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Mini-Review: A Hitchhiker's Guide to long-read genomic analysis
- Medhat Mahmoud,
- Daniel P. Agustinho,
- and Fritz J. Sedlazeck
Genome Res. April 2025 35: 545-558; doi:10.1101/gr.279975.124
..., effectively tiling them together to create longer contiguous sequences (i.e., contigs) (Sedlazeck et al. 2018a). With modern long-read technologies, particularly PacBio HiFi reads, many assemblers can now produce highly contiguous assemblies directly from the assembly graph, often achieving chromosome...
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Perspective: Unraveling the hidden complexity of cancer through long-read sequencing
- Qiuhui Li,
- Ayse G. Keskus,
- Justin Wagner,
- Michal B. Izydorczyk,
- Winston Timp,
- Fritz J. Sedlazeck,
- Alison P. Klein,
- Justin M. Zook,
- Mikhail Kolmogorov,
- and Michael C. Schatz
Genome Res. April 2025 35: 599-620; Published in Advance March 20, 2025, doi:10.1101/gr.280041.124
...conformation capture technique, identifies large-scale rearrangements by capturing the spatial proximity of genomic regions, and has been widely used for variant phasing and assembly (Liao et al. 2023). A recent study used a combination of long-read and Hi-C sequencing to reveal chromosome-scale structure...
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Method: Reconstructing extrachromosomal DNA structural heterogeneity from long-read sequencing data using Decoil
- Mădălina Giurgiu,
- Nadine Wittstruck,
- Elias Rodriguez-Fos,
- Rocío Chamorro González,
- Lotte Brückner,
- Annabell Krienelke-Szymansky,
- Konstantin Helmsauer,
- Anne Hartebrodt,
- Philipp Euskirchen,
- Richard P. Koche,
- Kerstin Haase,
- Knut Reinert,
- and Anton G. Henssen
Genome Res. September 2024 34: 1355-1364; Published in Advance August 7, 2024, doi:10.1101/gr.279123.124
...with LASSO regression to reconstruct complex ecDNA and deconvolve co-occurring ecDNA elements with overlapping genomic footprints from long-read nanopore sequencing. Decoil outperforms de novo assembly and alignment-based methods in simulated long-read sequencing data for both simple and complex ec...
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Resource: Long-read assembly and comparative evidence-based reanalysis of Cryptosporidium genome sequences reveal expanded transporter repertoire and duplication of entire chromosome ends including subtelomeric regions
- Rodrigo P. Baptista,
- Yiran Li,
- Adam Sateriale,
- Mandy J. Sanders,
- Karen L. Brooks,
- Alan Tracey,
- Brendan R.E. Ansell,
- Aaron R. Jex,
- Garrett W. Cooper,
- Ethan D. Smith,
- Rui Xiao,
- Jennifer E. Dumaine,
- Peter Georgeson,
- Bernard J. Pope,
- Matthew Berriman,
- Boris Striepen,
- James A. Cotton,
- and Jessica C. Kissinger
Genome Res. January 2022 32: 203-213; Published in Advance November 11, 2021, doi:10.1101/gr.275325.121
...flanking each major inversion in each orientation using genomic DNA from an unsequenced isolate from 2006, C. parvum KSU-1 and CpBGF from 2019 validated the long-read CpIA assembly. Because the other species still lack physical evidence for their chromosomal structures, further long-read sequencing...
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Research: De novo genome assemblies of two cryptodiran turtles with ZZ/ZW and XX/XY sex chromosomes provide insights into patterns of genome reshuffling and uncover novel 3D genome folding in amniotes
- Basanta Bista,
- Laura González-Rodelas,
- Lucía Álvarez-González,
- Zhi-qiang Wu,
- Eugenia E. Montiel,
- Ling Sze Lee,
- Daleen B. Badenhorst,
- Srihari Radhakrishnan,
- Robert Literman,
- Beatriz Navarro-Dominguez,
- John B. Iverson,
- Simon Orozco-Arias,
- Josefa González,
- Aurora Ruiz-Herrera,
- and Nicole Valenzuela
Genome Res. October 2024 34: 1553-1569; Published in Advance October 16, 2024, doi:10.1101/gr.279443.124
...diversity of vertebrate chromatin conformation, here we generate de novo assemblies for two cryptodiran (hidden-neck) turtles via Illumina sequencing, chromosome conformation capture, and RNA-seq: Apalone spinifera (ZZ/ZW, 2n = 66) and Staurotypus triporcatus (XX/XY, 2n = 54). We detected differences...
