Dual-reference projection defines a callable core and reference-sensitive shell in a Qiantang River draft assembly

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

Article  PubMed  Google Scholar 

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

Article  Google Scholar 

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

Article  CAS  Google Scholar 

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

Article  CAS  Google Scholar 

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

Article  CAS  Google Scholar 

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

Article  Google Scholar 

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

Article  CAS  Google Scholar 

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

Article  CAS  Google Scholar 

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

Article  PubMed  Google Scholar 

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

Article  CAS  PubMed  PubMed Central  Google Scholar 

Comments (0)

No login
gif