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Muthusamy PV, Vakayil Mani R, Kumari S, Kaur M, Bhaskar B, Raghavan Pillai R, Sajeev Kumar T, Anilkumar TV, Singh NS. Hybrid de novo and haplotype-resolved genome assembly of Vechur cattle - elucidating genetic variation. Front Genet 2024; 15:1338224. [PMID: 38510276 PMCID: PMC10952100 DOI: 10.3389/fgene.2024.1338224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 01/29/2024] [Indexed: 03/22/2024] Open
Abstract
Cattle contribute to the nutritional needs and economy of a place. The performance and fitness of cattle depend on the response and adaptation to local climatic conditions. Genomic and genetic studies are important for advancing cattle breeding, and availability of relevant reference genomes is essential. In the present study, the genome of a Vechur calf was sequenced on both short-read Illumina and long-read Nanopore sequencing platforms. The hybrid de novo assembly approach was deployed to obtain an average contig length of 1.97 Mbp and an N50 of 4.94 Mbp. By using a short-read genome sequence of the corresponding sire and dam, a haplotype-resolved genome was also assembled. In comparison to the taurine reference genome, we found 28,982 autosomal structural variants and 16,926,990 SNVs, with 883,544 SNVs homozygous in the trio samples. Many of these SNPs have been reported to be associated with various QTLs including growth, milk yield, and milk fat content, which are crucial determinants of cattle production. Furthermore, population genotype data analysis indicated that the present sample belongs to an Indian cattle breed forming a unique cluster of Bos indicus. Subsequent FST analysis revealed differentiation of the Vechur cattle genome at multiple loci, especially those regions related to whole body growth and cell division, especially IGF1, HMGA2, RRM2, and CD68 loci, suggesting a possible role of these genes in its small stature and better disease resistance capabilities in comparison with the local crossbreeds. This provides an opportunity to select and engineer cattle breeds optimized for local conditions.
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Affiliation(s)
- Poorvishaa V. Muthusamy
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala, India
| | | | - Shivani Kumari
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala, India
| | - Manpreet Kaur
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala, India
| | - Balu Bhaskar
- Kerala Livestock Development Board, Thiruvananthapuram, Kerala, India
| | | | | | - Thapasimuthu Vijayamma Anilkumar
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala, India
- Division of Experimental Pathology, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, India
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Frommer B, Müllner S, Holtgräwe D, Viehöver P, Huettel B, Töpfer R, Weisshaar B, Zyprian E. Phased grapevine genome sequence of an Rpv12 carrier for biotechnological exploration of resistance to Plasmopara viticola. Front Plant Sci 2023; 14:1180982. [PMID: 37223784 PMCID: PMC10200900 DOI: 10.3389/fpls.2023.1180982] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 04/11/2023] [Indexed: 05/25/2023]
Abstract
The downy mildew disease caused by the oomycete Plasmopara viticola is a serious threat for grapevine and can cause enormous yield losses in viticulture. The quantitative trait locus Rpv12, mediating resistance against P. viticola, was originally found in Asian Vitis amurensis. This locus and its genes were analyzed here in detail. A haplotype-separated genome sequence of the diploid Rpv12-carrier Gf.99-03 was created and annotated. The defense response against P. viticola was investigated in an infection time-course RNA-seq experiment, revealing approximately 600 upregulated Vitis genes during host-pathogen interaction. The Rpv12 regions of the resistance and the sensitivity encoding Gf.99-03 haplotype were structurally and functionally compared with each other. Two different clusters of resistance-related genes were identified within the Rpv12 locus. One cluster carries a set of four differentially expressed genes with three ACCELERATED CELL DEATH 6-like genes. The other cluster carries a set of six resistance gene analogs related to qualitative pathogen resistance. The Rpv12 locus and its candidate genes for P. viticola resistance provide a precious genetic resource for P. viticola resistance breeding. Newly developed co-segregating simple sequence repeat markers in close proximity to the R-genes enable its improved applicability in marker-assisted grapevine breeding.
