{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,7]],"date-time":"2026-08-07T16:49:29Z","timestamp":1786121369979,"version":"build-2736575974"},"reference-count":72,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2026,8,7]],"date-time":"2026-08-07T00:00:00Z","timestamp":1786060800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2026,8,7]],"date-time":"2026-08-07T00:00:00Z","timestamp":1786060800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"funder":[{"name":"Hangzhou Science and Technology Commissioner Program","award":["2025TPY0034"],"award-info":[{"award-number":["2025TPY0034"]}]},{"name":"Science & Technology Innovation Program of Hangzhou Academy of Agricultural Sciences","award":["2025HNCT-01"],"award-info":[{"award-number":["2025HNCT-01"]}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Mol Genet Genomics"],"published-print":{"date-parts":[[2026,12]]},"DOI":"10.1007\/s00438-026-02489-x","type":"journal-article","created":{"date-parts":[[2026,8,7]],"date-time":"2026-08-07T04:35:40Z","timestamp":1786077340000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Pan-SSR architecture in Acrossocheilus fasciatus links cross-assembly repeat conservation, repeat-unit count variation, and genomic context"],"prefix":"10.1007","volume":"301","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7034-7235","authenticated-orcid":false,"given":"Kai","family":"Liu","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nan","family":"Xie","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,8,7]]},"reference":[{"issue":"1","key":"2489_CR1","doi-asserted-by":"publisher","first-page":"258","DOI":"10.1186\/s13059-022-02823-7","volume":"23","author":"M Alonge","year":"2022","unstructured":"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","journal-title":"Genome Biol"},{"key":"2489_CR2","doi-asserted-by":"publisher","DOI":"10.3389\/fgene.2024.1474611","volume":"15","author":"SIA Alves","year":"2024","unstructured":"Alves SIA, Dantas CWD, Macedo DB, Ramos RTJ (2024) What are microsatellites and how to choose the best tool: a user-friendly review of SSR and 74 SSR mining tools. Front Genet 15:1474611. https:\/\/doi.org\/10.3389\/fgene.2024.1474611","journal-title":"Front Genet"},{"key":"2489_CR3","doi-asserted-by":"publisher","first-page":"31","DOI":"10.3389\/fbioe.2015.00031","volume":"3","author":"M Anisimova","year":"2015","unstructured":"Anisimova M, Pecerska J, Schaper E (2015) Statistical approaches to detecting and analyzing tandem repeats in genomic sequences. Front Bioeng Biotechnol 3:31. https:\/\/doi.org\/10.3389\/fbioe.2015.00031","journal-title":"Front Bioeng Biotechnol"},{"issue":"1","key":"2489_CR4","doi-asserted-by":"publisher","first-page":"136","DOI":"10.1006\/geno.1995.1224","volume":"29","author":"SS Arcot","year":"1995","unstructured":"Arcot SS, Wang Z, Weber JL, Deininger PL, Batzer MA (1995) Alu repeats: a source for the genesis of primate microsatellites. Genomics 29(1):136\u2013144. https:\/\/doi.org\/10.1006\/geno.1995.1224","journal-title":"Genomics"},{"issue":"9","key":"2489_CR5","doi-asserted-by":"publisher","first-page":"2428","DOI":"10.1093\/gbe\/evx164","volume":"9","author":"ATM Bagshaw","year":"2017","unstructured":"Bagshaw ATM (2017) Functional mechanisms of microsatellite DNA in eukaryotic genomes. Genome Biol Evol 9(9):2428\u20132443. https:\/\/doi.org\/10.1093\/gbe\/evx164","journal-title":"Genome Biol Evol"},{"issue":"1","key":"2489_CR6","doi-asserted-by":"publisher","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","volume":"57","author":"Y Benjamini","year":"1995","unstructured":"Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J Roy Stat Soc: Ser B (Methodol) 57(1):289\u2013300. https:\/\/doi.org\/10.1111\/j.2517-6161.1995.tb02031.x","journal-title":"J Roy Stat Soc: Ser B (Methodol)"},{"issue":"2","key":"2489_CR7","doi-asserted-by":"publisher","first-page":"573","DOI":"10.1093\/nar\/27.2.573","volume":"27","author":"G Benson","year":"1999","unstructured":"Benson G (1999) Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res 