Comparison of whole-genome assemblies of European river lamprey (Lampetra fluviatilis) and brook lamprey (Lampetra planeri)

Sep 29, 2026

We present haplotype-resolved whole-genome assemblies from one individual European river lamprey (Lampetra fluviatilis) and one individual brook lamprey (Lampetra planeri), usually regarded as sister species. The L. fluviatilis assembly includes two pseudo-haplotypes spanning 1073 Mb and 963 Mb, while the L. planeri assembly spans 1049 Mb and 960 Mb. Both species’ pseudo-haplotypes were scaffolded into 82 pseudochromosomes and annotated to identify 21,479/16,973 genes for L. fluviatilis and 24,961/21,668 genes for L. planeri. Genome comparisons and phylogenetics suggest a species complex, potentially reflecting distinct ecotypes.

LanguageEnglish

CategoryResearch & Report

FormatPDF

Pages11

Reading Time28 min

AccessFree to download

Abstract

Key words

Introduction

Genome Resources Comparison of whole-genome assemblies of European river lamprey (Lampetra fluviatilis) and brook lamprey (Lampetra planeri) Ole K. Tørresen1,§, Benedicte Garmann-Aarhus1,5,§, Siv Nam Khang Hoff1, Sissel Jentoft1, Mikael Svensson2, Eivind Schartum3, Ave Tooming-Klunderud1, Morten Skage1, Anders Krabberød1,4, Leif Asbjørn Vøllestad1, Kjetill S. Jakobsen1,* 1Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway 2SLU Artdatabanken, SLU-Swedish Species Information Centre, Uppsala, Sweden 3Department of Natural Sciences and Environmental Health, University of South-Eastern Norway, Bø i Telemark, Norway 4Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Norway 5 Present address: Natural History Museum, University of Oslo, Oslo, Norway §Equal contributions. * Corresponding author: Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, NO-0316 Oslo, Norway. Email: [k.s.jakobsen@ibv.uio.no](k.s.jakobsen@ibv.uio.no) Corresponding Editor: William Murphy Abstract We present haplotype-resolved whole-genome assemblies from one individual European river lamprey (Lampetra fluviatilis) and one individual brook lamprey (Lampetra planeri), usually regarded as sister species. The genome assembly of L. fluviatilis consists of pseudo-haplotype one, spanning 1073 Mb and pseudo-haplotype two, spanning 963 Mb. Likewise for the L. planeri specimen, the genome assembly spans 1049 Mband 960 Mb for pseudo-haplotypes one and two, respectively. Both the L. fluviatilis pseudo-haplotypes have been scaffolded into 82 pseudochromosomes, with the same number for the L. planeri pseudo-haplotypes. All four pseudo-haplotype assemblies were annotated, identifying 21,479 and 16,973 genes in pseudo-haplotypes one and two for L. fluviatilis, and 24,961 and 21,668 genes in pseudo-haplotypes one and two for L. planeri. A comparison of the genomes of L. fluviatilis and L. planeri, alongside a separate chromosome level assembly of L. fluviatilis from the UK, indicates that they form a species complex, potentially representing distinct ecotypes. This is further supported by phylogenetic analyses of the three reference Lampetra genomes in addition to sea lamprey (Petromyzon marinus) . Key words: brook lamprey, chromosomal assemblies, European river lamprey, genome sequence, Lampetra fluviatilis, Lampetra planeri Introduction Freshwater fishes reside in lakes, rivers, and streams and often migrate between different habitats, such as within and between rivers and lakes. Diadromous fishes can also sometimes migrate between freshwater and marine environments. In particular, many species in postglacial lakes show large phenotypic plasticity and also possess many morphotypes—sometimes regarded as different species. Determining what constitutes a species has been challenging for many freshwater fishes; a typical example is Salmoniformes, such as trout, charr, and whitefish (Whiteley et al., 2019). The genetic structuring following glaciations and subsequent post-glacial invasions, together with phenotypic plasticity, has led to large among-population variations in morphology, behavior, and life history. In Petromyzontidae lampreys, this has led to the evolution of so-called species pairs consisting of closely related large migratory parasitic and non-parasitic freshwater-resident species (Docker 2009). The migratory and parasitic European river lamprey (Lampetra fluviatilis) and the non-migratory and non-parasitic brook lamprey (Lampetra planeri) are regarded as sister species. They have been the subject of several genetic studies, using mtDNA (mitochondrial DNA) (Bracken et al., 2015; Cahsan et al., 2020), RADseq (restriction-site associated DNA sequencing) (Mateus et al., 2013; Rougemontet al., 2017; Hume et al., 2018), and microsatellite markers (Rougemont et al., 2015) . There is nonetheless

FAQs

What genomes were assembled in the study?

The study generated haplotype-resolved whole-genome assemblies for one European river lamprey (Lampetra fluviatilis) and one brook lamprey (Lampetra planeri).

How were the assemblies structured and scaffolded?

Each assembly comprised two pseudo-haplotypes, which were scaffolded into 82 pseudochromosomes for both species.

What main biological interpretation is supported by the genome comparison?

Comparisons between the two genomes, together with reference genome phylogenetics, indicate they form a species complex and may represent distinct ecotypes.

Sep 29, 2026

Upload by Chumphorn