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Affiliation(s)
- Bianca Frommer
- Genetics and Genomics of Plants, Faculty of Biology and Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
- Computational Biology, Faculty of Biology and Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Sophia Müllner
- Institute for Grapevine Breeding Geilweilerhof, Julius Kühn-Institute, Siebeldingen, Germany
| | - Daniela Holtgräwe
- Genetics and Genomics of Plants, Faculty of Biology and Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Prisca Viehöver
- Genetics and Genomics of Plants, Faculty of Biology and Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Bruno Huettel
- Max Planck-Genome-Centre Cologne, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Reinhard Töpfer
- Institute for Grapevine Breeding Geilweilerhof, Julius Kühn-Institute, Siebeldingen, Germany
| | - Bernd Weisshaar
- Genetics and Genomics of Plants, Faculty of Biology and Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Eva Zyprian
- Institute for Grapevine Breeding Geilweilerhof, Julius Kühn-Institute, Siebeldingen, Germany
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Heaton MP, Smith TPL, Bickhart DM, Vander Ley BL, Kuehn LA, Oppenheimer J, Shafer WR, Schuetze FT, Stroud B, McClure JC, Barfield JP, Blackburn HD, Kalbfleisch TS, Davenport KM, Kuhn KL, Green RE, Shapiro B, Rosen BD. A Reference Genome Assembly of Simmental Cattle, Bos taurus taurus. J Hered 2021; 112:184-191. [PMID: 33438035 PMCID: PMC8006815 DOI: 10.1093/jhered/esab002] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 01/11/2021] [Indexed: 12/22/2022] Open
Abstract
Genomics research has relied principally on the establishment and curation of a reference genome for the species. However, it is increasingly recognized that a single reference genome cannot fully describe the extent of genetic variation within many widely distributed species. Pangenome representations are based on high-quality genome assemblies of multiple individuals and intended to represent the broadest possible diversity within a species. A Bovine Pangenome Consortium (BPC) has recently been established to begin assembling genomes from more than 600 recognized breeds of cattle, together with other related species to provide information on ancestral alleles and haplotypes. Previously reported de novo genome assemblies for Angus, Brahman, Hereford, and Highland breeds of cattle are part of the initial BPC effort. The present report describes a complete single haplotype assembly at chromosome-scale for a fullblood Simmental cow from an F1 bison-cattle hybrid fetus by trio binning. Simmental cattle, also known as Fleckvieh due to their red and white spots, originated in central Europe in the 1830s as a triple-purpose breed selected for draught, meat, and dairy production. There are over 50 million Simmental cattle in the world, known today for their fast growth and beef yields. This assembly (ARS_Simm1.0) is similar in length to the other bovine assemblies at 2.86 Gb, with a scaffold N50 of 102 Mb (max scaffold 156.8 Mb) and meets or exceeds the continuity of the best Bos taurus reference assemblies to date.
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Affiliation(s)
| | | | | | - Brian L Vander Ley
- Great Plains Veterinary Educational Center, University of Nebraska-Lincoln, Lincoln, NE
| | - Larry A Kuehn
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE
| | - Jonas Oppenheimer
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA
| | | | | | - Brad Stroud
- Stroud Veterinary Embryo Services, Weatherford, TX
| | | | - Jennifer P Barfield
- College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO
| | | | | | - Kimberly M Davenport
- Department of Animal, Veterinary, and Food Science, University of Idaho, Moscow, ID
| | - Kristen L Kuhn
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE
| | - Richard E Green
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA
| | - Benjamin D Rosen
- USDA, ARS, Animal Genomics and Improvement Laboratory, Beltsville, MD
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Oppenheimer J, Rosen BD, Heaton MP, Vander Ley BL, Shafer WR, Schuetze FT, Stroud B, Kuehn LA, McClure JC, Barfield JP, Blackburn HD, Kalbfleisch TS, Bickhart DM, Davenport KM, Kuhn KL, Green RE, Shapiro B, Smith TPL. A Reference Genome Assembly of American Bison, Bison bison bison. J Hered 2021; 112:174-183. [PMID: 33595645 PMCID: PMC8006816 DOI: 10.1093/jhered/esab003] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 01/13/2021] [Indexed: 11/14/2022] Open
Abstract
Bison are an icon of the American West and an ecologically, commercially, and culturally important species. Despite numbering in the hundreds of thousands today, conservation concerns remain for the species, including the impact on genetic diversity of a severe bottleneck around the turn of the 20th century and genetic introgression from domestic cattle. Genetic diversity and admixture are best evaluated at genome-wide scale, for which a high-quality reference is necessary. Here, we use trio binning of long reads from a bison-Simmental cattle (Bos taurus taurus) male F1 hybrid to sequence and assemble the genome of the American plains bison (Bison bison bison). The male haplotype genome is chromosome-scale, with a total length of 2.65 Gb across 775 scaffolds (839 contigs) and a scaffold N50 of 87.8 Mb. Our bison genome is ~13× more contiguous overall and ~3400× more contiguous at the contig level than the current bison reference genome. The bison genome sequence presented here (ARS-UCSC_bison1.0) will enable new research into the evolutionary history of this iconic megafauna species and provide a new tool for the management of bison populations in federal and commercial herds.
