Akopyan M, Genchev M, Armstrong EE, Mooney JA (2025) Reference genome choice compromises population genetic analyses. Cell 188(24):6939-6952.e11. https://doi.org/10.1016/j.cell.2025.08.034
Article CAS PubMed Google Scholar
Alonge M, Soyk S, Ramakrishnan S, Wang X, Goodwin S, Sedlazeck FJ et al (2019) RaGOO: fast and accurate reference-guided scaffolding of draft genomes. Genome Biol 20(1):224. https://doi.org/10.1186/s13059-019-1829-6
Article PubMed PubMed Central Google Scholar
Alonge M, Lebeigle L, Kirsche M, Jenike K, Ou S, Aganezov S et al (2022) Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing. Genome Biol 23(1):258. https://doi.org/10.1186/s13059-022-02823-7
Article CAS PubMed PubMed Central Google Scholar
Andersson L, Bekkevold D, Berg F, Farrell ED, Felkel S, Ferreira MS et al (2024) How fish population genomics can promote sustainable fisheries: a road map. Annu Rev Anim Biosci 12:1–20. https://doi.org/10.1146/annurev-animal-021122-102933
Chen S (2023) Ultrafast one‐pass FASTQ data preprocessing, quality control, and deduplication using fastp. iMeta 2(2):e107. https://doi.org/10.1002/imt2.107
Article CAS PubMed PubMed Central Google Scholar
Chen J, Wang W (2021) Genetic diversity and genetic differentiation of Megalobrama populations inferred by mitochondrial markers. Genes Genom 43(10):1119–1132. https://doi.org/10.1007/s13258-021-01126-8
Chen J, Guo J, Wang ZQ, Wang WM (2020) Morphological variation among the four Megalobrama species inferred by X-ray photography. Aquac Res 51(10):3999–4010. https://doi.org/10.1111/are.14743
Chen J, Liu H, Gooneratne R, Wang Y, Wang W (2022) Population genomics of Megalobrama provides insights into evolutionary history and dietary adaptation. Biology (Basel) 11(2):186. https://doi.org/10.3390/biology11020186
Article CAS PubMed PubMed Central Google Scholar
Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO et al (2021) Twelve years of SAMtools and BCFtools. Gigascience 10(2):1–4. https://doi.org/10.1093/gigascience/giab008
Ding R, Yu D, Yang K, Wu X, Liu H (2025) Chromosome-level genome assembly and whole-genome resequencing revealed contrasting population genetic differentiation of black bream (Megalobrama skolkovii) (teleostei: Cyprinidae) allopatric and sympatric to its kin species. Ecol Evol 15(1):e70874. https://doi.org/10.1002/ece3.70874
Article PubMed PubMed Central Google Scholar
Fan G, Song Y, Yang L, Huang X, Zhang S, Zhang M et al (2020) Initial data release and announcement of the 10,000 fish genomes project (Fish10K). Gigascience 9(8):giaa080. https://doi.org/10.1093/gigascience/giaa080
Article PubMed PubMed Central Google Scholar
Fricke R, Eschmeyer W, Van der Laan R (2026) Eschmeyer's catalog of fishes: genera, species, references. http://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp. Accessed 01/2026
Froese R, Pauly D (2025) FishBase. https://www.fishbase.org/. Accessed 11/2025
Gong D, Wang X, Yang J, Liang J, Tao M, Hu F et al (2023) Protection and utilization status of Parabramis and Megalobrama germplasm resources. Reprod Breed 3(1):26–34. https://doi.org/10.1016/j.repbre.2023.01.003
Hu X, Luan P, Cao C, Li C, Jia Z, Ge Y et al (2019) Characterization of the mitochondrial genome of Megalobrama terminalis in the Heilong River and a clearer phylogeny of the genus Megalobrama. Sci Rep 9(1):8509. https://doi.org/10.1038/s41598-019-44721-2
Article CAS PubMed PubMed Central Google Scholar
