Archegozetes longisetosus, Aoki, 1965

Brückner, Adrian, Barnett, Austen A., Bhat, Prashant, Antoshechkin, Igor A. & Kitchen, Sheila A., 2022, Molecular evolutionary trends and biosynthesis pathways in the Oribatida revealed by the genome of Archegozetes longisetosus, Acarologia 62 (2), pp. 532-573 : 536-537

Archegozetes longisetosus ( Figure 1 ) has a diploid chromosome number (2n) of 18 ( Heethoff et al., 2006), most likely comprising 9 autosomal pairs, the typical number of nearly all studied oribatid mite species ( Figure 1d ) ( Norton et al., 1993). There are no distinct sex chromosomes in Archegozetes ; this appears to be ancestral in the Acariformes and persisted in the Oribatida

( Norton et al., 1993 ; Wrensch et al., 1994 ; Heethoff et al., 2006). Even though some XX:XO and XX:XY genetic systems have been described in the closely related Astigmata , the sex determination mechanism in oribatids, including Archegozetes , remains unknown ( Oliver Jr,

1983; Norton et al., 1993 ; Wrensch et al., 1994 ; Heethoff et al., 2006 ; Heethoff et al., 2013).

To provide genetic resources, we sequenced and assembled the genome using both Illumina short-read and Nanopore MinION long-read sequencing approaches followed by scaffolding with Hi-C technology ( Figure 1d ; Table 1 ; see also “ Materials and Methods ”). Analyses of the k-mer frequency distribution of short reads ( Table 1 ; Supplementary Figure S1 ) resulted in an estimated genome size range of 135-180 Mb, encompassing the final HiC assembled size of 143 Mb ( Table 1 ; see also “ Materials and Methods ”). Compared to genome assemblies of other acariform mites, the assembled genome size of Archegozetes is on the large end of the spectrum (with Opiella nova and O. subpectinata representing notable exceptions)( Brandt et al.,

2021), but is smaller than that of most mesostigmatid mites, ticks and spiders that on average range from ~250 Mb up to 2.5 Gb ( Grbić et al., 2011 ; Bast et al., 2016 ; Gulia-Nuss et al., 2016 ;

Hoy et al., 2016 ; Dong et al., 2017 ; Schwager et al., 2017 ; Dong et al., 2018). In the context of arthropods in general, Archegozetes ’ genome ( Table 1) is among the smaller ones and shares this feature with other arthropod model species like Tetranychus urticae (hereafter called ‘spider mite’), Drosophila , clonal raider ant and red flour beetle ( Consortium, 2008 ; Grbić et al., 2011 ;

Oxley et al., 2014 ; dos Santos et al., 2015). Even though we surface-washed the mites and only used specimens with empty alimentary tracts for sequencing, we removed a total 532 sequences

(438 long-read contigs and 94 Hi-C scaffolds) with high bacterial or fugal homology making up approximately 9 Mb of contamination in the final assembly (see supplementary Table S1).

The final filtered Hi-C genome assembly was composed of 164 scaffolds, the majority of which is composed of nine pseudochromosomes with an N 50 contiguity of 16.25 Mb ( Table 1 and

Figure 1d ).

Genome scaffolding and the analysis of genome structure in arthropods by all-vs-all chromosome conformation capture (Hi-C) is a relatively new field that has grown in recent years ( Richards, 2019). Like other arthropods, the Archegozetes genome is organized into chromosome territories, compartments, and sub-compartment structures ( Figure 1d ). Classic microscopy and fluorescent staining previously revealed that Archegozetes has a diploid set of 18 (2n) highly condensed chromosomes, and we recovered nine pseudo-chromosomes in our haploid assembly ( Heethoff et al., 2006). Even though Hi-C is often not able to resolve inter-chromosomal interactions and long range-contacts ( Quinodoz et al., 2022), we discovered multiple such contacts between different chromosomes, for instance chromosome

1 is interacting with parts of each chromosome except chromosome 5 ( Figure 1d ). One hypothesis which could explain this pattern is that the Archegozetes genome is highly compact, and chromatin is densely packed in the nucleus (see also the genome of the tomato russet mite; Greenhalgh et al., 2020).

Figures

Figure 1 The mite, Archegozetes longisetosus, in its phylogenetic and natural environment. a – Species tree of selected oribatid mites of the family Trhypochthoniidae based on phylogenetic analyses and divergence time estimates (Heethoff et al., 2011b). b – Two adults and one tritonymph of Archegozeteson a piece of leaf litter. The algae growing on the leaf serves as a food source for the mites. c – Habitus of an adult mite based on a surface rendering of a µCT-scan reconstruction. Image courtesy of Sebastian Schmelzle. d – Hi-C interaction matrix maps of the nine Archegozeteschromosomes. The corrected contacts are indicated by the color scale on the right from red (high density) to blue (low density)