27(2):573\u2013580. https:\/\/doi.org\/10.1093\/nar\/27.2.573","journal-title":"Nucleic Acids Res"},{"issue":"12","key":"2489_CR8","doi-asserted-by":"publisher","first-page":"5825","DOI":"10.1093\/molbev\/msab293","volume":"38","author":"CP Cantalapiedra","year":"2021","unstructured":"Cantalapiedra CP, Hern\u00e1ndez-Plaza A, Letunic I, Bork P, Huerta-Cepas J (2021) EggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale. Mol Biol Evol 38(12):5825\u20135829. https:\/\/doi.org\/10.1093\/molbev\/msab293","journal-title":"Mol Biol Evol"},{"issue":"2","key":"2489_CR9","doi-asserted-by":"publisher","first-page":"567","DOI":"10.1093\/gbe\/evv005","volume":"7","author":"D Chalopin","year":"2015","unstructured":"Chalopin D, Naville M, Plard F, Galiana D, Volff J-N (2015) Comparative analysis of transposable elements highlights mobilome diversity and evolution in vertebrates. Genome Biol Evol 7(2):567\u2013580. https:\/\/doi.org\/10.1093\/gbe\/evv005","journal-title":"Genome Biol Evol"},{"issue":"2","key":"2489_CR10","doi-asserted-by":"publisher","DOI":"10.1002\/imt2.107","volume":"2","author":"S Chen","year":"2023","unstructured":"Chen S (2023) Ultrafast one\u2010pass FASTQ data preprocessing, quality control, and deduplication using fastp. iMeta 2(2):e107. https:\/\/doi.org\/10.1002\/imt2.107","journal-title":"iMeta"},{"issue":"2","key":"2489_CR11","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1093\/gigascience\/giab008","volume":"10","author":"P Danecek","year":"2021","unstructured":"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\u20134. https:\/\/doi.org\/10.1093\/gigascience\/giab008","journal-title":"Gigascience"},{"issue":"4","key":"2489_CR12","doi-asserted-by":"publisher","first-page":"3545","DOI":"10.1093\/mnras\/stu2219","volume":"446","author":"L Delchambre","year":"2015","unstructured":"Delchambre L (2015) Weighted principal component analysis: a weighted covariance eigendecomposition approach. Mon Not R Astron Soc 446(4):3545\u20133555. https:\/\/doi.org\/10.1093\/mnras\/stu2219","journal-title":"Mon Not R Astron Soc"},{"issue":"1","key":"2489_CR13","doi-asserted-by":"publisher","first-page":"151","DOI":"10.1186\/s12859-025-06168-3","volume":"26","author":"L Du","year":"2025","unstructured":"Du L, Sun D, Chen J, Zhou X, Zhao K, Zeng Q et al (2025) Pytrf: a python package for finding tandem repeats from genomic sequences. BMC Bioinformatics 26(1):151. https:\/\/doi.org\/10.1186\/s12859-025-06168-3","journal-title":"BMC Bioinformatics"},{"issue":"3","key":"2489_CR14","doi-asserted-by":"publisher","first-page":"241","DOI":"10.2307\/1266041","volume":"6","author":"OJ Dunn","year":"1964","unstructured":"Dunn OJ (1964) Multiple comparisons using rank sums. Technometrics 6(3):241\u2013252. https:\/\/doi.org\/10.2307\/1266041","journal-title":"Technometrics"},{"issue":"3","key":"2489_CR15","doi-asserted-by":"publisher","first-page":"308","DOI":"10.1007\/BF00163235","volume":"40","author":"L Duret","year":"1995","unstructured":"Duret L, Mouchiroud D, Gautier C (1995) Statistical analysis of vertebrate sequences reveals that long genes are scarce in GC-rich isochores. J Mol Evol 40(3):308\u2013317. https:\/\/doi.org\/10.1007\/BF00163235","journal-title":"J Mol Evol"},{"issue":"Volume 21, 2020","key":"2489_CR16","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1146\/annurev-genom-120219-080406","volume":"21","author":"JM Eizenga","year":"2020","unstructured":"Eizenga JM, Novak AM, Sibbesen JA, Heumos S, Ghaffaari A, Hickey G et al (2020) Pangenome graphs. Annu Rev Genomics Hum Genet 21(Volume 21, 2020):139\u2013162. https:\/\/doi.org\/10.1146\/annurev-genom-120219-080406","journal-title":"Annu Rev Genomics Hum Genet"},{"issue":"6","key":"2489_CR17","doi-asserted-by":"publisher","first-page":"435","DOI":"10.1038\/nrg1348","volume":"5","author":"H Ellegren","year":"2004","unstructured":"Ellegren H (2004) Microsatellites: simple sequences with complex evolution. Nat Rev Genet 5(6):435\u2013445. https:\/\/doi.org\/10.1038\/nrg1348","journal-title":"Nat