Biology subjects

Kiontke, K.

Publications and source records attributed to Kiontke, K..

5 recordsLinked to original sources

bioRxiv2025

Genome evolution in parthenogenetic nematodes shaped by chromosome rearrangements and rare sex

In contrast to their dioecious relatives, members of the parthenogenetic Diploscapter nematode genus harbour their entire genome within a single pair of highly heterozygous chromosomes. To examine how this unusual karyotype relates to the evolution of parthenogenesis, we generated chromosome-level assemblies for two species in this clade: Diploscapter pachys and Diploscapter coronatus. Sequence comparisons revealed that the two genomes are colinear across their entirety, and that multiple ancestral chromosome fusions and extensive genomic rearrangements preceded the divergence of these two species. The presence of shortened telomeres and extended subtelomeric repeats suggests that the fusions arose from defects in telomere function in the lineage. Our analysis also identified an introgression event after divergence of the two species, suggesting that their parthenogenetic lifestyle may have been punctuated by rare sexual reproduction. These findings shed new light on how telomere loss, chromatin architecture, and reproductive strategies interconnect in shaping chromosome evolution.

genomics↗

bioRxiv2024

Transcriptional control of C. elegans male tail tip morphogenesis by DMD-3

Sexual dimorphic morphogenesis is governed by DM-domain transcription factors (TFs) in many animals, but how these transcriptional control links to the morphogenetic mechanisms is insufficiently known. The DM-domain TF DMD-3 in C. elegans is the master regulator of a male-specific development that changes the shape of the tail tip from long and pointed in larvae to short and round in adults. This tail tip morphogenesis (TTM) requires cell-shape changes, cell migration and fusion. To understand how transcriptional regulation by DMD-3 governs TTM, we used male-specific ChIP-seq to identify its direct targets. We found 1,755 DMD-3 bound sites. We identify a DMD-3 associated binding motif and validate its function in TTM. This motif is similar to the binding motif of EOR-1, and we suggest that DMD-3 acts cooperatively with EOR-1 and possibly other TFs. DMD-3 targets 270 genes that play a role in TTM. These genes include other TFs but also effectors and components of morphogenetic mechanisms. By deleting the DMD-3 bound region endogenously and observing changes in reporter expression and tail tip phenotypes, we identify tissue specific enhancers in the cis-regulatory region of fos-1, pan-1, nmy-2 and hmr-1 that play a role in TTM. For fos-1, we propose that a feed-forward loop is responsible for tail-tip specific increase of gene-expression. This study provides insights into the architecture of the genetic regulatory network controlling a morphogenetic process. Article SummaryDM domain transcription factors are often responsible for sexually dimorphic morphogenesis, but how they connect to morphogenetic mechanisms is insufficiently known. Here, we use ChIP-seq to determine the direct targets of DMD-3, which is the master regulator of male-specific tail tip morphogenesis (TTM) in C. elegans. We find that DMD-3 targets 270 TTM genes which include other transcription factors but also effectors and components of morphogenetic mechanisms. This study provides insights into the architecture of the genetic regulatory network controlling a morphogenetic process.

developmental biology↗

bioRxiv2023

Homologies and evolution of male tail characters in rhabditid and diplogastrid nematodes

A major question in evolutionary biology is how often the same developmental events, mechanisms and genes are reused in the recurrent evolution of similar phenotypes. If this happens frequently, it would suggest that evolution is often constrained by developmental genetic mechanisms. To help address this question, we used adherens junction staining and laser ablation to analyze the development underlying several features of nematode male tails have evolved recurrently. We find that recurrent evolution has sometimes employed similar developmental events (parallel evolution) and sometimes different events (convergent evolution). Specifically, phasmid position changed four times via cell migration and never by switches in cell lineage polarity; different genital papillae are missing in species with less than nine; and tail tip morphogenesis was gained at least twice (once with tail tip cell fusions and once without) and lost at least twice. As in previous analyses, we also find that genital papilla positions have shifted differently in different lineages relative to their conserved positions of origin in the lateral hypodermis. In particular, the v1 papilla homolog in diplogastrids has moved dorsally relative to the other v-papillae and lies posterior to the v2 papilla. The prevalence of recurrently evolved characters (homoplasy) suggests that caution should be exercised when using these characters for phylogenetic inference. On the other hand, because of their recurrent evolution, these characters provide good models for investigating how developmental and genetic systems may bias, constrain or allow phenotypic evolution.

