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Hosaka AJ, Sanetomo R, Hosaka K. A de novo genome assembly of Solanum bulbocastanum Dun., a Mexican diploid species reproductively isolated from the A-genome species, including cultivated potatoes. G3 (Bethesda) 2024:jkae080. [PMID: 38608140 DOI: 10.1093/g3journal/jkae080] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 03/23/2024] [Accepted: 04/06/2024] [Indexed: 04/14/2024]
Abstract
Potato and its wild relatives are distributed mainly in the Mexican highlands and central Andes of South America. The South American A-genome species, including cultivated potatoes, are reproductively isolated from Mexican diploid species. Whole-genome sequencing has disclosed genome structure and similarity, mostly in cultivated potatoes and their closely related species. In this study, we generated a chromosome-scale assembly of the genome of a Mexican diploid species, Solanum bulbocastanum Dun., using PacBio long-read sequencing, Optical mapping, and Hi-C scaffolding technologies. The final sequence assembly consisted of 737.9 Mb, among which 647.0 Mb were anchored to the 12 chromosomes. Compared with chromosome-scale assemblies of S. lycopersicum (tomato), S. etuberosum (non-tuber-bearing species with E genome), S. verrucosum, S. chacoense, S. multidissectum, and S. phureja (all four are A-genome species), the S. bulbocastnum genome was the shortest. It contained fewer transposable elements (56.2%) than A-genome species. A cluster analysis was performed based on pairwise ratios of syntenic regions among the seven chromosome-scale assemblies, showing that the A-genome species were first clustered as a distinct group. Then, this group was clustered with S. bulbocastanum. Sequence similarity in 1,624 single-copy orthologous gene groups among 36 Solanum species and clones separated S. bulbocastanum as a specific group, including other Mexican diploid species, from the A-genome species. Therefore, the S. bulbocastanum genome differs in genome structure and gene sequences from the A-genome species. These findings provide important insights into understanding and utilizing the genetic diversity of S. bulbocastanum and the other Mexican diploid species in potato breeding.
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Affiliation(s)
- Awie J Hosaka
- Nihon BioData Corporation, Takatsu, Kawasaki, Kanagawa 213-0012, Japan
- Kihara Institute for Biological Research, Yokohama City University, Yokohama 244-0813, Japan
| | - Rena Sanetomo
- Potato Germplasm Enhancement Laboratory, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido 080-8555, Japan
| | - Kazuyoshi Hosaka
- Potato Germplasm Enhancement Laboratory, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido 080-8555, Japan
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2
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Wolf M, Greve C, Schell T, Janke A, Schmitt T, Pauls SU, Aspöck H, Aspöck U. The de novo genome of the Black-necked Snakefly (Venustoraphidia nigricollis Albarda, 1891): A resource to study the evolution of living fossils. J Hered 2024; 115:112-119. [PMID: 37988623 PMCID: PMC10838129 DOI: 10.1093/jhered/esad074] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 11/15/2023] [Accepted: 11/21/2023] [Indexed: 11/23/2023] Open
Abstract
Snakeflies (Raphidioptera) are the smallest order of holometabolous insects that have kept their distinct and name-giving appearance since the Mesozoic, probably since the Jurassic, and possibly even since their emergence in the Carboniferous, more than 300 million years ago. Despite their interesting nature and numerous publications on their morphology, taxonomy, systematics, and biogeography, snakeflies have never received much attention from the general public, and only a few studies were devoted to their molecular biology. Due to this lack of molecular data, it is therefore unknown, if the conserved morphological nature of these living fossils translates to conserved genomic structures. Here, we present the first genome of the species and of the entire order of Raphidioptera. The final genome assembly has a total length of 669 Mbp and reached a high continuity with an N50 of 5.07 Mbp. Further quality controls also indicate a high completeness and no meaningful contamination. The newly generated data was used in a large-scaled phylogenetic analysis of snakeflies using shared orthologous sequences. Quartet score and gene concordance analyses revealed high amounts of conflicting signals within this group that might speak for substantial incomplete lineage sorting and introgression after their presumed re-radiation after the asteroid impact 66 million years ago. Overall, this reference genome will be a door-opening dataset for many future research applications, and we demonstrated its utility in a phylogenetic analysis that provides new insights into the evolution of this group of living fossils.