Rev Genet"},{"issue":"8","key":"2489_CR18","doi-asserted-by":"publisher","DOI":"10.1093\/gigascience\/giaa080","volume":"9","author":"G Fan","year":"2020","unstructured":"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","journal-title":"Gigascience"},{"issue":"3","key":"2489_CR19","doi-asserted-by":"publisher","DOI":"10.1186\/1755-8794-8-S3-S5","volume":"8","author":"G Fertin","year":"2015","unstructured":"Fertin G, Jean G, Radulescu A, Rusu I (2015) Hybrid de novo tandem repeat detection using short and long reads. BMC Med Genomics 8(3):S5. https:\/\/doi.org\/10.1186\/1755-8794-8-S3-S5","journal-title":"BMC Med Genomics"},{"key":"2489_CR20","doi-asserted-by":"publisher","unstructured":"Fertin G, Jean G, Radulescu A, Rusu I DExTaR: Detection of exact tandem repeats based on the de bruijn graph. In: 2014 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2014\/11\/\/ 2014. pp 90\u201393. https:\/\/doi.org\/10.1109\/BIBM.2014.6999134","DOI":"10.1109\/BIBM.2014.6999134"},{"issue":"6","key":"2489_CR21","doi-asserted-by":"publisher","first-page":"1672","DOI":"10.1111\/1755-0998.13065","volume":"19","author":"G Fox","year":"2019","unstructured":"Fox G, Preziosi RF, Antwis RE, Benavides-Serrato M, Combe FJ, Harris WE et al (2019) Multi-individual microsatellite identification: a multiple genome approach to microsatellite design (MiMi). Mol Ecol Resour 19(6):1672\u20131680. https:\/\/doi.org\/10.1111\/1755-0998.13065","journal-title":"Mol Ecol Resour"},{"key":"2489_CR22","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1016\/j.gde.2017.01.012","volume":"44","author":"M Gymrek","year":"2017","unstructured":"Gymrek M (2017) A genomic view of short tandem repeats. Curr Opin Genet Dev 44:9\u201316. https:\/\/doi.org\/10.1016\/j.gde.2017.01.012","journal-title":"Curr Opin Genet Dev"},{"issue":"5","key":"2489_CR23","doi-asserted-by":"publisher","first-page":"286","DOI":"10.1038\/nrg.2017.115","volume":"19","author":"AJ Hannan","year":"2018","unstructured":"Hannan AJ (2018) Tandem repeats mediating genetic plasticity in health and disease. Nat Rev Genet 19(5):286\u2013298. https:\/\/doi.org\/10.1038\/nrg.2017.115","journal-title":"Nat Rev Genet"},{"issue":"7","key":"2489_CR24","doi-asserted-by":"publisher","first-page":"1001","DOI":"10.1093\/oxfordjournals.molbev.a026381","volume":"17","author":"B Harr","year":"2000","unstructured":"Harr B, Zangerl B, Schl\u00f6tterer C (2000) Removal of microsatellite interruptions by DNA replication slippage: phylogenetic evidence from Drosophila. Mol Biol Evol 17(7):1001\u20131009. https:\/\/doi.org\/10.1093\/oxfordjournals.molbev.a026381","journal-title":"Mol Biol Evol"},{"issue":"1","key":"2489_CR25","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-024-51854-0","volume":"15","author":"H He","year":"2024","unstructured":"He H, Leng Y, Cao X, Zhu Y, Li X, Yuan Q et al (2024) The pan-tandem repeat map highlights multiallelic variants underlying gene expression and agronomic traits in rice. Nat Commun 15(1):7291. https:\/\/doi.org\/10.1038\/s41467-024-51854-0","journal-title":"Nat Commun"},{"issue":"6664","key":"2489_CR26","doi-asserted-by":"publisher","DOI":"10.1126\/science.add1250","volume":"381","author":"CA Horton","year":"2023","unstructured":"Horton CA, Alexandari AM, Hayes MGB, Marklund E, Schaepe JM, Aditham AK et al (2023) Short tandem repeats bind transcription factors to tune eukaryotic gene expression. Science 381(6664):eadd1250. https:\/\/doi.org\/10.1126\/science.add1250","journal-title":"Science"},{"issue":"4","key":"2489_CR27","doi-asserted-by":"publisher","first-page":"593","DOI":"10.1093\/bioinformatics\/btr708","volume":"28","author":"W Huang","year":"2012","unstructured":"Huang W, Li L, Myers JR, Marth GT (2012) ART: a next-generation sequencing read simulator. Bioinformatics 28(4):593\u2013594. https:\/\/doi.org\/10.1093\/bioinformatics\/btr708","journal-title":"Bioinformatics"},{"issue":"2","key":"2489_CR28","doi-asserted-by":"publisher","first-page":"291","DOI":"10.1089\/cmb.1995.2.291","volume":"2","author":"RM