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

Abstract

2017). Rapid recovery of nuclear and mitochondrial genes by genome skimming from Northern Hemisphere freshwater crayfish. -Zoologica Scripta, 46, 718-728. 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.

Salmo macrostigma(Teleostei, Salmonidae): Nothing more than a brown trout (S. trutta) lineage?

“…New techniques may facilitate the retrieval of more complete mitochondrial (van der Valk et al, 2017) and nuclear data (e.g. Grandjean et al, 2017) from museum specimens.…”

Comparative morphology of crayfish mandibles, with insight into their evolution

“…Studies based on morphology (cf. Braband, Kawai, & Scholtz, ; Kawai, ) are consistent in that the two general Holarctic branches (ie, the European astacids with American Pacifastacus and the American cambarids together with the East Asiatic Cambaroides ) form sister monophyletic assemblages, and subsequent molecular studies (Braband et al, ; Bracken‐Grissom et al, ; Breinholt, Perez‐Losada, & Crandall, ; Crandall, ; Grandjean et al, ; Owen et al, ) have instead shown a wide variety of relationships among these four key taxa.…”

“…Similar results were revealed in molecular studies by Ahn et al (), Johnson, Elder Jr., Thompson, Hightower, and Bechler (), and Owen et al (). Recent molecular phylogenies (Crandall & De Grave, ; Grandjean et al, ) based on extensive genetic sampling have confirmed that Cambaroides is the most basally separated Holarctic taxon, and the American cambarids are sister to the clade of European and American astacids. Based on not only own molecular analysis but also morphological distinctions and geographic affiliations, Crandall and De Grave () established for the genus Cambaroides the third Holarctic crayfish family, Cambaroididae.…”

“…During the evolution of the Holarctic crayfish, the molar ridge of the mandibles revealed a feeble subdivision into two plesiomorphic corneous molar fields in the phylogenetically most basally derivative Cambaroides (see Grandjean et al, ; Kawai, ; Kawai et al, ); the caudal molar field was further subdivided into two short ridges in Cambaroides . This characteristic is largely shared by representatives of the genera Cambarellus and Cambarus , members of the American cambarids derived from the second evolutionary division of the Holarctic crayfish.…”

Whole genome sequencing of Rhodotorula mucilaginosa isolated from the chewing stick (Distemonanthus benthamianus): insights into Rhodotorula phylogeny, mitogenome dynamics and carotenoid biosynthesis

“…Given the high abundance of 252 mitochondrial organelle in an actively dividing cell, the depth of mitochondrial-derived 253 sequencing reads will be substantially higher than that of the nuclear genome. While this 254 genomic feature has been used to rapidly recover complete mitogenome via the genome 255 skimming approach (Gan et al 2014;Grandjean et al 2017), overly high read depth of 256 the mitogenome obtained from a full genome sequencing data is likely to be detrimental 257 to de novo assembly due to the accumulation of sequencing errors, leading to the 258 generation of fragmented and/or incomplete mitogenome assembly (Mirebrahim et al 259 2015). In this work, we demonstrate that a simple subsampling approach followed by de 260 novo assembly could be an effective way to recover complete mitogenome from fungal 261 genome sequencing data.…”