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Research: Plant genome evolution in the genus Eucalyptus is driven by structural rearrangements that promote sequence divergence
- Scott Ferguson,
- Ashley Jones,
- Kevin Murray,
- Rose Andrew,
- Benjamin Schwessinger,
- and Justin Borevitz
Genome Res. April 2024 34: 606-619; Published in Advance April 8, 2024, doi:10.1101/gr.277999.123
...contigs (contigs that span the same genomic region but originate from different parental chromosomes) using BlobTools (Laetsch and Blaxter 2017) and Purge Haplotigs (version 1.1.0) (Roach et al. 2018). Next, all assemblies were long-read and then short-read polished, using assembly reads and Illumina...
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Research: Chromosome-scale assemblies of Acanthamoeba castellanii genomes provide insights into Legionella pneumophila infection–related chromatin reorganization
- Cyril Matthey-Doret,
- Morgan J. Colp,
- Pedro Escoll,
- Agnès Thierry,
- Pierrick Moreau,
- Bruce Curtis,
- Tobias Sahr,
- Matt Sarrasin,
- Michael W. Gray,
- B. Franz Lang,
- John M. Archibald,
- Carmen Buchrieser,
- and Romain Koszul
Genome Res. September 2022 32: 1698-1710; Published in Advance September 15, 2022, doi:10.1101/gr.276375.121
...-dimensional organization of its . We combined Illumina, Oxford Nanopore long-read, and Hi-C data to generate high-quality reference sequence of the C3 strain, as well as a new and improved reference assembly of the Neff (Neff-v2). We next analyzed the folding and expression changes of A. castellanii C3 strain in response...
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Research: Combination of short-read, long-read, and optical mapping assemblies reveals large-scale tandem repeat arrays with population genetic implications
- Matthias H. Weissensteiner,
- Andy W.C. Pang,
- Ignas Bunikis,
- Ida Höijer,
- Olga Vinnere-Petterson,
- Alexander Suh,
- and Jochen B.W. Wolf
Genome Res. May 2017 27: 697-708; Published in Advance March 30, 2017, doi:10.1101/gr.215095.116
...et al. 1986). The long-read sequence assembly using FALCON (https://github.com/PacificBiosciences/FALCON), for which only subreads >8 kb were considered, yielded a cumulative length of 1.093 Gb assembled in 3100 contigs. This provided an 89.1-fold improvement in contiguity metrics compared...
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Method: Gapless assembly of complete human and plant chromosomes using only nanopore sequencing
- Sergey Koren,
- Zhigui Bao,
- Andrea Guarracino,
- Shujun Ou,
- Sara Goodwin,
- Katharine M. Jenike,
- Julian Lucas,
- Brandy McNulty,
- Jimin Park,
- Mikko Rautiainen,
- Arang Rhie,
- Dick Roelofs,
- Harrie Schneiders,
- Ilse Vrijenhoek,
- Koen Nijbroek,
- Olle Nordesjo,
- Sergey Nurk,
- Mike Vella,
- Katherine R. Lawrence,
- Doreen Ware,
- Michael C. Schatz,
- Erik Garrison,
- Sanwen Huang,
- William Richard McCombie,
- Karen H. Miga,
- Alexander H.J. Wittenberg,
- and Adam M. Phillippy
Genome Res. November 2024 34: 1919-1930; Published in Advance November 6, 2024, doi:10.1101/gr.279334.124
.... 2022) and 47.0 Mbp (Zm-B73-NAM-5.0, based on PacBio CLR long reads and BioNano optical maps) (Hufford et al. 2021). The tomato assembly resolved 5 of 12 chromosomes as T2T contigs while maize resolved 2 of 10 chromosomes. As with HG002, we investigated the source of the remaining gaps. In the tomato...
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Research: Fusion, fission, and scrambling of the bilaterian genome in Bryozoa
- Thomas D. Lewin,
- Isabel Jiah-Yih Liao,
- Mu-En Chen,
- John D.D. Bishop,
- Peter W.H. Holland,
- and Yi-Jyun Luo
Genome Res. January 2025 35: 78-92; Published in Advance January 6, 2025, doi:10.1101/gr.279636.124
...-level using Pacific Biosciences (PacBio) HiFi long reads and high-throughput chromosome conformation capture (Hi-C) scaffolding (Wood et al. 2023; Bishop et al. 2023a,b, 2024).View larger version: In this window In a new window Figure 1. Comparative genomics of five chromosome-scale bryozoan s. (A...
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