Idury","year":"1995","unstructured":"Idury RM, Waterman MS (1995) A new algorithm for DNA sequence assembly. J Comput Biol 2(2):291\u2013306. https:\/\/doi.org\/10.1089\/cmb.1995.2.291","journal-title":"J Comput Biol"},{"key":"2489_CR29","doi-asserted-by":"publisher","first-page":"620","DOI":"10.1093\/gbe\/evq046","volume":"2","author":"YD Kelkar","year":"2010","unstructured":"Kelkar YD, Strubczewski N, Hile SE, Chiaromonte F, Eckert KA, Makova KD (2010) What is a microsatellite: a computational and experimental definition based upon repeat mutational behavior at a\/T and GT\/AC repeats. Genome Biol Evol 2:620\u2013635. https:\/\/doi.org\/10.1093\/gbe\/evq046","journal-title":"Genome Biol Evol"},{"issue":"1","key":"2489_CR30","doi-asserted-by":"publisher","first-page":"421","DOI":"10.1186\/s12864-021-07752-6","volume":"22","author":"Y Lei","year":"2021","unstructured":"Lei Y, Zhou Y, Price M, Song Z (2021) Genome-wide characterization of microsatellite DNA in fishes: survey and analysis of their abundance and frequency in genome-specific regions. BMC Genomics 22(1):421. https:\/\/doi.org\/10.1186\/s12864-021-07752-6","journal-title":"BMC Genomics"},{"issue":"3","key":"2489_CR31","doi-asserted-by":"publisher","first-page":"203","DOI":"10.1093\/oxfordjournals.molbev.a040442","volume":"4","author":"G Levinson","year":"1987","unstructured":"Levinson G, Gutman GA (1987) Slipped-strand mispairing: A major mechanism for DNA sequence evolution. Mol Biol Evol 4(3):203\u2013221. https:\/\/doi.org\/10.1093\/oxfordjournals.molbev.a040442","journal-title":"Mol Biol Evol"},{"issue":"18","key":"2489_CR32","doi-asserted-by":"publisher","first-page":"3094","DOI":"10.1093\/bioinformatics\/bty191","volume":"34","author":"H Li","year":"2018","unstructured":"Li H (2018) Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34(18):3094\u20133100. https:\/\/doi.org\/10.1093\/bioinformatics\/bty191","journal-title":"Bioinformatics"},{"issue":"12","key":"2489_CR33","doi-asserted-by":"publisher","first-page":"2453","DOI":"10.1046\/j.1365-294X.2002.01643.x","volume":"11","author":"YC Li","year":"2002","unstructured":"Li YC, Korol AB, Fahima T, Beiles A, Nevo E (2002) Microsatellites: genomic distribution, putative functions and mutational mechanisms: a review. Mol Ecol 11(12):2453\u20132465. https:\/\/doi.org\/10.1046\/j.1365-294X.2002.01643.x","journal-title":"Mol Ecol"},{"issue":"1","key":"2489_CR34","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-017-03330-7","volume":"7","author":"Z Li","year":"2017","unstructured":"Li Z, Chen F, Huang C, Zheng W, Yu C, Cheng H et al (2017) Genome-wide mapping and characterization of microsatellites in the swamp eel genome. Sci Rep 7(1):3157. https:\/\/doi.org\/10.1038\/s41598-017-03330-7","journal-title":"Sci Rep"},{"key":"2489_CR35","doi-asserted-by":"publisher","unstructured":"Liu K, Xie N (2024) 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","DOI":"10.21203\/rs.3.rs-4621443\/v1"},{"issue":"1","key":"2489_CR36","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-24378-0","volume":"12","author":"T-Y Lu","year":"2021","unstructured":"Lu T-Y, Chaisson MJP (2021) Profiling variable-number tandem repeat variation across populations using repeat-pangenome graphs. Nat Commun 12(1):4250. https:\/\/doi.org\/10.1038\/s41467-021-24378-0","journal-title":"Nat Commun"},{"key":"2489_CR37","doi-asserted-by":"publisher","first-page":"1","DOI":"10.4137\/ebo.s420","volume":"4","author":"A Merkel","year":"2008","unstructured":"Merkel A, Gemmell NJ (2008) Detecting microsatellites in genome data: variance in definitions and bioinformatic approaches cause systematic bias. Evol Bioinform Online 4:1\u20136. https:\/\/doi.org\/10.4137\/ebo.s420","journal-title":"Evol Bioinform Online"},{"issue":"5","key":"2489_CR38","doi-asserted-by":"publisher","first-page":"612","DOI":"10.1093\/bioinformatics\/btaa865","volume":"37","author":"S Morishita","year":"2021","unstructured":"Morishita S, Ichikawa K, Myers EW (2021) Finding long