利用连锁图谱校正和搭建从头基因组组装：方法、挑战及计算工具
Using linkage maps to correct and scaffold de novo genome assemblies: methods, challenges, and computational tools.
作者信息
Fierst Janna L
机构信息
Department of Biological Sciences, University of Alabama Tuscaloosa, AL, USA.
出版信息
Front Genet. 2015 Jun 19;6:220. doi: 10.3389/fgene.2015.00220. eCollection 2015.
Abstract
Modern high-throughput DNA sequencing has made it possible to inexpensively produce genome sequences, but in practice many of these draft genomes are fragmented and incomplete. Genetic linkage maps based on recombination rates between physical markers have been used in biology for over 100 years and a linkage map, when paired with a de novo sequencing project, can resolve mis-assemblies and anchor chromosome-scale sequences. Here, I summarize the methodology behind integrating de novo assemblies and genetic linkage maps, outline the current challenges, review the available software tools, and discuss new mapping technologies.
摘要
现代高通量DNA测序使得低成本生成基因组序列成为可能，但实际上许多这些草图基因组是碎片化且不完整的。基于物理标记之间重组率的遗传连锁图谱在生物学中已使用了100多年，并且当与从头测序项目配对时，连锁图谱可以解决错误组装问题并锚定染色体规模的序列。在这里，我总结了整合从头组装和遗传连锁图谱背后的方法，概述了当前的挑战，回顾了可用的软件工具，并讨论了新的作图技术。
相似文献
1
Using linkage maps to correct and scaffold de novo genome assemblies: methods, challenges, and computational tools.
Front Genet. 2015 Jun 19;6:220. doi: 10.3389/fgene.2015.00220. eCollection 2015.
2
Improving Nelumbo nucifera genome assemblies using high-resolution genetic maps and BioNano genome mapping reveals ancient chromosome rearrangements.
Plant J. 2018 May;94(4):721-734. doi: 10.1111/tpj.13894. Epub 2018 Apr 15.
3
Hybrid de novo genome assembly and centromere characterization of the gray mouse lemur (Microcebus murinus).
BMC Biol. 2017 Nov 16;15(1):110. doi: 10.1186/s12915-017-0439-6.
4
Enhancing genome assemblies by integrating non-sequence based data.
BMC Proc. 2011 May 28;5 Suppl 2(Suppl 2):S7. doi: 10.1186/1753-6561-5-S2-S7.
5
Lep-Anchor: automated construction of linkage map anchored haploid genomes.
Bioinformatics. 2020 Apr 15;36(8):2359-2364. doi: 10.1093/bioinformatics/btz978.
6
Construction of Ultradense Linkage Maps with Lep-MAP2: Stickleback F2 Recombinant Crosses as an Example.
Genome Biol Evol. 2015 Dec 14;8(1):78-93. doi: 10.1093/gbe/evv250.
7
OMGS: Optical Map-Based Genome Scaffolding.
J Comput Biol. 2020 Apr;27(4):519-533. doi: 10.1089/cmb.2019.0310. Epub 2019 Dec 3.
8
De novo assembly of Dekkera bruxellensis: a multi technology approach using short and long-read sequencing and optical mapping.
Gigascience. 2015 Nov 26;4:56. doi: 10.1186/s13742-015-0094-1. eCollection 2015.
9
High-throughput physical mapping of chromosomes using automated in situ hybridization.
J Vis Exp. 2012 Jun 28(64):4007. doi: 10.3791/4007.
10
Lep-MAP3: robust linkage mapping even for low-coverage whole genome sequencing data.
Bioinformatics. 2017 Dec 1;33(23):3726-3732. doi: 10.1093/bioinformatics/btx494.
引用本文的文献
1
The impact of telomere-to-telomere genome assembly in the plant pan-genomics era.
Breed Sci. 2025 Mar;75(1):3-12. doi: 10.1270/jsbbs.24065. Epub 2025 Feb 21.
2
A high-density linkage map reveals broad- and fine-scale sex differences in recombination in the hihi (stitchbird; Notiomystis cincta).