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Affiliation(s)
- Jonas Oppenheimer
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Benjamin D Rosen
- USDA, ARS, Animal Genomics and Improvement Laboratory, Beltsville, MD, USA
| | - Michael P Heaton
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, USA
| | - Brian L Vander Ley
- Great Plains Veterinary Educational Center, University of Nebraska-Lincoln, Lincoln, NE, USA
| | | | | | - Brad Stroud
- Stroud Veterinary Embryo Services, Weatherford, TE, USA
| | - Larry A Kuehn
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, USA
| | | | - Jennifer P Barfield
- College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | | | | | | | - Kimberly M Davenport
- Department of Animal, Veterinary, and Food Science, University of Idaho, Moscow, ID, USA
| | - Kristen L Kuhn
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, USA
| | - Richard E Green
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA.,Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, USA
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Montgomery JS, Giacomini D, Waithaka B, Lanz C, Murphy BP, Campe R, Lerchl J, Landes A, Gatzmann F, Janssen A, Antonise R, Patterson E, Weigel D, Tranel PJ. Draft Genomes of Amaranthus tuberculatus, Amaranthus hybridus, and Amaranthus palmeri. Genome Biol Evol 2020; 12:1988-1993. [PMID: 32835372 PMCID: PMC7643611 DOI: 10.1093/gbe/evaa177] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/15/2020] [Indexed: 12/15/2022] Open
Abstract
Amaranthus tuberculatus, Amaranthus hybridus, and Amaranthus palmeri are agronomically important weed species. Here, we present the most contiguous draft assemblies of these three species to date. We utilized a combination of Pacific Biosciences long-read sequencing and chromatin contact mapping information to assemble and order sequences of A. palmeri to near-chromosome-level resolution, with scaffold N50 of 20.1 Mb. To resolve the issues of heterozygosity and coassembly of alleles in diploid species, we adapted the trio binning approach to produce haplotype assemblies of A. tuberculatus and A. hybridus. This approach resulted in an improved assembly of A. tuberculatus, and the first genome assembly for A. hybridus, with contig N50s of 2.58 and 2.26 Mb, respectively. Species-specific transcriptomes and information from related species were used to predict transcripts within each assembly. Syntenic comparisons of these species and Amaranthus hypochondriacus identified sites of genomic rearrangement, including duplication and translocation, whereas genetic map construction within A. tuberculatus highlighted the need for further ordering of the A. hybridus and A. tuberculatus contigs. These multiple reference genomes will accelerate genomic studies in these species to further our understanding of weedy evolution within Amaranthus.