tandem repeats in long noisy reads. Bioinformatics 37(5):612\u2013621. https:\/\/doi.org\/10.1093\/bioinformatics\/btaa865","journal-title":"Bioinformatics"},{"issue":"15","key":"2489_CR39","doi-asserted-by":"publisher","first-page":"e90","DOI":"10.1093\/nar\/gkz501","volume":"47","author":"N Mousavi","year":"2019","unstructured":"Mousavi N, Shleizer-Burko S, Yanicky R, Gymrek M (2019) Profiling the genome-wide landscape of tandem repeat expansions. Nucleic Acids Res 47(15):e90. https:\/\/doi.org\/10.1093\/nar\/gkz501","journal-title":"Nucleic Acids Res"},{"key":"2489_CR40","doi-asserted-by":"publisher","DOI":"10.1093\/bioadv\/vbae149","author":"DR Olson","year":"2024","unstructured":"Olson DR, Wheeler TJ (2024) ULTRA-effective labeling of tandem repeats in genomic sequence. Bioinformatics Adv. https:\/\/doi.org\/10.1093\/bioadv\/vbae149","journal-title":"Bioinformatics Adv"},{"issue":"5","key":"2489_CR41","doi-asserted-by":"publisher","first-page":"665","DOI":"10.1101\/gr.214155.116","volume":"27","author":"B Paten","year":"2017","unstructured":"Paten B, Novak AM, Eizenga JM, Garrison E (2017) Genome graphs and the evolution of genome inference. Genome Res 27(5):665\u2013676. https:\/\/doi.org\/10.1101\/gr.214155.116","journal-title":"Genome Res"},{"issue":"17","key":"2489_CR42","doi-asserted-by":"publisher","first-page":"9748","DOI":"10.1073\/pnas.171285098","volume":"98","author":"PA Pevzner","year":"2001","unstructured":"Pevzner PA, Tang H, Waterman MS (2001) An eulerian path approach to DNA fragment assembly. Proc Natl Acad Sci U S A 98(17):9748\u20139753. https:\/\/doi.org\/10.1073\/pnas.171285098","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2489_CR43","doi-asserted-by":"publisher","DOI":"10.2202\/1544-6115.1585","author":"B Phipson","year":"2010","unstructured":"Phipson B, Smyth GK (2010) Permutation P-values should never be zero: calculating exact P-values when permutations are randomly drawn. Stat Appl Genet Mol Biol. https:\/\/doi.org\/10.2202\/1544-6115.1585","journal-title":"Stat Appl Genet Mol Biol"},{"issue":"7","key":"2489_CR44","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0133667","volume":"10","author":"W-H Qi","year":"2015","unstructured":"Qi W-H, Jiang X-M, Du L-M, Xiao G-S, Hu T-Z, Yue B-S et al (2015) Genome-wide survey and analysis of microsatellite sequences in bovid species. PLoS ONE 10(7):e0133667. https:\/\/doi.org\/10.1371\/journal.pone.0133667","journal-title":"PLoS ONE"},{"issue":"4","key":"2489_CR45","doi-asserted-by":"publisher","first-page":"415","DOI":"10.1046\/j.1365-313X.1999.00392.x","volume":"17","author":"L Ramsay","year":"1999","unstructured":"Ramsay L, Macaulay M, Cardle L, Morgante M, Ivanissevich S, Maestri E et al (1999) Intimate association of microsatellite repeats with retrotransposons and other dispersed repetitive elements in barley. Plant J 17(4):415\u2013425. https:\/\/doi.org\/10.1046\/j.1365-313X.1999.00392.x","journal-title":"Plant J"},{"issue":"1","key":"2489_CR46","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-024-55276-w","volume":"15","author":"WB Reinar","year":"2024","unstructured":"Reinar WB, Krabber\u00f8d AK, Lalun VO, Butenko MA, Jakobsen KS (2024) Short tandem repeats delineate gene bodies across eukaryotes. Nat Commun 15(1):10902. https:\/\/doi.org\/10.1038\/s41467-024-55276-w","journal-title":"Nat Commun"},{"issue":"20","key":"2489_CR47","doi-asserted-by":"publisher","first-page":"10005","DOI":"10.1093\/nar\/gks726","volume":"40","author":"E Schaper","year":"2012","unstructured":"Schaper E, Kajava AV, Hauser A, Anisimova M (2012) Repeat or not repeat?