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Herzog KS, Wu R, Hawdon JM, Nejsum P, Fauver JR. Assessing de novo parasite genomes assembled using only Oxford Nanopore Technologies MinION data. iScience 2024; 27:110614. [PMID: 39211578 PMCID: PMC11357801 DOI: 10.1016/j.isci.2024.110614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 06/09/2024] [Accepted: 07/26/2024] [Indexed: 09/04/2024] Open
Abstract
In this study, we assessed the quality of de novo genome assemblies for three species of parasitic nematodes (Brugia malayi, Trichuris trichiura, and Ancylostoma caninum) generated using only Oxford Nanopore Technologies MinION data. Assemblies were compared to current reference genomes and against additional assemblies that were supplemented with short-read Illumina data through polishing or hybrid assembly approaches. For each species, assemblies generated using only MinION data had similar or superior measures of contiguity, completeness, and gene content. In terms of gene composition, depending on the species, between 88.9 and 97.6% of complete coding sequences predicted in MinION data only assemblies were identical to those predicted in assemblies polished with Illumina data. Polishing MinION data only assemblies with Illumina data therefore improved gene-level accuracy to a degree. Furthermore, modified DNA extraction and library preparation protocols produced sufficient genomic DNA from B. malayi and T. trichiura to generate de novo assemblies from individual specimens.
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Affiliation(s)
- Kaylee S. Herzog
- Department of Epidemiology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Rachel Wu
- Department of Epidemiology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - John M. Hawdon
- Department of Microbiology, Immunology, and Tropical Medicine, The George Washington University, Washington, DC 20037, USA
| | - Peter Nejsum
- Department of Clinical Medicine, Aarhus University, 8200 Aarhus, Denmark
| | - Joseph R. Fauver
- Department of Epidemiology, University of Nebraska Medical Center, Omaha, NE 68198, USA
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Puritz JB, Guo X, Hare M, He Y, Hillier LW, Jin S, Liu M, Lotterhos KE, Minx P, Modak T, Proestou D, Rice ES, Tomlinson C, Warren WC, Witkop E, Zhao H, Gomez-Chiarri M. A second unveiling: Haplotig masking of the eastern oyster genome improves population-level inference. Mol Ecol Resour 2024; 24:e13801. [PMID: 37186213 DOI: 10.1111/1755-0998.13801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 12/16/2022] [Accepted: 03/20/2023] [Indexed: 05/17/2023]
Abstract
Genome assembly can be challenging for species that are characterized by high amounts of polymorphism, heterozygosity, and large effective population sizes. High levels of heterozygosity can result in genome mis-assemblies and a larger than expected genome size due to the haplotig versions of a single locus being assembled as separate loci. Here, we describe the first chromosome-level genome for the eastern oyster, Crassostrea virginica. Publicly released and annotated in 2017, the assembly has a scaffold N50 of 54 mb and is over 97.3% complete based on BUSCO analysis. The genome assembly for the eastern oyster is a critical resource for foundational research into molluscan adaptation to a changing environment and for selective breeding for the aquaculture industry. Subsequent resequencing data suggested the presence of haplotigs in the original assembly, and we developed a post hoc method to break up chimeric contigs and mask haplotigs in published heterozygous genomes and evaluated improvements to the accuracy of downstream analysis. Masking haplotigs had a large impact on SNP discovery and estimates of nucleotide diversity and had more subtle and nuanced effects on estimates of heterozygosity, population structure analysis, and outlier detection. We show that haplotig masking can be a powerful tool for improving genomic inference, and we present an open, reproducible resource for the masking of haplotigs in any published genome.
