Next-generation sequencing as means to retrieve tick systematic markers, with the focus on Nuttalliella namaqua (Ixodoidea: Nuttalliellidae)

Abstract

Nuclear ribosomal RNA (18S and 28S rRNA) and mitochondrial genomes are commonly used in tick systematics. The ability to retrieve these markers using nextgeneration sequencing was investigated using the tick Nuttalliella namaqua. Issues related to nuclear markers may be resolved using this approach, notably, the monotypic status of N. namaqua and its basal relationship to other tick families. Four different Illumina datasets (~55 million, 100 bp reads each) were generated from a single tick specimen and assembled to give 350k-390k contigs. A genome size of ~1 Gbp was estimated with low levels of repetitive elements. Contigs (>1000 bp, >50-fold coverage) present in most assemblies (n=69), included host-derived 18S and 28S rRNA, tick and host-derived transposable elements, full-length tick 18S and 28 rRNA, the mitochondrial genome in single contig assemblies and the histone cassette.Coverage for the nuclear rRNA genes was above 1000-fold confirming previous sequencing errors in the 18S rRNA gene, thereby maintaining the monotypic status of this tick. Nuclear markers for the soft tick Argas africolumbae were also retrieved from next-generation data. Phylogenetic analysis of a concatenated 18S-28S rRNA dataset supported the grouping of N. namaqua at the base of the tick tree and the two main tick families in separate clades. This study confirmed the monotypic status of N. namaqua and its basal relationship to other tick families. Next-generation sequencing of genomic material to retrieve high quality nuclear and mitochondrial systematic markers for ticks is viable and may resolve issues around conventional sequencing errors when comparing closely related tick species.

Ancestral reconstruction of tick lineages

“…In both these cases, N. namaqua would be incorporated into the respective families, with no resolution to their disparate lifestyle histories. Nuttalliella namaqua may also group basal to the argasid and ixodid families thereby retaining the three tick families as well as the monophyletic nature of the Ixodida, as was observed for 18S, 18S-28S rRNA and mitochondrial genome analysis (Chen et al 2014;Gu et al 2014;Mans et al 2015Mans et al , 2012Mans et al , 2011. Parsimony considerations of the latter position on the tick tree suggest a monophyletic origin for hematophagy in ticks ).…”

“…Reconstruction of the evolutionary history of the tick lineage (Ixodida) in broad terms have previously been addressed on various levels Murrell, 2004, 2002;Black et al 1997;Burger et al 2014aBurger et al , 2013Burger et al , 2012de la Fuente et al 2015;Dobson and Barker, 1999;Durden and Beati, 2014;Hoogstraal, 1985;Klompen and Oliver, 1993;Klompen et al 2000Klompen et al , 1996aMans, 2014;Mans, 2011;Mans and Neitz, 2004a;Mans et al 2015;, 2011, 2003a, 2002aMurrell et al 2005;Oliver, 1989), but no critical review regarding progress in this field in recent years exist. The current review will assess our knowledge regarding ancestral reconstruction of the tick lineage, as well as challenges faced for successful reconstruction in the future.…”

“…The Acari is composed of the Acariformes Figure 1: The lineage specific history of the Ixodida. Indicated are a current phylogenetic relationships for Eukaryotes (Adl, et al 2012), Metazoa , Arthropoda (Giribet and Edgecombe, 2012), Acari (Klompen et al 2007) and Ixodida (Mans, 2011;Mans et al 2015). Numbers in brackets indicate current number of species according to as updated (Mans, 2011). and the Parasitiformes, the latter divided into Opilioacarida, Holothyrida, Ixodida and Mesostigmata ( Fig.…”

“…It should also be noted that the nuclear dataset analysis did not correlate in all studies, notably because incomplete 18S-28S rRNA datasets were used in some studies (Burger et al 2014a, while inclusion of a complete 18S-28S dataset for N. namaqua supports its basal position (Mans et al 2015). Nuclear ribosomal genes are generally considered more informative at family and subfamily level, while mitochondrial data may be better at resolving intrageneric and intraspecific relationships (Durden and Beati, 2014;Mans et al 2015).…”

“…Incomplete taxon sampling may bias phylogenies (Wiens and Morrill, 2011) and this may be a fundamental problem in tick systematics, since only five basal lineages can be recognized (Nuttalliellidae, Argasinae, Ornithodorinae, Prostriata and Metastriata) (Mans et al 2015). The possibility exists that significant lineage specific extinctions occurred, within extant lineages and even among basal lineages .…”