\u2014statistical validation of tandem repeat prediction in genomic sequences. Nucleic Acids Res 40(20):10005\u201310017. https:\/\/doi.org\/10.1093\/nar\/gks726","journal-title":"Nucleic Acids Res"},{"issue":"6","key":"2489_CR48","doi-asserted-by":"publisher","first-page":"365","DOI":"10.1007\/s004120000089","volume":"109","author":"C Schl\u00f6tterer","year":"2000","unstructured":"Schl\u00f6tterer C (2000) Evolutionary dynamics of microsatellite DNA. Chromosoma 109(6):365\u2013371. https:\/\/doi.org\/10.1007\/s004120000089","journal-title":"Chromosoma"},{"issue":"3","key":"2489_CR49","doi-asserted-by":"publisher","DOI":"10.1002\/imt2.191","volume":"3","author":"W Shen","year":"2024","unstructured":"Shen W, Sipos B, Zhao L (2024) SeqKit2: a swiss army knife for sequence and alignment processing. iMeta 3(3):e191. https:\/\/doi.org\/10.1002\/imt2.191","journal-title":"iMeta"},{"issue":"12","key":"2489_CR50","doi-asserted-by":"publisher","first-page":"1639","DOI":"10.1093\/bioinformatics\/btaa1016","volume":"37","author":"A Shumate","year":"2021","unstructured":"Shumate A, Salzberg SL (2021) Liftoff: accurate mapping of gene annotations. Bioinformatics 37(12):1639\u20131643. https:\/\/doi.org\/10.1093\/bioinformatics\/btaa1016","journal-title":"Bioinformatics"},{"key":"2489_CR51","unstructured":"Smit A, Hubley R, Green P (2015) RepeatMasker open-4.0. 2013\u20132015. http:\/\/www.repeatmasker.org. Accessed 21 Dec 2025"},{"issue":"1","key":"2489_CR52","doi-asserted-by":"publisher","first-page":"161","DOI":"10.1093\/gbe\/evw264","volume":"9","author":"CG Sotero-Caio","year":"2017","unstructured":"Sotero-Caio CG, Platt RN II, Suh A, Ray DA (2017) Evolution and diversity of transposable elements in vertebrate genomes. Genome Biol Evol 9(1):161\u2013177. https:\/\/doi.org\/10.1093\/gbe\/evw264","journal-title":"Genome Biol Evol"},{"issue":"1","key":"2489_CR53","doi-asserted-by":"publisher","first-page":"153","DOI":"10.1186\/s12864-019-5516-5","volume":"20","author":"S Srivastava","year":"2019","unstructured":"Srivastava S, Avvaru AK, Sowpati DT, Mishra RK (2019) Patterns of microsatellite distribution across eukaryotic genomes. BMC Genomics 20(1):153. https:\/\/doi.org\/10.1186\/s12864-019-5516-5","journal-title":"BMC Genomics"},{"issue":"D1","key":"2489_CR54","doi-asserted-by":"publisher","first-page":"D516","DOI":"10.1093\/nar\/gkae987","volume":"53","author":"F Tegenfeldt","year":"2025","unstructured":"Tegenfeldt F, Kuznetsov D, Manni M, Berkeley M, Zdobnov EM, Kriventseva EV (2025) OrthoDB and BUSCO update: annotation of orthologs with wider sampling of genomes. Nucleic Acids Res 53(D1):D516\u2013D522. https:\/\/doi.org\/10.1093\/nar\/gkae987","journal-title":"Nucleic Acids Res"},{"issue":"8","key":"2489_CR55","doi-asserted-by":"publisher","first-page":"1441","DOI":"10.1101\/gr.184001","volume":"11","author":"S Temnykh","year":"2001","unstructured":"Temnykh S, DeClerck G, Lukashova A, Lipovich L, Cartinhour S, McCouch S (2001) Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. Genome Res 11(8):1441\u20131452. https:\/\/doi.org\/10.1101\/gr.184001","journal-title":"Genome Res"},{"issue":"39","key":"2489_CR56","doi-asserted-by":"publisher","first-page":"13950","DOI":"10.1073\/pnas.0506758102","volume":"102","author":"H Tettelin","year":"2005","unstructured":"Tettelin H, Masignani V, Cieslewicz MJ, Donati C, Medini D, Ward NL et al (2005) Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial \u201cpan-genome.\u201d Proc Natl Acad Sci U S A 102(39):13950\u201313955. https:\/\/doi.org\/10.1073\/pnas.0506758102","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"3","key":"2489_CR57","doi-asserted-by":"publisher","first-page":"411","DOI":"10.1007\/s00122-002-1031-0","volume":"106","author":"T Thiel","year":"2003","unstructured":"Thiel T, Michalek W, Varshney RK, Graner A (2003) Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor Appl Genet 106(3):411\u2013422. https:\/\/doi.org\/10.1007\/s00122-002-1031-0","journal-title":"Theor Appl Genet"},{"issue":"7","key":"2489_CR58","doi-asserted-by":"publisher","first-page":"967","DOI":"10.1101\/gr.10.7.967","volume":"10","author":"G T\u00f3th","year":"2000","unstructured":"T\u00f3th G, G\u00e1sp\u00e1ri Z, Jurka J (2000) Microsatellites in different eukaryotic genomes: survey and analysis. Genome Res 10(7):967\u2013981. https:\/\/doi.org\/10.1101\/gr.10.7.967","journal-title":"Genome