Caenorhabditis monodelphis Slos &amp; Sudhaus 2017
Creators: name: Slos, Dieter
name: Sudhaus, Walter
name: Stevens, Lewis
name: Bert, Wim
name: Blaxter, Mark
Publisher: name: Zenodo
Year: 2017
Subjects: Biodiversity
Taxonomy
Animalia
Nematoda
Secernentea
Rhabditida
Rhabditidae
Caenorhabditis
Caenorhabditis monodelphis

description: <i>Caenorhabditis monodelphis</i> 1 sp. n. Slos &amp; Sudhaus = <i>Caenorhabditis</i> sp. SB341 [7] = <i>Caenorhabditis</i> sp. SB341 and <i>Caenorhabditis</i> sp. n. SB341 [36] = <i>Caenorhabditis</i> sp. n. 1 (SB341) and (lapse) <i>Caenorhabditis</i> sp. n. 4 (SB341) [10] = <i>Caenorhabditis</i> sp. 1 SB341 [6, 8, 37] = <i>Caenorhabditis</i> sp. 4 SB341 [38] (Figs. 1, 2, 3 and 4; Table 1) Adult Small species (female 0.72 - 1.04 mm, male 0.65 - 0.77 mm); cuticle thin, ca. 1 pm wide and finely annulated, 0.8 pm wide at midbody. Lateral field inconspicuous, about 9% of body width, consisting one ridge that can be <b>traced</b> anteriorly to the level of the median bulb and posteriorly at level of rectum in females and about 1% spicules length anterior of the cloacal aperture in males. Six lips slightly protruding, each with one apical papilliform labial sensillum and a second circle of four sublateral cephalic sensilla in both <b>sexes</b>; amphids opening on the lateral lips, hardly discernible. Buccal tube long and slender, more than twice the width in lip region, pharyngeal sleeve envelopes nearly half of the stoma, the anterior as well as the posterior end of the tube appear slightly thickened, <b>cheilostom</b> inconspicuous, arcade cells forming the gymnostom sometimes visible; glottoid apparatus completely absent. Pharynx with a prominent median bulb, diameter more than 90% of diameter of terminal bulb; terminal bulb pyriform, with double chambered haustrulum, the anterior chamber smallish; cardia conspicuous, opens funnel-like in intestine. Nerve ring encircles isthmus in its anterior part in living specimens, m ore to the middle of the isthmus in heat relaxed or preserved specimens; deirids usually conspicuous in the lateral field at level of beginning of terminal bulb, sometimes not visible in heat relaxed animals; pore of excretory-secretory system hard to discern posterior of deirid level. Two gland cells ventral and slightly posterior of term inal bulb conspicuous in live specimens. Lateral canals visible in live specimens extending anteriorly to two stoma length from the anterior end and ending at rectum level in the female. Postdeirids usually very conspicuous dorsally of the lateral field at about 75% of body length in both <b>sexes</b> and about half the length between vulva and beginning of rectum (or at level of posterior end of uterus remnant) in females, sometimes not visible in heat relaxed specimens. Female Maximum body diameter clearly anterior of the vulva, vulva position 65% body length, a transverse slit, bordered in both ends by cuticular longitudinal flaps, vulva lips moderately protruding, four diagonal vulval muscles conspicuous; one pseudocoelomocyte exists anterior of gonad flexure ventrally. Genital tracts asymmetrical; posterior branch rudimentary, sac like, on the left hand side of intestine, without flexure, almost as long as body diameter at the level of the vulva, containing spermatozoa (Fig. 2); anterior branch right of intestine, reflexed dorsally close to the pharynx, flexure more than half the length of the gonad (measured from vulva to flexure); at the flexure oocytes in several rows, downstream in one row, oocytes predominantly growing in the last position, where granules are stored inside; sphincter between oviduct and uterus, only a few sperm cells in oviduct, most of them in uterus and blind sac; oviparous, one egg at a time in uterus (rarely two), segmentation starts in the uterus. Rectum a little S-shaped, rectal gland cells very small, posterior anal lip slightly protuberant. Tail short, panagrolaimid, dorsally convex, with offset tip tapering, smooth to somewhat telescope-like by cuticle