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Affiliation(s)
- Magnus Wolf
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt am Main, Germany
- Institute for Ecology, Evolution and Diversity, Goethe University, Frankfurt am Main, Germany
| | - Carola Greve
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt am Main, Germany
- LOEWE-Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
| | - Tilman Schell
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt am Main, Germany
- LOEWE-Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
| | - Axel Janke
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt am Main, Germany
- Institute for Ecology, Evolution and Diversity, Goethe University, Frankfurt am Main, Germany
- LOEWE-Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
| | - Thomas Schmitt
- Senckenberg German Entomological Institute, Müncheberg, Germany
- Entomology and Biogeography, Faculty of Science, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Steffen U Pauls
- LOEWE-Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
- Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt am Main, Germany
- Institute of Insects Biotechnology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Horst Aspöck
- Institute of Specific Prophylaxis and Tropical Medicine, Medical Parasitology, Medical University of Vienna (MUW), Vienna, Austria
| | - Ulrike Aspöck
- Department of Evolutionary Biology, University of Vienna, Vienna, Austria
- Department of Entomology, Natural History Museum Vienna, Vienna, Austria
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3
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Ballard JWO, Field MA, Edwards RJ, Wilson LAB, Koungoulos LG, Rosen BD, Chernoff B, Dudchenko O, Omer A, Keilwagen J, Skvortsova K, Bogdanovic O, Chan E, Zammit R, Hayes V, Aiden EL. The Australasian dingo archetype: de novo chromosome-length genome assembly, DNA methylome, and cranial morphology. Gigascience 2023; 12:giad018. [PMID: 36994871 PMCID: PMC10353722 DOI: 10.1093/gigascience/giad018] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 01/13/2023] [Accepted: 02/28/2023] [Indexed: 03/29/2023] Open
Abstract
BACKGROUND One difficulty in testing the hypothesis that the Australasian dingo is a functional intermediate between wild wolves and domesticated breed dogs is that there is no reference specimen. Here we link a high-quality de novo long-read chromosomal assembly with epigenetic footprints and morphology to describe the Alpine dingo female named Cooinda. It was critical to establish an Alpine dingo reference because this ecotype occurs throughout coastal eastern Australia where the first drawings and descriptions were completed. FINDINGS We generated a high-quality chromosome-level reference genome assembly (Canfam_ADS) using a combination of Pacific Bioscience, Oxford Nanopore, 10X Genomics, Bionano, and Hi-C technologies. Compared to the previously published Desert dingo assembly, there are large structural rearrangements on chromosomes 11, 16, 25, and 26. Phylogenetic analyses of chromosomal data from Cooinda the Alpine dingo and 9 previously published de novo canine assemblies show dingoes are monophyletic and basal to domestic dogs. Network analyses show that the mitochondrial DNA genome clusters within the southeastern lineage, as expected for an Alpine dingo. Comparison of regulatory regions identified 2 differentially methylated regions within glucagon receptor GCGR and histone deacetylase HDAC4 genes that are unmethylated in the Alpine dingo genome but hypermethylated in the Desert dingo. Morphologic data, comprising geometric morphometric assessment of cranial morphology, place dingo Cooinda within population-level variation for Alpine dingoes. Magnetic resonance imaging of brain tissue shows she had a larger cranial capacity than a similar-sized domestic dog. CONCLUSIONS These combined data support the hypothesis that the dingo Cooinda fits the spectrum of genetic and morphologic characteristics typical of the Alpine ecotype. We propose that she be considered the archetype specimen for future research investigating the evolutionary history, morphology, physiology, and ecology of dingoes. The female has been taxidermically prepared and is now at the Australian Museum, Sydney.