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Affiliation(s)
- Jonathan B Puritz
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, USA
| | - Ximing Guo
- Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, Port Norris, New Jersey, USA
| | - Matthew Hare
- Department of Natural Resources and the Environment, Cornell University, Ithaca, New York, USA
| | - Yan He
- Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, Port Norris, New Jersey, USA
| | - LaDeana W Hillier
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Shubo Jin
- Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, Port Norris, New Jersey, USA
| | - Ming Liu
- Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, Port Norris, New Jersey, USA
| | - Katie E Lotterhos
- Department of Marine and Environmental Sciences, Northeastern University Marine Science Center, Nahant, Massachusetts, USA
| | - Pat Minx
- Donald Danforth Plant Science Center, Olivette, Missouri, USA
| | - Tejashree Modak
- Department of Cell and Molecular Biology, University of Rhode Island, Kingston, Rhode Island, USA
| | - Dina Proestou
- USDA Agricultural Research Service, National Cold Water Marine Aquaculture Center, Kingston, Rhode Island, USA
| | - Edward S Rice
- Bond Life Sciences Center, University of Missouri, Columbia, Missouri, USA
| | - Chad Tomlinson
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, Missouri, USA
| | - Wesley C Warren
- Departments of Animal Sciences and Surgery, Institute of Informatics and Data Sciences, Bond Life Sciences Center, University of Missouri, Columbia, Missouri, USA
| | - Erin Witkop
- Department of Fisheries, Animal and Veterinary Sciences, University of Rhode Island, Kingston, Rhode Island, USA
| | - Honggang Zhao
- Department of Natural Resources and the Environment, Cornell University, Ithaca, New York, USA
| | - Marta Gomez-Chiarri
- Department of Fisheries, Animal and Veterinary Sciences, University of Rhode Island, Kingston, Rhode Island, USA
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Schelkunov MI. Mabs, a suite of tools for gene-informed genome assembly. BMC Bioinformatics 2023; 24:377. [PMID: 37794322 PMCID: PMC10548655 DOI: 10.1186/s12859-023-05499-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 09/26/2023] [Indexed: 10/06/2023] Open
Abstract
BACKGROUND Despite constantly improving genome sequencing methods, error-free eukaryotic genome assembly has not yet been achieved. Among other kinds of problems of eukaryotic genome assembly are so-called "haplotypic duplications", which may manifest themselves as cases of alleles being mistakenly assembled as paralogues. Haplotypic duplications are dangerous because they create illusions of gene family expansions and, thus, may lead scientists to incorrect conclusions about genome evolution and functioning. RESULTS Here, I present Mabs, a suite of tools that serve as parameter optimizers of the popular genome assemblers Hifiasm and Flye. By optimizing the parameters of Hifiasm and Flye, Mabs tries to create genome assemblies with the genes assembled as accurately as possible. Tests on 6 eukaryotic genomes showed that in 6 out of 6 cases, Mabs created assemblies with more accurately assembled genes than those generated by Hifiasm and Flye when they were run with default parameters. When assemblies of Mabs, Hifiasm and Flye were postprocessed by a popular tool for haplotypic duplication removal, Purge_dups, genes were better assembled by Mabs in 5 out of 6 cases. CONCLUSIONS Mabs is useful for making high-quality genome assemblies. It is available at https://github.com/shelkmike/Mabs.
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Chakraborty M, Lara AG, Dang A, McCulloch KJ, Rainbow D, Carter D, Ngo LT, Solares E, Said I, Corbett-Detig RB, Gilbert LE, Emerson JJ, Briscoe AD. Sex-linked gene traffic underlies the acquisition of sexually dimorphic UV color vision in Heliconius butterflies. Proc Natl Acad Sci U S A 2023; 120:e2301411120. [PMID: 37552755 PMCID: PMC10438391 DOI: 10.1073/pnas.2301411120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 06/16/2023] [Indexed: 08/10/2023] Open
Abstract
The acquisition of novel sexually dimorphic traits poses an evolutionary puzzle: How do new traits arise and become sex-limited? Recently acquired color vision, sexually dimorphic in animals like primates and butterflies, presents a compelling model for understanding how traits become sex-biased. For example, some Heliconius butterflies uniquely possess UV (ultraviolet) color vision, which correlates with the expression of two differentially tuned UV-sensitive rhodopsins, UVRh1 and UVRh2. To discover how such traits become sexually dimorphic, we studied Heliconius charithonia, which exhibits female-specific UVRh1 expression. We demonstrate that females, but not males, discriminate different UV wavelengths. Through whole-genome shotgun sequencing and assembly of the H. charithonia genome, we discovered that UVRh1 is present on the W chromosome, making it obligately female-specific. By knocking out UVRh1, we show that UVRh1 protein expression is absent in mutant female eye tissue, as in wild-type male eyes. A PCR survey of UVRh1 sex-linkage across the genus shows that species with female-specific UVRh1 expression lack UVRh1 gDNA in males. Thus, acquisition of sex linkage is sufficient to achieve female-specific expression of UVRh1, though this does not preclude other mechanisms, like cis-regulatory evolution from also contributing. Moreover, both this event, and mutations leading to differential UV opsin sensitivity, occurred early in the history of Heliconius. These results suggest a path for acquiring sexual dimorphism distinct from existing mechanistic models. We propose a model where gene traffic to heterosomes (the W or the Y) genetically partitions a trait by sex before a phenotype shifts (spectral tuning of UV sensitivity).