forming a sleeve-like structure; tail tip with tiny hooks, mostly one dorsal, but also subventral (compare with <i>Poikilolaimus);</i> opening of phasmids located at 60-65% of tail length, shortly anterior of tip, phasmid glands not reaching anus level. Male Testis right of intestine, ventrally reflexed in a certain distance posterior of pharynx; flexure relatively short. One pseudocoelomocyte between pharynx and flexure ventrally. Bursa well developed, peloderan, anteriorly open, with smooth margin and sometimes terminally indented, posterior part of velum transversely striated. Nine pairs of genital papillae (GP) present, two of them anterior of the cloaca, genital papilla 1 (GP1) and GP2 spaced, GP3 to GP6 and GP7 to GP9 clustered, GP5 and GP7 point to the dorsal side of the velum, GP6 slightly bottle shaped, GP8 and GP9 fused at base, GP2 and GP8 not reaching the margin of velum. Phasmids forming small tubercles to the ventral side posterior of the last GP; formula of GPs: vl,v2/(v3,v4,ad,v5) (pd,v6,v7)ph. Precloacal sensillum small, precloacal lip simple (according to type A of W Sudhaus and K Kiontke [39]), postcloacal sensilla long filamentous. Spicules short and stout, tawny, separate, slightly curved, with prominent head; shaft with a transverse seam, with a prominent longitudinal ridge, a dorsal lamella, and an oval “window”, the tip notched. Gubernaculum dorsally projecting, flexible, in the distal part following the contour of the spicules, spoon shaped in ventral view. Dauer larva Unsheathed, mouth closed; stoma long, slender. Pharyngeal sleeve covering about half of the stoma; pharynx with welldeveloped median and terminal bulbs; corpus length ca. 52% of pharynx length. Nerve ring somewhat in the middle between the middle and terminal bulb. Genital primordium at about 60% of body length, elongated oval in shape. Tail conical. Amphids, lateral lines, position excretory pore, deirids and phasmids not observed. <i>Aberration</i> In one female a second set of “sensilla” were observed a short distance posterior to postdeirids, possibly a duplication of the postdeirids. <b>Type</b> <i>carrier and <i>locality</i> </i> Holotype and paratypes of <i>Caenorhabditis monodelphis</i> sp. n. were isolated from the tunnels of <i>Cis castaneus</i> (Herbst, 1793) (Ciidae, Coleoptera) in the bracket fungus <i>Ganoderma applanatum</i> (Polyporales) on a stump of the common beech (<i>Fagus sylvatica)</i> a few centimetres above the ground in Berlin-Grunewald in April 2001. The same sample included individuals of <i>Diploscapter</i> sp., <i>Plectus</i> sp., <i>Oscheius dolichura</i> and one individual dorylaimid and mononchid. <b>Type</b> <i>material</i> Holotype male (collection num ber <i>W</i> T 3684) and five female and four male paratypes (WT 3685, W T 3686) are deposited in the National Plant Protection Organization Wageningen, The Netherlands. In addition, four female and four male paratypes, are deposited in the collection of Museum Voor Dierkunde at Ghent University, Ghent, Belgium, five female and three male paratypes in Museum für Naturkunde an der Humboldt-Universität zu Berlin, Berlin, Germany. Additional paratypes are available in the UGent Nematode Collection (slides UGnem158, 159 &amp; 160) of the Nematology Research Unit, Department of Biology, Ghent University, Ghent, Belgium. <i>Diagnosis and relationship</i> <i>Caenorhabditis monodelphis</i> sp. n. can be recognised as a <i>Caenorhabditis</i> based on the thickened GP6 and the clearly visible postdeirids. <i>Caenorhabditis monodelphis</i> sp. n. is distinguished from all other described <i>Caenorhabditis</i> species by the presence of a monodelphic genital tract in the female with a blind sac posterior the vulva, a panagrolaimid female tail shape, adults with only one ridge on the lateral field, a very long and slender stoma without visible glottoid apparatus and male with short, stout spicule with bifurcate tip. <i> <i>Ecology</i> and</i> biology <i>Caenorhabditis monodelphis</i> sp. n. is a gonochoristic