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Affiliation(s)
| | | | - Bridgit Waithaka
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Christa Lanz
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Brent P Murphy
- Department of Crop Sciences, University of Illinois, Urbana
| | | | | | | | | | | | | | - Eric Patterson
- Department of Plant, Soil and Microbial Sciences, Michigan State University
| | - Detlef Weigel
- Max Planck Institute for Developmental Biology, Tübingen, Germany
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Yen EC, McCarthy SA, Galarza JA, Generalovic TN, Pelan S, Nguyen P, Meier JI, Warren IA, Mappes J, Durbin R, Jiggins CD. A haplotype-resolved, de novo genome assembly for the wood tiger moth (Arctia plantaginis) through trio binning. Gigascience 2020; 9:giaa088. [PMID: 32808665 PMCID: PMC7433188 DOI: 10.1093/gigascience/giaa088] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 07/03/2020] [Accepted: 07/27/2020] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Diploid genome assembly is typically impeded by heterozygosity because it introduces errors when haplotypes are collapsed into a consensus sequence. Trio binning offers an innovative solution that exploits heterozygosity for assembly. Short, parental reads are used to assign parental origin to long reads from their F1 offspring before assembly, enabling complete haplotype resolution. Trio binning could therefore provide an effective strategy for assembling highly heterozygous genomes, which are traditionally problematic, such as insect genomes. This includes the wood tiger moth (Arctia plantaginis), which is an evolutionary study system for warning colour polymorphism. FINDINGS We produced a high-quality, haplotype-resolved assembly for Arctia plantaginis through trio binning. We sequenced a same-species family (F1 heterozygosity ∼1.9%) and used parental Illumina reads to bin 99.98% of offspring Pacific Biosciences reads by parental origin, before assembling each haplotype separately and scaffolding with 10X linked reads. Both assemblies are contiguous (mean scaffold N50: 8.2 Mb) and complete (mean BUSCO completeness: 97.3%), with annotations and 31 chromosomes identified through karyotyping. We used the assembly to analyse genome-wide population structure and relationships between 40 wild resequenced individuals from 5 populations across Europe, revealing the Georgian population as the most genetically differentiated with the lowest genetic diversity. CONCLUSIONS We present the first invertebrate genome to be assembled via trio binning. This assembly is one of the highest quality genomes available for Lepidoptera, supporting trio binning as a potent strategy for assembling heterozygous genomes. Using our assembly, we provide genomic insights into the geographic population structure of A. plantaginis.
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Affiliation(s)
- Eugenie C Yen
- Department of Zoology, University of Cambridge, Downing
Street, Cambridge CB2 3EJ, UK
| | - Shane A McCarthy
- Department of Genetics, University of Cambridge, Downing
Street, Cambridge CB2 3EH, UK
- Wellcome Sanger Institute, Wellcome Trust Genome Campus,
Hinxton, Saffron Walden CB10 1SA, UK
| | - Juan A Galarza
- Department of Biological and Environmental Science, University of
Jyväskylä, FI-40014 Jyväskylä, Finland
| | - Tomas N Generalovic
- Department of Zoology, University of Cambridge, Downing
Street, Cambridge CB2 3EJ, UK
| | - Sarah Pelan
- Wellcome Sanger Institute, Wellcome Trust Genome Campus,
Hinxton, Saffron Walden CB10 1SA, UK
| | - Petr Nguyen
- Biology Centre of the Czech Academy of Sciences, Institute of
Entomology, Branišovská 1160/31, 370 05 České Budějovice, Czech
Republic
- University of South Bohemia, Faculty of Science, Branišovská
1645/31A, 370 05 České Budějovice, Czech Republic
| | - Joana I Meier
- Department of Zoology, University of Cambridge, Downing
Street, Cambridge CB2 3EJ, UK
- St John's College, University of Cambridge, St John's Street,
Cambridge CB2 1TP, UK
| | - Ian A Warren
- Department of Zoology, University of Cambridge, Downing
Street, Cambridge CB2 3EJ, UK
| | - Johanna Mappes
- Department of Biological and Environmental Science, University of
Jyväskylä, FI-40014 Jyväskylä, Finland
| | - Richard Durbin
- Department of Genetics, University of Cambridge, Downing
Street, Cambridge CB2 3EH, UK
- Wellcome Sanger Institute, Wellcome Trust Genome Campus,
Hinxton, Saffron Walden CB10 1SA, UK
| | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Downing
Street, Cambridge CB2 3EJ, UK
- St John's College, University of Cambridge, St John's Street,
Cambridge CB2 1TP, UK
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