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Journal articles on the topic 'Deep genome skimming'

Author: Grafiati

Published: 7 June 2025

Last updated: 16 July 2025

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1

Hiley, Avery S., Nicolás Mongiardino Koch, and Greg W. Rouse. "Phylogenetics of Lepidonotopodini (Macellicephalinae, Polynoidae, Annelida) and Comparative Mitogenomics of Shallow-Water vs. Deep-Sea Scaleworms (Aphroditiformia)." Biology 13, no. 12 (2024): 979. http://dx.doi.org/10.3390/biology13120979.

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Within Polynoidae, a diverse aphroditiform family, the subfamily Macellicephalinae comprises anchialine cave-dwelling and deep-sea scaleworms. In this study, Lepidonotopodinae is synonymized with Macellicephalinae, and the tribe Lepidonotopodini is applied to a well-supported clade inhabiting deep-sea chemosynthetic-based ecosystems. Newly sequenced “genome skimming” data for 30 deep-sea polynoids and the comparatively shallow living Eulagisca gigantea is used to bioinformatically assemble their mitogenomes. When analyzed with existing scaleworm mitogenomes, deep-sea scaleworms exhibit increas

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Lin, Xiao-Hua, Si-Yu Xie, Guang-Ning Liu, et al. "Plastome-based subgenus-level phylogenetic backbone of hawthorns: insights into the maternal position and taxonomic synopsis of Crataegus shandongensis (Rosaceae, Maleae)." PhytoKeys 252 (February 12, 2025): 87–108. https://doi.org/10.3897/phytokeys.252.136506.

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The recent recognition of the five-subgenera classification within <i>Crataegus</i> has prompted discussion about the maternal phylogenetic relationships among these subgenera, with inconsistencies in taxon sampling, marker selection, and inference methods contributing to differing interpretations. In this study, we performed deep genome skimming sequencing and assembled 63 whole plastomes, including 58 from <i>Crataegus</i> and five from related genera as the outgroups. We employed multiple phylogenetic inference methods (Maximum Likelihood and Bayesian Inference) to reconstruct an accurate p

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3

Zhang, Ning, Jun Wen, and Elizabeth A. Zimmer. "Congruent Deep Relationships in the Grape Family (Vitaceae) Based on Sequences of Chloroplast Genomes and Mitochondrial Genes via Genome Skimming." PLOS ONE 10, no. 12 (2015): e0144701. http://dx.doi.org/10.1371/journal.pone.0144701.

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4

Zhang, Ning, Jun Wen, and Elizabeth A. Zimmer. "Correction: Congruent Deep Relationships in the Grape Family (Vitaceae) Based on Sequences of Chloroplast Genomes and Mitochondrial Genes via Genome Skimming." PLOS ONE 11, no. 3 (2016): e0152059. http://dx.doi.org/10.1371/journal.pone.0152059.

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5

McCartin, Luke, Emma Saso, Samuel A. Vohsen, et al. "Nuclear eDNA metabarcoding primers for anthozoan coral biodiversity assessment." PeerJ 12 (November 26, 2024): e18607. http://dx.doi.org/10.7717/peerj.18607.

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The distributions of anthozoan corals are undercharacterized due to their wide bathymetric ranges, occurrences in remote locales, and difficulties of identification from morphology alone. Environmental DNA (eDNA) sequencing promises to be a noninvasive strategy to complement conventional approaches for mapping and monitoring the distribution and biodiversity of coral communities. Primers for eDNA metabarcoding have been designed to amplify nuclear and mitochondrial DNA barcodes in shallow scleractinians and mitochondrial MutS in deep-sea octocorals. However, a comprehensive method for eDNA met

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Lin, Xiao-Hua, Si-Yu Xie, Guang-Ning Liu, et al. "Plastome-based subgenus-level phylogenetic backbone of hawthorns: insights into the maternal position and taxonomic synopsis of Crataegus shandongensis (Rosaceae, Maleae)." PhytoKeys 252 (February 12, 2025): 87–108. https://doi.org/10.3897/phytokeys.252.136506.