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Affiliation(s)
- Mahul Chakraborty
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA92697
- Department of Biology, Texas A&M University, College Station, TX77843
| | | | - Andrew Dang
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA92697
| | - Kyle J. McCulloch
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA92697
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN55108
| | - Dylan Rainbow
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA92697
| | - David Carter
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, CA92521
| | - Luna Thanh Ngo
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA92697
| | - Edwin Solares
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA92697
| | - Iskander Said
- Department of Biomolecular Engineering and Genomics Institute, University of California, Santa Cruz, CA95064
| | - Russell B. Corbett-Detig
- Department of Biomolecular Engineering and Genomics Institute, University of California, Santa Cruz, CA95064
| | | | - J. J. Emerson
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA92697
| | - Adriana D. Briscoe
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA92697
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Solares E, Morales-Cruz A, Balderas RF, Focht E, Ashworth VETM, Wyant S, Minio A, Cantu D, Arpaia ML, Gaut BS. Insights into the domestication of avocado and potential genetic contributors to heterodichogamy. G3 (BETHESDA, MD.) 2023; 13:jkac323. [PMID: 36477810 PMCID: PMC9911064 DOI: 10.1093/g3journal/jkac323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 11/11/2022] [Accepted: 11/15/2022] [Indexed: 12/13/2022]
Abstract
The domestication history of the avocado (Persea americana) remains unclear. We created a reference genome from the Gwen varietal, which is closely related to the economically dominant Hass varietal. Our genome assembly had an N50 of 3.37 megabases, a BUSCO score of 91%, and was scaffolded with a genetic map, producing 12 pseudo-chromosomes with 49,450 genes. We used the Gwen genome as a reference to investigate population genomics, based on a sample of 34 resequenced accessions that represented the 3 botanical groups of P. americana. Our analyses were consistent with 3 separate domestication events; we estimated that the Mexican group diverged from the Lowland (formerly known as "West Indian") and Guatemalan groups >1 million years ago. We also identified putative targets of selective sweeps in domestication events; within the Guatemalan group, putative candidate genes were enriched for fruit development and ripening. We also investigated divergence between heterodichogamous flowering types, providing preliminary evidence for potential candidate genes involved in pollination and floral development.
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Affiliation(s)
- Edwin Solares
- Deptartment of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA 92697-2525, USA
| | - Abraham Morales-Cruz
- Deptartment of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA 92697-2525, USA
| | - Rosa Figueroa Balderas
- Department of Viticulture and Enology, University of California, Davis, Davis, CA 95616, USA
| | - Eric Focht
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Vanessa E T M Ashworth
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Skylar Wyant
- Deptartment of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA 92697-2525, USA
| | - Andrea Minio
- Department of Viticulture and Enology, University of California, Davis, Davis, CA 95616, USA
| | - Dario Cantu
- Department of Viticulture and Enology, University of California, Davis, Davis, CA 95616, USA
| | - Mary Lu Arpaia
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Brandon S Gaut
- Deptartment of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA 92697-2525, USA
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