Res"},{"issue":"1","key":"2489_CR59","doi-asserted-by":"publisher","first-page":"36","DOI":"10.1038\/nrg3117","volume":"13","author":"TJ Treangen","year":"2012","unstructured":"Treangen TJ, Salzberg SL (2012) Repetitive DNA and next-generation sequencing: computational challenges and solutions. Nat Rev Genet 13(1):36\u201346. https:\/\/doi.org\/10.1038\/nrg3117","journal-title":"Nat Rev Genet"},{"issue":"9","key":"2489_CR60","doi-asserted-by":"publisher","first-page":"1037","DOI":"10.1038\/s41431-024-01666-z","volume":"32","author":"K Uguen","year":"2024","unstructured":"Uguen K, Michaud JL, G\u00e9nin E (2024) Short tandem repeats in the era of next-generation sequencing: from historical loci to population databases. Eur J Hum Genet 32(9):1037\u20131044. https:\/\/doi.org\/10.1038\/s41431-024-01666-z","journal-title":"Eur J Hum Genet"},{"key":"2489_CR61","doi-asserted-by":"crossref","unstructured":"Vasimuddin M, Misra S, Li H, Aluru S (2019) Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems. In: Paper presented at the 2019 IEEE International Parallel and Distributed Processing Symposium (IPDPS), May 20","DOI":"10.1109\/IPDPS.2019.00041"},{"issue":"2","key":"2489_CR62","doi-asserted-by":"publisher","first-page":"321","DOI":"10.1111\/jeb.14106","volume":"36","author":"M Verbiest","year":"2023","unstructured":"Verbiest M, Maksimov M, Jin Y, Anisimova M, Gymrek M, Sonay TB (2023) Mutation and selection processes regulating short tandem repeats give rise to genetic and phenotypic diversity across species. J Evol Biol 36(2):321\u2013336. https:\/\/doi.org\/10.1111\/jeb.14106","journal-title":"J Evol Biol"},{"issue":"5","key":"2489_CR63","doi-asserted-by":"publisher","DOI":"10.3390\/fishes7050251","volume":"7","author":"P Wattanadilokchatkun","year":"2022","unstructured":"Wattanadilokchatkun P, Panthum T, Jaisamut K, Ahmad SF, Dokkaew S, Muangmai N et al (2022) Characterization of microsatellite distribution in siamese fighting fish genome to promote conservation and genetic diversity. Fishes 7(5):251. https:\/\/doi.org\/10.3390\/fishes7050251","journal-title":"Fishes"},{"issue":"6","key":"2489_CR64","doi-asserted-by":"publisher","first-page":"590","DOI":"10.1038\/nmeth.4267","volume":"14","author":"T Willems","year":"2017","unstructured":"Willems T, Zielinski D, Yuan J, Gordon A, Gymrek M, Erlich Y (2017) Genome-wide profiling of heritable and de novo STR variations. Nat Methods 14(6):590\u2013592. https:\/\/doi.org\/10.1038\/nmeth.4267","journal-title":"Nat Methods"},{"issue":"4","key":"2489_CR65","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0124432","volume":"10","author":"S Xiao","year":"2015","unstructured":"Xiao S, Han Z, Wang P, Han F, Liu Y, Li J et al (2015) Functional marker detection and analysis on a comprehensive transcriptome of large yellow croaker by next generation sequencing. PLoS ONE 10(4):e0124432. https:\/\/doi.org\/10.1371\/journal.pone.0124432","journal-title":"PLoS ONE"},{"issue":"1","key":"2489_CR66","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s42003-021-01716-y","volume":"4","author":"J Yuan","year":"2021","unstructured":"Yuan J, Zhang X, Wang M, Sun Y, Liu C, Li S et al (2021) Simple sequence repeats drive genome plasticity and promote adaptive evolution in penaeid shrimp. Commun Biol 4(1):1\u201314. https:\/\/doi.org\/10.1038\/s42003-021-01716-y","journal-title":"Commun Biol"},{"issue":"1","key":"2489_CR67","doi-asserted-by":"publisher","DOI":"10.1038\/s41597-024-03504-9","volume":"11","author":"Y Yuan","year":"2024","unstructured":"Yuan Y, Zhong T, Wang Y, Yang J, Gui L, Shen Y et al (2024) Chromosome-scale genome assemblies of sexually dimorphic male and female Acrossocheilus fasciatus. Sci Data 11(1):653. https:\/\/doi.org\/10.1038\/s41597-024-03504-9","journal-title":"Sci Data"},{"issue":"3","key":"2489_CR68","doi-asserted-by":"publisher","first-page":"317","DOI":"10.1080\/23802359.2025.2606443","volume":"11","author":"Y Yuan","year":"2026","unstructured":"Yuan Y, Zhang H, Jiang S, Yang X, Chung-Davidson Y-W, Li W et al (2026) Mitogenomic analyses uncover significant genetic