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The recent recognition of the five-subgenera classification within Crataegus has prompted discussion about the maternal phylogenetic relationships among these subgenera, with inconsistencies in taxon sampling, marker selection, and inference methods contributing to differing interpretations. In this study, we performed deep genome skimming sequencing and assembled 63 whole plastomes, including 58 from Crataegus and five from related genera as the outgroups. We employed multiple phylogenetic inference methods (Maximum Likelihood and Bayesian Inference) to reconstruct an accurate phylogeny. The

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7

Golightly, Charles, Danielle M. DeLeo, Nicole Perez, Tin-Yam Chan, José M. Landeira, and Heather D. Bracken‐Grissom. "Tracing the evolution of bioluminescent light organs across the deep-sea shrimp family Sergestidae using a genomic skimming and phylogenetic approach." Invertebrate Systematics 36, no. 1 (2022): 22–35. http://dx.doi.org/10.1071/is21013.

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Deep-sea shrimp of the family Sergestidae Dana, 1852 provide a unique system for studying the evolution of bioluminescence. Most species within the family possess autogenic bioluminescent photophores in one of three distinct forms: lensed photophores; non-lensed photophores; or internal organs of Pesta. This morphological diversity across the Sergestidae has resulted in recent major taxonomic revisions, dividing the two major genera (Sergia Stimpson, 1860 and Sergestes Milne Edwards, 1830) into 15. The present study capitalises on molecular data to construct an updated genus-level phylogeny of

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8

Horowitz, Jeremy, Mina Barajas, Luke J. McCartin, Samuel A. Vohsen, and Santiago Herrera. "Description of a new species of Stauropathes (Anthozoa, Antipatharia, Schizopathidae) from Puerto Rico." ZooKeys 1231 (March 13, 2025): 331–46. https://doi.org/10.3897/zookeys.1231.136967.

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A new species of black coral, <i>Stauropathes monopinnata</i> sp. nov., represented by two specimens collected 738 m and 1604 m deep off Puerto Rico and Hawaii, respectively, is recognized in the family Schizopathidae. The new species is characterized by a monopodial, unbranched corallum; simple, suboppositely arranged pinnules in two anterolateral rows along the stem with nearly 90° distal angles, spaced 12–17 mm apart in a row, and with smooth and triangular spines 0.05–0.08 mm tall; and polyps 4–9 mm in transverse diameter. A phylogeny composed of 90 taxa representing species in Schizopathi

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9

Horowitz, Jeremy, Dennis M. Opresko, Santiago Herrera, Colleen M. Hansel, and Andrea M. Quattrini. "Ameripathidae, a new family of antipatharian corals (Cnidaria, Anthozoa, Hexacorallia, Antipatharia)." ZooKeys 1203 (May 31, 2024): 355–75. https://doi.org/10.3897/zookeys.1203.121411.

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A new family of antipatharian corals, Ameripathidae (Cnidaria: Anthozoa: Antipatharia), is established for <i>Ameripathes pseudomyriophylla</i> Opresko & Horowitz, gen. et sp. nov. The new family resembles Myriopathidae and Stylopathidae in terms of the morphology of the polyps and tentacles and the pinnulate branching of the corallum. Phylogenetic analysis using a genomic data set of 741 conserved element loci indicates that the new family is sister to a clade containing the Myriopathidae, Stylopathidae, Antipathidae, and Aphanipathidae.

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10

Reginato, Marcelo, Kurt M. Neubig, Lucas C. Majure, and Fabian A. Michelangeli. "The first complete plastid genomes of Melastomataceae are highly structurally conserved." PeerJ 4 (November 29, 2016): e2715. http://dx.doi.org/10.7717/peerj.2715.

