More from less: genome skimming for nuclear markers for animal phylogenomics, a case study using decapod crustaceans

Tan, Mun Hua, Gan, Han Ming, Bracken-Grissom, Heather, Chan, Tin-Yam, Grandjean, Frederic and Austin, Christopher M 2021, More from less: genome skimming for nuclear markers for animal phylogenomics, a case study using decapod crustaceans, Journal of crustacean biology, vol. 41, no. 2, pp. 1-7, doi: 10.1093/jcbiol/ruab009.

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Title More from less: genome skimming for nuclear markers for animal phylogenomics, a case study using decapod crustaceans
Author(s) Tan, Mun HuaORCID iD for Tan, Mun Hua orcid.org/0000-0003-3396-8213
Gan, Han MingORCID iD for Gan, Han Ming orcid.org/0000-0001-7987-738X
Bracken-Grissom, Heather
Chan, Tin-Yam
Grandjean, Frederic
Austin, Christopher MORCID iD for Austin, Christopher M orcid.org/0000-0003-1848-6267
Journal name Journal of crustacean biology
Volume number 41
Issue number 2
Start page 1
End page 7
Total pages 7
Publisher Oxford University Press
Place of publication Oxford, Eng.
Publication date 2021-06
ISSN 0278-0372
1937-240X
Keyword(s) freshwater crayfishes
histones
mitochondria
NGS
phylogenetics
ribosomal genes
Summary Low coverage genome sequencing is rapid and cost-effective for recovering complete mitochondrial genomes for crustacean phylogenomics. The recovery of high-copy-number nuclear genes, including histone H3, 18S and 28S ribosomal RNAs, is also possible using this approach based on our research with freshwater crayfishes (Astacidea). We explored the potential of genome skimming (GS) to recover additional nuclear genes from shallow sequencing projects using decapod crustaceans. Using an in silico-baited approach, we recovered three additional core histone genes (H2A, H2B, and H4) from our low-coverage decapod dataset (99 species, 69 genera, 38 families, 10 infraorders). Phylogenetic analyses using various combinations of mitochondrial and nuclear genes for the entire decapod dataset and a subset of 40 species of crayfishes showed that the evolutionary rates for different classes of genes varied widely. A very high level of congruence was nevertheless found between trees from the six nuclear genes and those derived from the mitogenome sequences for freshwater crayfish. These findings indicate that nuclear genes recovered from the same genome skimming datasets designed to obtain mitogenomes can be used to support more robust and comprehensive phylogenetic analyses. Further, a search for additional intron-less nuclear genes identified several high-copy-number genes across the decapod dataset, and recovery of NaK, PEPCK, and GAPDH gene fragments is possible at slightly elevated coverage, suggesting the potential and utility of GS in recovering even more nuclear genetic information for phylogenetic studies from these inexpensive and increasingly abundant datasets.
Language eng
DOI 10.1093/jcbiol/ruab009
Indigenous content off
Field of Research 0602 Ecology
0603 Evolutionary Biology
0608 Zoology
HERDC Research category C1 Refereed article in a scholarly journal
ERA Research output type C Journal article
Persistent URL http://hdl.handle.net/10536/DRO/DU:30152796

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