evolutionary biology↗

bioRxiv2023

Pellioditis pelhami n. sp. (Nematoda: Rhabditidae) and Pellioditis pellio (Schneider, 1866), earthworm associates from different subclades within Pellioditis (syn. Phasmarhabditis Andrassy, 1976)

Recently, much attention has been focused on a group of rhabditid nematodes called Phasmarhabditis, a junior synonym of Pellioditis, as a promising source of biocontrol agents for invasive slugs. Pellioditis pelhami n. sp. was first isolated from earthworms near Pelham Bay Park in Bronx, New York, USA, in 1990 and has been found to be pathogenic to slugs as well as some earthworms. It has also been used in several comparative developmental studies. Here, we provide a description of this species, as well as a redescription of a similar earthworm-associated nematode, Pellioditis pellio Schneider, 1866, re-isolated from the type locality. Although P. pelhami n. sp. and P. pellio are morphologically similar, they are reproductively isolated. Molecular phylogenetic analysis places both species in a clade that includes all species previously described as Phasmarhabditis which are associated with gastropods. Phasmarhabditis Andrassy, 1976 is therefore a junior synonym of Pellioditis Dougherty, 1953. Also, P. bohemica Nermut, P[u][z]a, Mekete & Mra[c]ek, 2017, described to be a facultative parasite of slugs, is found to be a junior synonym of Pellioditis pellio (Schneider, 1866), adding to evidence that P. pellio is associated with both slugs and earthworms. The earthworm-associated species P. pelhami n. sp. and P. pellio represent different subclades within Pellioditis, suggesting that Pellioditis species in general have a broader host range than just slugs. Because of this, caution is warranted in using these species as biological control agents until more is understood about their ecology.

zoology↗

bioRxiv2020

EUAdb: a resource for COVID-19 test development

Due to the sheer number of COVID-19 (coronavirus disease 2019) cases, the prevalence of asymptomatic cases and the fact that undocumented cases appear to be significant for transmission of the causal virus, SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), there is an urgent need for increased SARS-CoV-2 testing capability that is both efficient and effective1. In response to the growing threat of the COVID-19 pandemic in February, 2020, the FDA (US Food and Drug Administration) began issuing Emergency Use Authorizations (EUAs) to laboratories and commercial manufacturers for the development and implementation of diagnostic tests1. So far, the gold standard assay for SARS-CoV-2 detection is the RT-qPCR (real-time quantitative polymerase chain reaction) test2. However, the authorized RT-qPCR test protocols vary widely, not only in the reagents, controls, and instruments they use, but also in the SARS-CoV-2 genes they target, what results constitute a positive SARS-CoV-2 infection, and their limit of detection (LoD). The FDA has provided a web site that lists most of the tests that have been issued EUAs, along with links to the authorization letters and summary documents describing these tests1. However, it is very challenging to use this site to compare or replicate these tests for a variety of reasons. First, at least 12 of 18 tests for EUA submissions made prior to March 31, 2020, are not listed there. To our knowledge, no EUAs have been issued for these applications. Second, the data are not standardized and are only provided as longhand prose in the summary documents. Third, some details (e.g. primer sequences) are absent from several of the test descriptions. Fourth, for tests provided by commercial manufacturers, summary documents are completely missing. To address at least the first three issues, we have developed a database, EUAdb (EUAdb.org), that holds standardized information about EUA-issued tests and is focused on RT-qPCR diagnostic tests, or "high complexity molecular-based laboratory developed tests"1. By providing a standardized ontology and curated data in a relational architecture, we seek to facilitate comparability and reproducibility, with the ultimate goal of consistent, universal and high-quality testing nationwide. Here, we document the basics of the EUAdb data architecture and simple data queries. The source files can be provided to anyone who wants to modify the database for his/her own research purposes. We ask that the original source of the files be made clear and that the database not be used in its original or modified forms for commercial purposes.

bioinformatics↗