Biology subjects

Prochotta, D.

Publications and source records attributed to Prochotta, D..

4 recordsLinked to original sources

bioRxiv2025

Chromosome-level genome assembly of the lemon sole Microstomus kitt (Pleuronectiformes: Pleuronectidae)

BackgroundThe lemon sole (Microstomus kitt) is a culinary fish from the family of righteye flounders (Pleuronectidae) inhabiting sandy and shallow offshore grounds of the North Sea, the western Baltic Sea, the English Channel, the shallow waters of Great Britain and Ireland as well as the Bay of Biscay and the coastal waters of Norway. FindingsHere, we present the chromosome-level genome assembly of the lemon sole. We applied PacBio HiFi sequencing on the PacBio Revio system to generate a highly complete and contiguous reference genome. The resulting assembly has a contig N50 of 17.2 Mbp and a scaffold N50 of 27.2 Mbp. The total assembly length is 628 Mbp, of which 616 Mbp were scaffolded into 24 chromosome-length scaffolds. The identification of 99.7% complete BUSCO genes indicates a high assembly completeness. ConclusionsThe chromosome-level genome assembly of the lemon sole provides a high-quality reference genome for future population genomic analyses of a commercially valuable edible fish.

evolutionary biology↗

bioRxiv2024

High-speed whole-genome sequencing of a Whippet: Rapid chromosome-level assembly and annotation of an extremely fast dog's genome

BackgroundThe time required for sequencing and de novo assembly of genomes is highly dependent on the interaction between laboratory work, sequencing capacity, and the bioinformatics workflow. As a result, genome projects are often not only limited by financial, computational and sequencing platform resources, but also delayed by second party sequencing service providers. By bringing together academic biodiversity institutes and a medical diagnostics company with extensive sequencing capabilities and know-how, we aimed at generating a high-quality mammalian de novo genome in the shortest possible time period. Therefore, we streamlined all processes involved and chose a very fast dog as a model: The Whippet. FindingsWe present the first chromosome-level genome assembly of the Whippet. We used PacBio long-read HiFi sequencing and reference-guided scaffolding to generate a high-quality genome assembly. The final assembly has a contig N50 of 55 Mbp and a scaffold N50 of 65.7 Mbp. The total assembly length is 2.47 Gbp, of which 2.43 Gpb were scaffolded into 39 chromosome-length scaffolds. In addition, we used available mammalian genomes and transcriptome data to annotate the genome assembly. The annotation resulted in 28,383 transcripts resembling a total of 90.9% complete BUSCO genes and identified a repeat content of 36.5%. ConclusionsSequencing, assembling, and scaffolding the chromosome-level genome of the Whippet took less than a week and adds a high-quality reference genome to the list of domestic dog breeds sequenced to date.

genomics↗

bioRxiv2023

Near chromosome-level and highly repetitive genome assembly of the snake pipefish Entelurus aequoreus (Syngnathiformes: Syngnathidae)

The snake pipefish, Entelurus aequoreus (Linnaeus, 1758), is a slender, up to 60 cm long, northern Atlantic fish that dwells in open seagrass habitats and has recently expanded its distribution range. The snake pipefish is part of the family Syngnathidae (seahorses and pipefish) that has undergone several characteristic morphological changes, such as loss of pelvic fins and elongated snout. Here, we present a highly contiguous, near chromosome-scale genome of the snake pipefish assembled as part of a university masters course. The final assembly has a length of 1.6 Gbp in 7,391 scaffolds, a scaffold and contig N50 of 62.3 Mbp and 45.0 Mbp and L50 of 12 and 14, respectively. The largest 28 scaffolds (>21 Mbp) span 89.7% of the assembly length. A BUSCO completeness score of 94.1% and a mapping rate above 98% suggest a high assembly completeness. Repetitive elements cover 74.93% of the genome, one of the highest proportions so far identified in vertebrate genomes. Demographic modeling using the PSMC framework indicates a peak in effective population size (50 - 100 kya) during the last interglacial period and suggests that the species might largely benefit from warmer water conditions, as seen today. Our updated snake pipefish assembly forms an important foundation for further analysis of the morphological and molecular changes unique to the family Syngnathidae.

genomics↗

bioRxiv2020

Chromosome-level genome assembly of a benthic associated Syngnathiformes species: the common dragonet, Callionymus lyra

BackgroundThe common dragonet, Callionymus lyra, is one of three Callionymus species inhabiting the North Sea. All three species show strong sexual dimorphism. The males show strong morphological differentiation, e.g., species-specific colouration and size relations, while the females of different species have few distinguishing characters. Callionymus belongs to the benthic associated clade of the order Syngnathiformes. The benthic associated clade so far is not represented by genome data and serves as an important outgroup to understand the morphological transformation in long-snouted syngnatiforms such as seahorses and pipefishes. FindingsHere, we present the chromosome-level genome assembly of C. lyra. We applied Oxford Nanopore Technologies long-read sequencing, short-read DNBseq, and proximity-ligation-based scaffolding to generate a high-quality genome assembly. The resulting assembly has a contig N50 of 2.2 Mbp, a scaffold N50 of 26.7 Mbp. The total assembly length is 568.7 Mbp, of which over 538 Mbp were scaffolded into 19 chromosome-length scaffolds. The identification of 94.5% of complete BUSCO genes indicates high assembly completeness. Additionally, we sequenced and assembled a multi-tissue transcriptome with a total length of 255.5 Mbp that was used to aid the annotation of the genome assembly. The annotation resulted in 19,849 annotated transcripts and identified a repeat content of 27.66%. ConclusionsThe chromosome-level assembly of C. lyra provides a high-quality reference genome for future population genomic, phylogenomic, and phylogeographic analyses.

genomics↗