Reference genomes of the Chinese perch (Siniperca chuatsi), the Eurasian perch (Perca fluviatilis) and three related fish species of the family Sinipercidae for comparative genomics and marker assisted breeding in aquaculture
General Genetics and Functional Genome Biology
Bioinformatics and Theoretical Biology
Final Report Abstract
In this international project, reference genomes for the Chinese perch (Siniperca chuatsi) and the European perch (Perca fluviatilis) were successfully created. Both reference genomes meet the highest quality requirements (assembly of whole chromosomes and very high sequence continuity). Another 4 genomes of related species (Siniperca kneri, Siniperca scherzeri, Coreoperca whiteheadi and Perca schrenkii) could be created with the help of the reference genomes. In this context, efficient bioinformatic tools were developed which enable the rapid assembly of a large number of vertebrate genomes. The genome-wide data enabled new insights into the origin of Sinipercidae and Percidae, which had a last common ancestor at the end of the Cretaceous period about 66 million years ago. For this purpose, efficient methods for phylogenetic analyzes of hundreds of genomes and transcriptomes have been developed. It was shown that this phylogenomic method can also be used to process phylogenies that are very difficult to resolve (e.g. family tree of birds). The analysis of evolving genes (positive selection) between the different species identified candidate genes which can be correlated with different phenotypic properties. For this purpose, new bioinformatic pipelines have been developed here, which enable a fast comparative annotation of genomes and the subsequent analysis of episodically evolving genes and thus allow statements to be made about which properties have developed at which point in the evolution of a respective species family. This methodology has been applied to the large number of new perch (Percidae) genomes that have been published in recent years. As an important contribution to the application in aquaculture, genetic sex markers for Siniperca sp. and Perca sp. have been developed. Lessons learned from these analyses have recently led us to the discovery of a conserved sex marker in sturgeons which before has remained undiscovered for decades despite intensive research.
Publications
- An unbiased molecular approach using 3'UTRs resolves the avian family-level tree of life. Mol Biol Evol 2020
Kuhl H, Frankl-Vilches C, Bakker A, Mayr G, Nikolaus G, Boerno ST, Klages S, Timmermann B, Gahr M
(See online at https://doi.org/10.1093/molbev/msaa191) - CSA: A high-throughput chromosome-scale assembly pipeline for vertebrate genomes. Gigascience 2020, 9(5)
Kuhl H, Li L, Wuertz S, Stock M, Liang XF, Klopp C
(See online at https://doi.org/10.1093/gigascience/giaa034) - Mandarin fish (Sinipercidae) genomes provide insights into innate predatory feeding. Commun Biol 2020, 3(1)
He S, Li L, Lv LY, Cai WJ, Dou YQ, Li J, Tang SL, Chen X, Zhang Z, Xu J, Zhang YP, Yin Z, Wuertz S, Tao YX, Kuhl H, Liang XF
(See online at https://doi.org/10.1038/s42003-020-1094-y) - A 180 My-old female-specific genome region in sturgeon reveals the oldest known vertebrate sex determining system with undifferentiated sex chromosomes, Philos Trans R Soc Lond B Biol Sci. 2021 Aug 30;376(1832):20200089
Kuhl H, Guiguen Y, Höhne C, Kreuz E, Du K, Klopp C, Lopez-Roques C, Yebra- Pimentel ES, Ciorpac M, Gessner J, Holostenco D, Kleiner W, Kohlmann K, Lamatsch DK, Prokopov D, Bestin A, Bonpunt E, Debeuf B, Haffray P, Morvezen R, Patrice P, Suciu R, Dirks R, Wuertz S, Kloas W, Schartl M, Stöck M
(See online at https://doi.org/10.1098/rstb.2020.0089)