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BackgroundIn the past three decades, several studies have predominantly relied on a small sample of the plastome to infer deep phylogenetic relationships in the species-rich Melastomataceae. Here, we report the first full plastid sequences of this family, compare general features of the sampled plastomes to other sequenced Myrtales, and survey the plastomes for highly informative regions for phylogenetics.MethodsGenome skimming was performed for 16 species spread across the Melastomataceae. Plastomes were assembled, annotated and compared to eight sequenced plastids in the Myrtales. Phylogenet

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11

Hu, Xiang-Zhou, Cen Guo, Sheng-Yuan Qin, De-Zhu Li, and Zhen-Hua Guo. "Deep genome skimming reveals the hybrid origin of Pseudosasa gracilis (Poaceae: Bambusoideae)." Plant Diversity, June 2023. http://dx.doi.org/10.1016/j.pld.2023.06.001.

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12

Nauheimer, Lars, Lujing Cui, Charles Clarke, Darren M. Crayn, Greg Bourke, and Katharina Nargar. "Genome skimming provides well resolved plastid and nuclear phylogenies, showing patterns of deep reticulate evolution in the tropical carnivorous plant genus Nepenthes (Caryophyllales)." Australian Systematic Botany, 2019. http://dx.doi.org/10.1071/sb18057.

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Nepenthes is a genus of carnivorous plants consisting of ~160 species that are distributed in the paleotropics. Molecular systematics has so far not been able to resolve evolutionary relationships of most species because of the limited genetic divergence in previous studies. In the present study, we used a genome-skimming approach to infer phylogenetic relationships on the basis of 81 plastid genes and the highly repetitive rRNA (external transcribed spacer (ETS)–26S) for 39 accessions representing 34 species from eight sections. Maximum-likelihood analysis and Bayesian inference were performe

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13

Ahuja, Namrata, Xuwen Cao, Darrin T. Schultz, et al. "Giants among Cnidaria: large nuclear genomes and rearranged mitochondrial genomes in siphonophores." Genome Biology and Evolution, March 19, 2024. http://dx.doi.org/10.1093/gbe/evae048.

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Abstract Siphonophores (Cnidaria:Hydrozoa) are abundant predators found throughout the ocean and are important constituents of the global zooplankton community. They range in length from a few centimeters to tens of meters. They are gelatinous, fragile, and difficult to collect, so many aspects of the biology of these roughly 200 species remain poorly understood. To survey siphonophore genome diversity, we performed Illumina sequencing of 32 species sampled broadly across the phylogeny. Sequencing depth was sufficient to estimate nuclear genome size from k-mer spectra in 6 specimens, ranging f

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14

Mo, Zhi-Qiong, Chao-Nan Fu, Alex D. Twyford, et al. "Evaluating the utility of deep genome skimming for phylogenomic analyses: a case study in the species-rich genus Rhododendron." Plant Diversity, May 2025. https://doi.org/10.1016/j.pld.2025.04.006.

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15

Liu, Bin‐Bin, Zhi‐Yao Ma, Chen Ren, et al. "Capturing single‐copy nuclear genes, organellar genomes, and nuclear ribosomal DNA from deep genome skimming data for plant phylogenetics: A case study in Vitaceae." Journal of Systematics and Evolution, September 2021. http://dx.doi.org/10.1111/jse.12806.

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16

Garrett, Phen, Hannes Becher, Galina Gussarova, et al. "Pervasive Phylogenomic Incongruence Underlies Evolutionary Relationships in Eyebrights (Euphrasia, Orobanchaceae)." Frontiers in Plant Science 13 (May 27, 2022). http://dx.doi.org/10.3389/fpls.2022.869583.

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Disentangling the phylogenetic relationships of taxonomically complex plant groups is often mired by challenges associated with recent speciation, hybridization, complex mating systems, and polyploidy. Here, we perform a phylogenomic analysis of eyebrights (Euphrasia), a group renowned for taxonomic complexity, with the aim of documenting the extent of phylogenetic discordance at both deep and at shallow phylogenetic scales. We generate whole-genome sequencing data and integrate this with prior genomic data to perform a comprehensive analysis of nuclear genomic, nuclear ribosomal (nrDNA), and

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17

Xie, Si‐Yu, Xiao‐Hua Lin, Jun‐Ru Wang, et al. "Unraveling evolutionary pathways: allopolyploidization and introgression in polyploid Prunus (Rosaceae)." Plant Journal 123, no. 1 (2025). https://doi.org/10.1111/tpj.70320.

