained from >95% of samples. Out of 99 circularized mitogenomes, 88% were recovered in samples from which we obtained >15M paired-end (PE) reads (>30M total reads); there was more variability in whether mitogenomes were circularized or not in samples with <15M PE reads. 4: Bioinformatically pulling UCEs, exons, mitochondrial genomes, and nuclear rRNA genes from genome skimming is a viable and low-cost option for phylogenetic studies. This approach can be used to review and support taxonomic revisions and reconstruct evolutionary histories, including historical museum and type specimens.

Nuclear eDNA Metabarcoding Primers for Anthozoan Coral Biodiversity Assessment

“…Many of these problematic cases, especially within the black corals, reflect incongruences between phylogenetic relationships and taxonomic nomenclature rather than the rate of evolution of the 28S barcode and its ability to distinguish taxonomic identity at the genus level. In black corals, phylogenetic evidence suggests that the genera Stichopathes and Cirrhipathes are polyphyletic (Bo et al 2018, Quattrini et al 2023). Likewise, Barret et al (2020) suggested that validations of the genera within Schizopathidae and Cladopathidae are necessary based on mitochondrial genome sequencing data.…”

“…Low coverage whole-genome sequencing (genome skimming) data were generated from specimens collected in the Gulf of Mexico following the methods described by Quattrini et al (2023). Several of these specimens were also barcoded with Sanger sequencing.…”

“…Consensus sequences from the assemblies were generated with a 90% identity threshold at each position, and the barcoding region was extracted from these consensus sequences. See Quattrini et al (2023) for further methodological details.…”

“…Data Availability: 28S DNA barcode sequences generated in this study using conventional PCR/Sanger sequencing and from target-capture data published in Quattrini et al (2020) will be made available on GenBank (Accession Numbers to be determined). 28S and mtMutS DNA barcode sequences trimmed from contigs generated from genome skimming data in Quattrini et al (2023) are being made available on GenBank (Accession Numbers to be determined). eDNA meta-barcoding amplicon sequencing data generated in this study will be made available on the Sequence Read Archive (Submission ID to be determined).…”

Analysis of mitogenomes from the family Keratoisididae reveals mitonuclear discordance and the presence of unknown open reading frames

“…Within Scleralcyonacea, the sister group to the Keratoisididae-Isidoidae clade is either Chrysogorgiidae or Primnoidae depending on whether the inference was constructed using nuclear or complete mitochondrial genomes respectively ). The ever-reducing cost of nextgeneration sequencing, and the ability to mine Sequence Read Archives (SRAs) for mitogenomic data (e.g., Muthye et al 2022;Hogan et al 2023) and conserved elements (Quattrini et al 2023a) will enable more comprehensive studies that can compare between alternative evolutionary histories and better explore the reasons as to why this discordance exists.…”