Heredity (Edinb). 2024 Oct;133(4):262-275. doi: 10.1038/s41437-024-00711-3. Epub 2024 Aug 2.
3
High-density linkage to physical mapping in a unique Tall × Dwarf coconut ( L.) outbred F uncovers a major QTL for flowering time colocalized with the .
Front Plant Sci. 2024 Jun 3;15:1408239. doi: 10.3389/fpls.2024.1408239. eCollection 2024.
4
Telomere-to-telomere genome assembly of an allotetraploid pernicious weed, Echinochloa phyllopogon.
DNA Res. 2023 Oct 1;30(5). doi: 10.1093/dnares/dsad023.
5
High-density linkage mapping and genetic dissection of resistance to broomrape ( Forsk.) in pea ( L.).
Front Plant Sci. 2023 Jul 10;14:1216297. doi: 10.3389/fpls.2023.1216297. eCollection 2023.
6
Chromosome-level assembly of the Rangifer tarandus genome and validation of cervid and bovid evolution insights.
BMC Genomics. 2023 Mar 23;24(1):142. doi: 10.1186/s12864-023-09189-5.
7
Smooth Descent: A ploidy-aware algorithm to improve linkage mapping in the presence of genotyping errors.
Front Genet. 2023 Mar 1;14:1049988. doi: 10.3389/fgene.2023.1049988. eCollection 2023.
8
Optimizing experimental design for genome sequencing and assembly with Oxford Nanopore Technologies.
GigaByte. 2021 Jul 13;2021:gigabyte27. doi: 10.46471/gigabyte.27. eCollection 2021.
9
A Novel Strategy for Constructing an Integrated Linkage Map in an F Hybrid Population of and .
Genes (Basel). 2022 Sep 26;13(10):1731. doi: 10.3390/genes13101731.
10
The first high-density genetic map of common cockle (Cerastoderma edule) reveals a major QTL controlling shell color variation.
Sci Rep. 2022 Oct 10;12(1):16971. doi: 10.1038/s41598-022-21214-3.
本文引用的文献
1
Chromosome-scale shotgun assembly using an in vitro method for long-range linkage.
Genome Res. 2016 Mar;26(3):342-50. doi: 10.1101/gr.193474.115. Epub 2016 Feb 4.
2
Rapid detection of structural variation in a human genome using nanochannel-based genome mapping technology.
Gigascience. 2014 Dec 30;3(1):34. doi: 10.1186/2047-217X-3-34. eCollection 2014.
3
De novo plant genome assembly based on chromatin interactions: a case study of Arabidopsis thaliana.
Mol Plant. 2015 Mar;8(3):489-92. doi: 10.1016/j.molp.2014.12.015. Epub 2014 Dec 30.
4
A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome.
Genome Biol. 2015 Jan 31;16(1):26. doi: 10.1186/s13059-015-0582-8.
5
A field guide to whole-genome sequencing, assembly and annotation.
Evol Appl. 2014 Nov;7(9):1026-42. doi: 10.1111/eva.12178. Epub 2014 Jun 24.
6
Extensive error in the number of genes inferred from draft genome assemblies.
PLoS Comput Biol. 2014 Dec 4;10(12):e1003998. doi: 10.1371/journal.pcbi.1003998. eCollection 2014 Dec.
7
One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly.
Curr Opin Microbiol. 2015 Feb;23:110-20. doi: 10.1016/j.mib.2014.11.014. Epub 2014 Dec 1.
8
Flexible and scalable genotyping-by-sequencing strategies for population studies.
BMC Genomics. 2014 Nov 18;15(1):979. doi: 10.1186/1471-2164-15-979.
9
A reference bacterial genome dataset generated on the MinION™ portable single-molecule nanopore sequencer.
Gigascience. 2014 Oct 20;3:22. doi: 10.1186/2047-217X-3-22. eCollection 2014.
10
High-resolution genetic maps of Eucalyptus improve Eucalyptus grandis genome assembly.
New Phytol. 2015 Jun;206(4):1283-96. doi: 10.1111/nph.13150. Epub 2014 Nov 10.
Zotero 插件