Hu J, Fan J, Sun Z, Liu S (2020a) NextPolish: a fast and efficient genome polishing tool for long-read assembly. Bioinformatics 36(7):2253–2255. https://doi.org/10.1093/bioinformatics/btz891
Article CAS PubMed Google Scholar
Hu X, Ma B, Li C, Jia Z, Jiang X, Ge Y et al (2020b) Genetic differentiation of an endangered Megalobrama terminalis population in the Heilong River within the genus Megalobrama. Diversity. https://doi.org/10.3390/d12100404
Hunt M, Kikuchi T, Sanders M, Newbold C, Berriman M, Otto TD (2013) REAPR: a universal tool for genome assembly evaluation. Genome Biol 14(5):R47. https://doi.org/10.1186/gb-2013-14-5-r47
Article PubMed PubMed Central Google Scholar
Kajitani R, Toshimoto K, Noguchi H, Toyoda A, Ogura Y, Okuno M et al (2014) Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads. Genome Res 24(8):1384–1395. https://doi.org/10.1101/gr.170720.113
Article CAS PubMed PubMed Central Google Scholar
Li H (2018) Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34(18):3094–3100. https://doi.org/10.1093/bioinformatics/bty191
Article CAS PubMed PubMed Central Google Scholar
Li H (2025) Seqtk: Toolkit for processing sequences in FASTA/Q formats. https://github.com/lh3/seqtk. Accessed 11/2025
Liu K, Xie N (2024a) Enhancing the accuracy of reference-guided genomic assemblies: Implementing RagTag correction for reference-guided scaffolds. Research Square [Preprint]. https://doi.org/10.21203/rs.3.rs-4621443/v1
Liu K, Xie N (2024b) Full-length transcriptome assembly of black amur bream (Megalobrama terminalis) as a reference resource. Mol Biol Rep 51(1):1101. https://doi.org/10.1007/s11033-024-10056-z
Article CAS PubMed Google Scholar
Liu H, Chen C, Lv M, Liu N, Hu Y, Zhang H et al (2021) A chromosome-level assembly of blunt snout bream (Megalobrama amblycephala) genome reveals an expansion of olfactory receptor genes in freshwater fish. Mol Biol Evol 38(10):4238–4251. https://doi.org/10.1093/molbev/msab152
Article CAS PubMed PubMed Central Google Scholar
Liu K, Xie N, Wang Y (2023) Exploring cross-species genetic diversity: unveiling new insights in Megalobrama through whole genome-wide simple sequence repeats. Conserv Genet 25(2):393–407. https://doi.org/10.1007/s10592-023-01575-6
Maurstad MF, Hoff SNK, Cerca J, Ravinet M, Bradbury I, Jakobsen KS et al (2025) Reference genome bias in light of species-specific chromosomal reorganization and translocations. Genome Biol 26(1):355. https://doi.org/10.1186/s13059-025-03761-w
Article CAS PubMed PubMed Central Google Scholar
Miga KH, Wang T (2021) The need for a human pangenome reference sequence. Annu Rev Genom Hum Genet 22:81–102. https://doi.org/10.1146/annurev-genom-120120-081921
Nevado B, Ramos-Onsins SE, Perez-Enciso M (2014) Resequencing studies of nonmodel organisms using closely related reference genomes: optimal experimental designs and bioinformatics approaches for population genomics. Mol Ecol 23(7):1764–1779. https://doi.org/10.1111/mec.12693
Article CAS PubMed Google Scholar
Prasad A, Lorenzen ED, Westbury MV (2022) Evaluating the role of reference-genome phylogenetic distance on evolutionary inference. Mol Ecol Resour 22(1):45–55. https://doi.org/10.1111/1755-0998.13457
Quinlan AR, Hall IM (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26(6):841–842. https://doi.org/10.1093/bioinformatics/btq033
Article CAS PubMed PubMed Central Google Scholar
Ranallo-Benavidez TR, Jaron KS, Schatz MC (2020) GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes. Nat Commun 11(1):1432. https://doi.org/10.1038/s41467-020-14998-3
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