Genetic and functional diversity of allorecognition receptors in the urochordate, .

Allorecognition in is controlled by a highly polymorphic locus (the ), and functionally similar to missing-self recognition utilized by Natural Killer cells-compatibility is determined by sharing a self-allele, and integration of activating and inhibitory signals determines outcome. We had found these signals were generated by two -encoded receptors, called and Here we show that genes are members of an extended family consisting of >37 loci, and co-expressed with an even more diverse gene family-the (). The are membrane proteins related to , but include conserved tyrosine motifs, including ITIMs and hemITAMs.

Haxe as a Swiss knife for bioinformatic applications: the SeqPHASE case story.

Haxe is a general purpose, object-oriented programming language supporting syntactic macros. The Haxe compiler is well known for its ability to translate the source code of Haxe programs into the source code of a variety of other programming languages including Java, C++, JavaScript, and Python. Although Haxe is more and more used for a variety of purposes, including games, it has not yet attracted much attention from bioinformaticians.

Do fish gut microbiotas vary across spatial scales? A case study of Diplodus vulgaris in the Mediterranean Sea.

Background: Biogeography has been linked to differences in gut microbiota in several animals. However, the existence of such a relationship in fish is not clear yet. So far, it seems to depend on the fish species studied.

Molecular analyses of groundwater amphipods (Crustacea: Niphargidae) from Luxembourg: new species reveal limitations of morphology-based checklists.

Niphargus amphipods were collected from 2007 to 2018 at 98 sites comprising artificial caverns, springs and interstitial waters in the Grand Duchy of Luxembourg. Opportunistic sampling was combined with passive trapping. Specimen identification was achieved using morphological keys and molecular data.

Cave Thiovulum (Candidatus Thiovulum stygium) differs metabolically and genomically from marine species.

Thiovulum spp. (Campylobacterota) are large sulfur bacteria that form veil-like structures in aquatic environments. The sulfidic Movile Cave (Romania), sealed from the atmosphere for ~5 million years, has several aqueous chambers, some with low atmospheric O (~7%).

Methanotrophy by a Mycobacterium species that dominates a cave microbial ecosystem.

So far, only members of the bacterial phyla Proteobacteria and Verrucomicrobia are known to grow methanotrophically under aerobic conditions. Here we report that this metabolic trait is also observed within the Actinobacteria. We enriched and cultivated a methanotrophic Mycobacterium from an extremely acidic biofilm growing on a cave wall at a gaseous chemocline interface between volcanic gases and the Earth's atmosphere.

Comparative genome analysis of Vagococcus fluvialis reveals abundance of mobile genetic elements in sponge-isolated strains.

Background: Vagococcus fluvialis is a species of lactic acid bacteria found both free-living in river and seawater and associated to hosts, such as marine sponges. This species has been greatly understudied, with no complete genome assembly available to date, which is essential for the characterisation of the mobilome.

Results: We sequenced and assembled de novo the complete genome sequences of five V.

Chromosome-level genome assembly reveals homologous chromosomes and recombination in asexual rotifer .

Bdelloid rotifers are notorious as a speciose ancient clade comprising only asexual lineages. Thanks to their ability to repair highly fragmented DNA, most bdelloid species also withstand complete desiccation and ionizing radiation. Producing a well-assembled reference genome is a critical step to developing an understanding of the effects of long-term asexuality and DNA breakage on genome evolution.

Solving the Coral Species Delimitation Conundrum.

Distinguishing coral species is not only crucial for physiological, ecological, and evolutionary studies but also to enable effective management of threatened reef ecosystems. However, traditional hypotheses that delineate coral species based on morphological traits from the coral skeleton are frequently at odds with tree-based molecular approaches. Additionally, a dearth of species-level molecular markers has made species delimitation particularly challenging in species-rich coral genera, leading to the widespread assumption that interspecific hybridization might be responsible for this apparent conundrum.

Genome Assembly of the Cold-Tolerant Leaf Beetle Gonioctena quinquepunctata, an Important Resource for Studying Its Evolution and Reproductive Barriers between Species.

Coleoptera is the most species-rich insect order, yet is currently underrepresented in genomic databases. An assembly was generated for ca. 1.

Overcoming uncollapsed haplotypes in long-read assemblies of non-model organisms.

Background: Long-read sequencing is revolutionizing genome assembly: as PacBio and Nanopore technologies become more accessible in technicity and in cost, long-read assemblers flourish and are starting to deliver chromosome-level assemblies. However, these long reads are usually error-prone, making the generation of a haploid reference out of a diploid genome a difficult enterprise. Failure to properly collapse haplotypes results in fragmented and structurally incorrect assemblies and wreaks havoc on orthology inference pipelines, yet this serious issue is rarely acknowledged and dealt with in genomic projects, and an independent, comparative benchmark of the capacity of assemblers and post-processing tools to properly collapse or purge haplotypes is still lacking.

An Indo-Pacific coral spawning database.

The discovery of multi-species synchronous spawning of scleractinian corals on the Great Barrier Reef in the 1980s stimulated an extraordinary effort to document spawning times in other parts of the globe. Unfortunately, most of these data remain unpublished which limits our understanding of regional and global reproductive patterns. The Coral Spawning Database (CSD) collates much of these disparate data into a single place.

Population genetics of the brooding coral Seriatopora hystrix reveals patterns of strong genetic differentiation in the Western Indian Ocean.

Coral reefs provide essential goods and services but are degrading at an alarming rate due to local and global anthropogenic stressors. The main limitation that prevents the implementation of adequate conservation measures is that connectivity and genetic structure of populations are poorly known. Here, the genetic diversity and connectivity of the brooding scleractinian coral Seriatopora hystrix were assessed at two scales by genotyping ten microsatellite markers for 356 individual colonies.

Computational Characterization of the mtORF of Pocilloporid Corals: Insights into Protein Structure and Function in Lineages from Contrasting Environments.

More than a decade ago, a new mitochondrial Open Reading Frame (mtORF) was discovered in corals of the family Pocilloporidae and has been used since then as an effective barcode for these corals. Recently, mtORF sequencing revealed the existence of two differentiated lineages occurring in sympatry along the environmental gradient of the Red Sea (18.5°C to 33.

Toward perfect reads: self-correction of short reads via mapping on de Bruijn graphs.

Motivation: Short-read accuracy is important for downstream analyses such as genome assembly and hybrid long-read correction. Despite much work on short-read correction, present-day correctors either do not scale well on large datasets or consider reads as mere suites of k-mers, without taking into account their full-length sequence information.

Results: We propose a new method to correct short reads using de Bruijn graphs and implement it as a tool called Bcool.