species with both males and females. Females are oviparous and carry only one egg (rarely two eggs). Development from egg to adult took about 5-6 days in juice prepared from brown algae at room temperature. Development from dauer larva to adults was completed in less than 3 days at 20 °C on NA seeded with OP50. The lifespan of adults is at m inim um 14 days for males and 17 days for females. One pair of adults produced 167 offspring in 8 days and the daily production of fertile eggs was 6-31 (mean 18; <i>n =</i> 14). After the reproductive phase, females lived 9-1 4 days <i>(n =</i> 3) with males present. <i>Caenorhabditis monodelphis</i> sp. n. has until now only been found in <i>Ganoderma</i> and <i>Fomes</i> in Germany and Belgium in relation with the ciid beetle <i>Cis castaneus.</i> The <i>Ganoderma</i> carrying <i>C</i>. <i>monodelphis</i> sp. n. from Oslo was not investigated for the presence of <i>C</i>. <i>castaneus.</i> In fungal fruiting bodies lacking the beetle C. <i>monodelphis</i> sp. n. was not found. Dauers of C. <i>monodelphis</i> sp. n. were found under the elytra of the beetle, but were not found internally when the beetle was further dissected. These findings indicate a phoretic association with the beetle. As only dauer larvae were isolated from beetles, while adults and larvae were present in the fruiting bodies, <i>we</i> infer that <i>C</i>. <i>monodelphis</i> sp. n. exit from dauer within the mushroom, develop to adulthood and start to reproduce. The food source of the species in natural conditions is not known, but they survive and reproduce easily on £ <i>coli</i> OP50 in <b>culture.</b> <i>Genome sequence</i> of <i>an inbred strain</i> of <i>Caenorhabditis</i> <i>monodelphis <i>sp.</i> n.</i> We sequenced the genome of an inbred strain (JU1677) of <i>C</i>. <i>monodelphis</i> sp. n. using Illumina sequencing technology to ~110 <b>x</b> coverage. The genome was assembled into 6,864 scaffolds, spanning 115.1 Mb with a scaffold N50 of 49.4 kb (Table 2). CEGMA (Core Eukaryotic Gene Mapping Approach) [40] scores suggested the assembly is of high completeness. W e predicted 17,180 protein coding gene models using RNA-Seq evidence. These statistics, and the overall gene content and structure of the assembly were largely in keeping with those determined for other <i>Caenorhabditis</i> species. The genome was larger than that of <i>C</i>. <i>elegans</i> and <i>C</i>. <i>briggsae,</i> which are hermaphroditic species, but smaller than that of C. <i>remanei,</i> a gonochoristic species. We carried out preliminary comparisons of the structure and <b>content</b> of the <i>C</i>. <i>monodelphis</i> sp. n. genome with those of other sequenced <i>Caenorhabditis</i> species. The number of genes identified was lower than estimates for most other <i>Caenorhabditis</i> species. To compare the gene structures of <i>C</i>. <i>monodelphis</i> sp. n. to that of <i>C</i>. <i>elegans,</i> we identified 6,174 orthologous gene pairs and calculated gene structure statistics (Table 3, Fig. 5.). To minimize bias from erroneous gene predictions (such as merged or split genes), orthologous gene pairs which differed in CDS length by 20% were considered outliers. <i>C</i>. <i>monodelphis</i> sp. n. genes were typically longer than their orthologues in <i>C</i>. <i>elegans.</i> W e also found a clear trend toward more coding exons per gene in <i>C</i>. <i>monodelphis</i> sp. n. than in <i>C</i>. <i>elegans</i> (Fig. 5 a). A few examples of <i>C</i>. <i>monodelphis</i> sp. n. gene models compared to those of orthologues in <i>C</i>. <i>elegans</i> are shown (Fig. 5 b). Although introns are, on average, shorter in <i>C</i>. <i>monodelphis</i> sp. n. than in <i>C</i>. <i>elegans,</i> <i>C. monodelphis</i> genes typically have a longer total span of introns than C. <i>elegans</i> transcripts (Table 3, Fig. 5.). afrom anus to flexure in the female; from <b>cloaca</b> to flexure in the male bn = 7 “Scaffolds shorter than 500 bp were not considered <i>C</i>. <i> <i>monodelphis</i> sp. n. is