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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
...methods.Two leading long-read sequencing technologies currently dominate the market and have significantly impacted the genomics field (Fig. 1A): Pacific Biosciences (PacBio) HiFi and Oxford Nanopore Technologies (ONT) sequencing. While both technologies produce continuous long reads, they present...
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Research: Independent expansion, selection, and hypervariability of the TBC1D3 gene family in humans
- Xavi Guitart,
- David Porubsky,
- DongAhn Yoo,
- Max L. Dougherty,
- Philip C. Dishuck,
- Katherine M. Munson,
- Alexandra P. Lewis,
- Kendra Hoekzema,
- Jordan Knuth,
- Stephen Chang,
- Tomi Pastinen,
- and Evan E. Eichler
Genome Res. November 2024 34: 1798-1810; Published in Advance August 6, 2024, doi:10.1101/gr.279299.124
...C), suggesting a nonrandom association of TBC1D3 SDs with large chromosomal rearrangements during primate evolution.To assess the origin of TBC1D3 gene clusters, we sequenced and assembled the of an outgroup primate species using HiFi data generated from a mouse lemur (Microcebus murinus...
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Method: Predicting human genes susceptible to genomic instability associated with Alu/Alu-mediated rearrangements
- Xiaofei Song,
- Christine R. Beck,
- Renqian Du,
- Ian M. Campbell,
- Zeynep Coban-Akdemir,
- Shen Gu,
- Amy M. Breman,
- Pawel Stankiewicz,
- Grzegorz Ira,
- Chad A. Shaw,
- and James R. Lupski
Genome Res. August 2018 28: 1228-1242; Published in Advance June 15, 2018, doi:10.1101/gr.229401.117
..., DNA repair–associated processes, and DNA replication–associated processes (Carvalho and Lupski 2016), and lead to human diseases often termed genomic disorders (Lupski 1998). Previously, repeated sequences (e.g., paralogous genes/pseudogenes, low-copy repeats [LCRs], etc.) and repetitive elements (e...
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Research: Large palindromes on the primate X Chromosome are preserved by natural selection
- Emily K. Jackson,
- Daniel W. Bellott,
- Ting-Jan Cho,
- Helen Skaletsky,
- Jennifer F. Hughes,
- Tatyana Pyntikova,
- and David C. Page
Genome Res. August 2021 31: 1337-1352; Published in Advance July 21, 2021, doi:10.1101/gr.275188.120
...Given that primate X-palindrome gene families are preserved by natural selection, we wondered whether deletions that remove one or more copies of human X-palindrome gene families negatively impact fitness. The two most common human X-palindrome spacer deletions from the 1000 Genomes Project each remove one copy...
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Resource: Inversion variants in human and primate genomes
- Claudia Rita Catacchio,
- Flavia Angela Maria Maggiolini,
- Pietro D'Addabbo,
- Miriana Bitonto,
- Oronzo Capozzi,
- Martina Lepore Signorile,
- Mattia Miroballo,
- Nicoletta Archidiacono,
- Evan E. Eichler,
- Mario Ventura,
- and Francesca Antonacci
Genome Res. May 18, 2018 ; Published in Advance May 18, 2018, doi:10.1101/gr.234831.118
..., sequence, and experimental analyses, we analyzed 109 of these loci and found 67 regions inverted in one ormultiple primates, including 28 newly identified inversions. These events overlap with 81 human genes at their breakpoints, and seven correspond to sites of recurrent rearrangements associated...
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Research: The grasshopper genome reveals long-term gene content conservation of the X Chromosome and temporal variation in X Chromosome evolution
- Xinghua Li,
- Judith E. Mank,
- and Liping Ban
Genome Res. July 2024 34: 997-1007; Published in Advance August 5, 2024, doi:10.1101/gr.278794.123
...conservation of the X Chromosome gene content across broad swathes of the insect phylogeny, as well as temporal dynamics to the rate of X Chromosome evolution (Meisel et al. 2019; Chauhan et al. 2021).ResultsGenome featuresWe used PacBio HiFi sequencing to generate sequences for a female (XX) migratory locust...
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Method: Gene prediction in the immunoglobulin loci
- Vikram Sirupurapu,
- Yana Safonova,
- and Pavel A. Pevzner
Genome Res. June 2022 32: 1152-1169; Published in Advance May 11, 2022, doi:10.1101/gr.276676.122
...cryptic RSSs are implicated in unusual genomic rearrangements outside the IG and TCR loci (Messier et al. 2003) and sometimes play an important role in antibody generation. For example, cryptic RSSs flanking the human LAIR1 gene participate in the off-target VDJ recombination and generate new types...
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Research: Genomic architecture constrained placental mammal X Chromosome evolution
- Wesley A. Brashear,
- Kevin R. Bredemeyer,
- and William J. Murphy
Genome Res. August 2021 31: 1353-1365; Published in Advance July 22, 2021, doi:10.1101/gr.275274.121
...from an F1 domestic cat/Asian leopard cat hybrid and demonstrated the formation of the bipartite structure found in primate and rodent inactivated X Chromosomes. Conservation of gene order and recombination patterns is attributable to strong selective constraints on three-dimensional genomic...
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Resource: Single-cell strand sequencing of a macaque genome reveals multiple nested inversions and breakpoint reuse during primate evolution
- Flavia Angela Maria Maggiolini,
- Ashley D. Sanders,
- Colin James Shew,
- Arvis Sulovari,
- Yafei Mao,
- Marta Puig,
- Claudia Rita Catacchio,
- Maria Dellino,
- Donato Palmisano,
- Ludovica Mercuri,
- Miriana Bitonto,
- David Porubský,
- Mario Cáceres,
- Evan E. Eichler,
- Mario Ventura,
- Megan Y. Dennis,
- Jan O. Korbel,
- and Francesca Antonacci
Genome Res. November 2020 30: 1680-1693; Published in Advance October 22, 2020, doi:10.1101/gr.265322.120
...s (Supplemental Fig. S8), which we identify as candidate nonallelic homologous recombination (NAHR)–mediated inversions that may undergo recurrent rearrangements in primate s.Analysis of genomic featuresBecause inversions can directly act on genes via direct breaking of structure and separation...
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Resource: GenTree, an integrated resource for analyzing the evolution and function of primate-specific coding genes
- Yi Shao,
- Chunyan Chen,
- Hao Shen,
- Bin Z. He,
- Daqi Yu,
- Shuai Jiang,
- Shilei Zhao,
- Zhiqiang Gao,
- Zhenglin Zhu,
- Xi Chen,
- Yan Fu,
- Hua Chen,
- Ge Gao,
- Manyuan Long,
- and Yong E. Zhang
Genome Res. April 2019 29: 682-696; Published in Advance March 12, 2019, doi:10.1101/gr.238733.118
..., including DNA- or RNA-mediated duplication and de novo origination, lead to a high rate of protein-coding gene gain in human evolution (Zhang et al. 2012; Zhang and Long 2014). Transcriptome profiling has revealed that new genes in the human postdating the human and mouse split (i.e., primate-specific genes...
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