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

2025/05/26 by Ole K. Tørresen, Benedicte Garmann-Aarhus, Siv Nam Khang Hoff +8 · 1 voice
Biochemistry, Genetics and Molecular Biology · Environmental Science · #Genetic and phenotypic traits in livestock #Fish Ecology and Management Studies

paper · pdf · doi:10.1093/jhered/esaf036

openalex publication_date 2025/05/26 · openalex created_date 2025/06/13 · openalex updated_date 2026/06/23

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 Mb and 960 Mb for pseudo-haplotypes one and two, respectively. Both the L. fluviatilis pseudo-haplotypes have been scaffolded into 82 pseudo-chromosomes, 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).

Citations

• MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
• IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era
• GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes
• Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm
• Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies
• UniProt: the Universal Protein Knowledgebase in 2023
• YaHS: yet another Hi-C scaffolding tool
• A draft human pangenome reference
• MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads
• Protein-to-genome alignment with miniprot
• BUSCO update: novel and streamlined workflows along with broader and\n deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and\n viral genomes
• STRIDE: Species Tree Root Inference from Gene Duplication Events
• KMC 3: counting and manipulating k-mer statistics
• Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM

Discussions

• These assemblies provide new insights into lamprey evolution and diversity. Paper: doi.org/10.1093/jher... Corresponding author: www.mn.uio.no/cees/e... #JHered #OpenAccess [bsky, 0 points, 0 comments]