sister</i> to <b>other</b> <i>known</i> <i>Caenorhabditis</i> We clustered a total of 634,564 protein sequences from <i>C. monodelphis</i> sp. n., twenty-two other <i>Caenorhabditis</i> species, and two rhabditomorph outgroup species (<i>Oscheius tipulae;</i> data courtesy of M. A. Félix, and <i>Heterorhabditis bacteriophora</i>) to define putative orthologues. We identified 34,425 putatively orthologous groups containing at least two members, 303 of which were either single copy or absent across all 25 species. These single copy orthologues were aligned, and the alignments concatenated and used to perform maximum-likelihood and Bayesian inference analysis using RAxML and PhyloBayes, respectively. Both analysis methods resulted in an identical topology, with the placement of <i>C</i>. <i>monodelphis</i> sp. n. arising basally to all other <i>Caenorhabditis</i> species (Fig. 6). All branches had maximal support except for three nodes within the <i>Elegans</i> super-group. Our analysis included data from several new and currently undescribed putative species of <i>Caenorhabditis,</i> including <i>C</i>. sp. 21 which is the sister taxon to the <i>Drosophilae</i> plus <i>Elegans</i> super-groups and <i>C</i>. sp. 31 which forms the first branch in the <i>Elegans</i> super-group. <i>C</i>. sp. 38 is placed within the <i>Drosophilae</i> super-group, while <i>C</i>. sp. 26, <i>C</i>. sp. 32 (sister to C. <i>afin)</i> and C. sp. 40 (sister to C. <i>sinica</i>) are all members of the <i>Elegans</i> super-group. From these analyses we conclude that <i>C</i>. <i>monodelphis</i> sp. n. is sister to all other known <i>Caenorhabditis.</i> <i>Stemspecies pattern reconstruction</i> Our phylogenetic analyses were based on species with whole genome data available, and thus did not include the full known diversity of the genus. The stemspecies pattern was reconstructed based on ingroup and outgroup comparison. Previous molecular phylogenetic analyses of <i>Caenorhabditis</i> species using a small num ber of marker genes [10] placed <i>C</i>. <i>monodelphis</i> sp. n. and <i>C</i>. <i>sonorae</i> [41] as sister species, again arising at the <b>base</b> of the genus. The following morphological synapomorphies can <b>be</b> hypothesised to support a <i>C</i>. <i>monodelphis</i> sp. n. - <i>C</i>. <i>sonorae</i> clade: m outh opening triangular (Fig. 4 b), spicule having a complicated tip (notched or dentated) and a longish thin walled “window” in the blade (Figs, li, 41), postcloacal sensilla being filiform (Fig. 4 k), and the female tail shortened to less than three times anal body width. Other similarities between both these species are plesiomorphic. <i>Caenorhabditis</i> and its sister group constitute the monophylum Anarhabditis within the Rhabditina. For convenience, we will call the sister clade of <i>Caenorhabditis</i> Protoscapter (Fig. 7): it comprises <i>“ Protorhabditis</i> ”, <i>Prodontorhabditis, Diploscapter</i> and <i>Sclerorhabditis</i> [42]. To reconstruct the characters of the stemspecies of <i>Caenorhabditis</i> it is necessary to consider the morphologies of all these taxa, and not only the taxa for which we have molecular data. <i>“ Protorhabditis ”</i> is paraphyletic. The <i>Oxyuroides</i> group is sister taxon of <i>Prodontorhabditis</i> [43, 44], and the <i>Xylocola</i> group may be sister taxon of <i>Diploscapter! Sclerorhabditis.</i> However, the two species <i>Protorhabditis elaphri (Hirschmann in Osche, 1952)</i> and <i>P. tristis</i> [45] appear to represent basal branches in Protoscapter (compare [43]). These last two species, despite the paucity of <b>information</b> available for them, are crucial for comparisons that will illuminate the stemspecies patterns of Anarhabditis, Protoscapter and <i>Caenorhabditis.