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Rapid recovery of nuclear and mitochondrial genes by genome skimming from Northern Hemisphere freshwater crayfish

journal contribution
posted on 2017-11-01, 00:00 authored by F Grandjean, Mun Hua Tan, Han Ming Gan, Yin Peng Lee, T Kawai, R J Distefano, M Blaha, A J Roles, Chris AustinChris Austin
Molecular phylogenetics has benefited tremendously from the advent of next-generation sequencing, enabling quick and cost-effective recovery of whole mitogenomes via an approach referred to as 'genome skimming'. Recently, genome skimming has been utilised to recover highly repetitive nuclear genes such as 18S and 28S ribosomal RNA genes that are useful for inferring deeper evolutionary relationships. To address some outstanding issues in the relationships among Northern Hemisphere freshwater crayfish (Astacoidea), we sequenced the partial genome of crayfish species from Asian, North American and European genera and report the successful recovery of whole mitogenome sequences in addition to three highly repetitive nuclear genes, namely histone H3, 18S and 28S ribosomal RNA. Consistent with some previous studies using short mtDNA and nuclear gene fragments, phylogenetic analyses based on the concatenation of recovered mitochondrial and/or nuclear sequences recovered the Asian cambarid lineage as basal to all astacids and North American cambarids, which conflicts with the current taxonomic classification based on morphological and reproduction-related characters. Lastly, we show that complete H3, 18S and 28S ribosomal RNA genes can also be consistently recovered from a diverse range of animal taxa, demonstrating the potential wide utility of genome skimming for nuclear markers. Zoologica Scripta

History

Journal

Zoologica scripta

Volume

46

Issue

6

Pagination

718 - 728

Publisher

Wiley

Location

London, Eng.

ISSN

0300-3256

eISSN

1463-6409

Language

eng

Publication classification

C Journal article; C1 Refereed article in a scholarly journal

Copyright notice

2017, Royal Swedish Academy of Sciences