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SUMMARYAllopolyploidization, resulting from hybridization and subsequent whole‐genome duplication (WGD), is a fundamental mechanism driving evolutionary diversification across various lineages within the Tree of Life. The polyploid Prunus (Rosaceae), significant for its economic and agricultural value, provides an ideal model for investigating the evolutionary dynamics associated with allopolyploidy. In this study, we utilized deep genome skimming (DGS) data to demonstrate a comprehensive analytical framework for elucidating the underlying allopolyploidy that includes a newly adapted tool (DGS

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18

Raza, Mustafa, Edgardo M. Ortiz, Lea Schwung, Gentaro Shigita, and Hanno Schaefer. "Resolving the phylogeny of Thladiantha (Cucurbitaceae) with three different target capture pipelines." BMC Ecology and Evolution 23, no. 1 (2023). http://dx.doi.org/10.1186/s12862-023-02185-z.

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Abstract Background Despite recent advances, reliable tools to simultaneously handle different types of sequencing data (e.g., target capture, genome skimming) for phylogenomics are still scarce. Here, we evaluate the performance of the recently developed pipeline Captus in comparison with the well-known target capture pipelines HybPiper and SECAPR. As test data, we analyzed newly generated sequences for the genus Thladiantha (Cucurbitaceae) for which no well-resolved phylogeny estimate has been available so far, as well as simulated reads derived from the genome of Arabidopsis thaliana. Resul

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19

Jin, Ze‐Tao, Dai‐Kun Ma, Guang‐Ning Liu, et al. "Advancing Pyrus phylogeny: Deep genome skimming‐based inference coupled with paralogy analysis yields a robust phylogenetic backbone and an updated infrageneric classification of the pear genus (Maleae, Rosaceae)." TAXON, March 28, 2024. http://dx.doi.org/10.1002/tax.13163.

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AbstractThe lack of a robust phylogenetic backbone has posed significant challenges to proposing an infrageneric taxonomic classification of the pear genus, Pyrus, a widely distributed Eurasian lineage of Rosaceae. This issue has been exacerbated by limited informative loci and inaccessible taxon sampling. To address these limitations, we conducted extensive taxon sampling, encompassing 78 Pyrus ingroup individuals representing 32 species, along with 4 outgroup species. This comprehensive sampling strategy covers a wide range of morphological and geographical variations. To enable accurate phy

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20

Xue, Tian-Tian, Steven B. Janssens, Bin-Bin Liu, and Sheng-Xiang Yu. "Phylogenomic conflict analyses of the plastid and mitochondrial genomes via deep genome skimming highlight their independent evolutionary histories: A case study in the cinquefoil genus Potentilla sensu lato (Potentilleae, Rosaceae)." Molecular Phylogenetics and Evolution, October 2023, 107956. http://dx.doi.org/10.1016/j.ympev.2023.107956.

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21

Jin, Xin‐Jie, Yan Yu, Han‐Yang Lin, et al. "Revisiting the backbone phylogeny and inferring the evolutionary trends in inflorescence of Elsholtzieae (Lamiaceae): new insights from orthologous nuclear genes." Cladistics, February 18, 2025. https://doi.org/10.1111/cla.12604.

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AbstractThe angiosperm tribe of Elsholtzieae (Lamiaceae) is characterized by complex inflorescences and has notable medicinal and economic significance. Relationships within Elsholtzieae, including the monophyly of Elsholtzia and Keiskea, and relationships among Mosla, Keiskea and Perilla, remain uncertain, hindering insights into inflorescence evolution within the tribe. Using hybridization capture sequencing and deep genome skimming data analysis, we reconstruct a phylogeny of Elsholtzieae using 279 orthologous nuclear loci from 56 species. We evaluated uncertainty among relationships using

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