</i> All values are medians aorthologous gene pairs which differed in CDS <b>length</b> by 20% were not included By ingroup comparison we reconstruct the following characters of the <b>stemspecies</b> of Anarhabditis without differentiating <b>them</b> into apo- or plesiomorphies (on apomorphies <b>see</b> the legend of Fig. 7): <b>- adults</b> of small size (less than 1 mm); - lips not offset from <b>anterior</b> end; - four cephalic sensilla present in male and female; - stoma with pharyngeal sleeve (<b>stegostom</b> length nearly that of gymnostom); - median bulb of pharynx strongly developed, corpus intima with transverse ridging, terminal bulb with double haustrulum; - gonochoristic; - female tail elongate conoid; - gonads amphidelphic, the anterior branch right and the posterior left of intestine; - vulva at midbody, a transverse slit; - oviparous, usually only one egg at a time in the uteri; - male gonad on the right side, reflexed to the ventral; - bursa peloderan and anteriorly open, oval-shaped in ventral view, with smooth margin, terminally not notched; - 9 pairs of even genital papillae, two precloacal largely spaced, GP <b>3</b> -6 evenly spaced, the last three GPs forming a tight cluster; GP1, GP5 and GP7 terminate on the dorsal surface of the bursa velum; - phasmids open behind GP9, inconspicuous; - bursa formula thus vl, <i>v</i> 2/v3,v4,ad,v5 (pd,v6,v7)ph; - male tail tip present; - 1 + 2 circumcloacal sensilla inconspicuous, precloacal lip simple; - spicules separate, stout, head not rounded, behind the shaft a slight ventral projection, dorsal part of blade weakly <b>cuticularised</b> (velum), its tip possibly not even (argued below); - gubernaculum simple spatulate; - dauerlarvae with double cuticle (ensheathed), not waving. Discussion <b>Taxonomy of <i>Caenorhabditis monodelphis</i></b> <b>sp.</b> n. <i>Caenorhabditis monodelphis</i> sp. n. is a new species of <i>Caenorhabditis</i> supported by its phylogenetic position as inferred from 303 molecular markers, morphology, <b>habitat</b> and specific association with <i>Cis castaneus</i> (Coleoptera). Morphologically, it could <b>be</b> confused with <i>“ Protorhabditis "</i> species because of the <b>absence</b> of a clear glottoid apparatus. A glottoid apparatus has <b>been</b> lost 5-6 <b>times</b> independently within “ Rhabditidae ” [46] and, <b>as</b> illustrated <b>here</b>, also in <i>C. monodelphis</i> sp. n. This <b>species</b> resembles <b>species</b> from <i>“ Protorhabditis "</i> With a <i>very</i> long stoma without glottoid <b>apparatus</b>, but differs from the <i>Oxyuroides-</i> group within <i>‘ Protorhabditis "</i> in having an open bursa and GP1 not anterior of the bursa. <b>It</b> is differentiated from the <i>Xylocola-</i> group within <i>“ Protorhabditis "</i> in having nine genital papillae. <b>Previously</b>, <i>Caenorhabditis</i> <b>has been</b> characterised <b>as</b> having the following apomorphic <b>characteristics: the</b> presence of a dorsal <b>velum</b> on the spicule, <b>a</b> lateral field <b>with</b> three ridges, an unsheathed dauer juvenile <b>and a slightly thickened</b> GP6 [42], W ith the discovery <b>and</b> description of <i>C</i>. <i>monodelphis</i> sp. n. the num <b>ber</b> of <b>lateral</b> ridges is no longer an apomorphic character of <i> <i>Caenorhabditis</i>,</i> since <i>C</i>. <i>monodelphis</i> sp. n. <b>only has</b> one <b>lateral</b> ridge. Association with fungivorous beetles Species of <i>Caenorhabditis</i> <b>are</b> known <b>to occur</b> in <b>soil</b>, compost, cadavers of insects, some <b>plant material</b> and the intestine of <b>birds</b> [10], and <b>can most easily be</b> <b>isolated</b> from rotting fruits, flowers and <b>stems [3], <i>Caenorhabditis elegans</i></b> has also <b>been</b> found <b>infesting cultures</b> of the m ushroom <i>Agaricus bisporus</i> [47
description: Published as part of <i>Dieter Slos, Walter Sudhaus, Lewis Stevens, Wim Bert &amp; Mark Blaxter, 2017, Caenorhabditis monodelphis sp. n.: defining CrossMark the stem morphology and genomics of the genus Caenorhabditis, pp. 1-15 in BMC Zoology 2 (4)</i> on pages 3-12, DOI: 10.1186/S40850-017-0013-2, http://zenodo.org/record/322316
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