differentiation between different geographic populations of Acrossocheilus fasciatus. Mitochondrial DNA B 11(3):317\u2013323. https:\/\/doi.org\/10.1080\/23802359.2025.2606443","journal-title":"Mitochondrial DNA B"},{"issue":"21","key":"2489_CR69","doi-asserted-by":"publisher","DOI":"10.3390\/cells11213373","volume":"11","author":"ML Zattera","year":"2022","unstructured":"Zattera ML, Bruschi DP (2022) Transposable elements as a source of novel repetitive DNA in the eukaryote genome. Cells 11(21):3373. https:\/\/doi.org\/10.3390\/cells11213373","journal-title":"Cells"},{"key":"2489_CR70","doi-asserted-by":"publisher","DOI":"10.1016\/j.xgen.2024.100699","author":"S Zhang","year":"2024","unstructured":"Zhang S, Song Q, Zhang P, Wang X, Guo R, Li Y et al (2024) Genome-wide investigation of VNTR motif polymorphisms in 8,222 genomes: implications for biological regulation and human traits. Cell Genom. https:\/\/doi.org\/10.1016\/j.xgen.2024.100699","journal-title":"Cell Genom"},{"issue":"1","key":"2489_CR71","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-025-03720-5","volume":"26","author":"Z-Q Zhang","year":"2025","unstructured":"Zhang Z-Q, Jiang J, Xu Y-C, Dent C, Sureshkumar S, Balasubramanian S et al (2025) Mutations of short tandem repeats explain abundant trait heritability in Arabidopsis. Genome Biol 26(1):242. https:\/\/doi.org\/10.1186\/s13059-025-03720-5","journal-title":"Genome Biol"},{"issue":"1","key":"2489_CR72","doi-asserted-by":"publisher","first-page":"166","DOI":"10.1038\/s41597-024-02999-6","volume":"11","author":"J Zheng","year":"2024","unstructured":"Zheng J, Jiang J, Rui Q, Li F, Liu S, Cheng S et al (2024) Chromosome-level genome assembly of Acrossocheilus fasciatus using PacBio sequencing and hi-C technology. Sci Data 11(1):166. https:\/\/doi.org\/10.1038\/s41597-024-02999-6","journal-title":"Sci Data"}],"container-title":["Molecular Genetics and Genomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s00438-026-02489-x.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s00438-026-02489-x","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s00438-026-02489-x.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,7]],"date-time":"2026-08-07T04:35:49Z","timestamp":1786077349000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s00438-026-02489-x"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,8,7]]},"references-count":72,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2026,12]]}},"alternative-id":["2489"],"URL":"https:\/\/doi.org\/10.1007\/s00438-026-02489-x","relation":{},"ISSN":["1617-4615","1617-4623"],"issn-type":[{"value":"1617-4615","type":"print"},{"value":"1617-4623","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,7]]},"assertion":[{"value":"6 May 2026","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"6 July 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"7 August 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","label":"Conflict of interest","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"This study utilized publicly available genomic data, precluding the need for novel biological sampling or animal experimentation. We conducted all analyses in strict adherence to the ethical guidelines and data use agreements governing the secondary analysis of these datasets.","order":2,"name":"Ethics","label":"Ethical approval","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"During the preparation of this work, the author(s) used DeepSeek in order to assist with language refinement, technical description optimization, and logical flow enhancement. After using this tool, the author(s) rigorously reviewed, fact-checked, and edited the content as needed, and take(s) full responsibility for the accuracy, integrity, and originality of all data, analyses, interpretations, and conclusions in this manuscript.","order":3,"name":"Ethics","label":"Declaration of generative AI and AI-assisted technologies in the writing process","group":{"name":"EthicsHeading","label":"Declarations"}}],"article-number":"167"}}