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Affiliation(s)
- J William O Ballard
- School of Biosciences, University of Melbourne, Royal Parade, Parkville, Victoria 3052, Australia
- Department of Environment and Genetics, SABE, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Matt A Field
- Centre for Tropical Bioinformatics and Molecular Biology, College of Public Health, Medical and Veterinary Science, James Cook University, Cairns, Queensland 4870, Australia
- Immunogenomics Lab, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
| | - Richard J Edwards
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Laura A B Wilson
- School of Archaeology and Anthropology, The Australian National University, Acton, ACT 2600, Australia
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Loukas G Koungoulos
- Department of Archaeology, School of Philosophical and Historical Inquiry, the University of Sydney, Sydney, NSW 2006, Australia
| | - Benjamin D Rosen
- Animal Genomics and Improvement Laboratory, Agricultural Research Service USDA, Beltsville, MD 20705, USA
| | - Barry Chernoff
- College of the Environment, Departments of Biology, and Earth & Environmental Sciences, Wesleyan University, Middletown, CT 06459, USA
| | - Olga Dudchenko
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Theoretical and Biological Physics, Rice University, Houston, TX 77005, USA
| | - Arina Omer
- Center for Theoretical and Biological Physics, Rice University, Houston, TX 77005, USA
| | - Jens Keilwagen
- Institute for Biosafety in Plant Biotechnology, Julius Kühn-Institut, Quedlinburg 06484, Germany
| | - Ksenia Skvortsova
- Developmental Epigenomics Lab, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Ozren Bogdanovic
- Developmental Epigenomics Lab, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Eva Chan
- Developmental Epigenomics Lab, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- Statewide Genomics, New South Wales Health Pathology, Newcastle, NSW 2300, Australia
| | - Robert Zammit
- Vineyard Veterinary Hospital,Vineyard, NSW 2765, Australia
| | - Vanessa Hayes
- Developmental Epigenomics Lab, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- Charles Perkins Centre, Faculty of Medical Sciences, University of Sydney, Camperdown, NSW 2006, Australia
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Theoretical and Biological Physics, Rice University, Houston, TX 77005, USA
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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4
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Tang T, Hutvagner G, Wang W, Li J. Simultaneous compression of multiple error-corrected short-read sets for faster data transmission and better de novo assemblies. Brief Funct Genomics 2022; 21:387-398. [PMID: 35848773 DOI: 10.1093/bfgp/elac016] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 06/10/2022] [Accepted: 06/14/2022] [Indexed: 11/14/2022] Open
Abstract
Next-Generation Sequencing has produced incredible amounts of short-reads sequence data for de novo genome assembly over the last decades. For efficient transmission of these huge datasets, high-performance compression algorithms have been intensively studied. As both the de novo assembly and error correction methods utilize the overlaps between reads data, a concern is that the will the sequencing errors bring up negative effects on genome assemblies also affect the compression of the NGS data. This work addresses two problems: how current error correction algorithms can enable the compression algorithms to make the sequence data much more compact, and whether the sequence-modified reads by the error-correction algorithms will lead to quality improvement for de novo contig assembly. As multiple sets of short reads are often produced by a single biomedical project in practice, we propose a graph-based method to reorder the files in the collection of multiple sets and then compress them simultaneously for a further compression improvement after error correction. We use examples to illustrate that accurate error correction algorithms can significantly reduce the number of mismatched nucleotides in the reference-free compression, hence can greatly improve the compression performance. Extensive test on practical collections of multiple short-read sets does confirm that the compression performance on the error-corrected data (with unchanged size) significantly outperforms that on the original data, and that the file reordering idea contributes furthermore. The error correction on the original reads has also resulted in quality improvements of the genome assemblies, sometimes remarkably. However, it is still an open question that how to combine appropriate error correction methods with an assembly algorithm so that the assembly performance can be always significantly improved.
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Affiliation(s)
- Tao Tang
- Data Science Institute, University of Technology Sydney, 81 Broadway, Ultimo, 2007, NSW, Australia.,School of Mordern Posts, Nanjing University of Posts and Telecommunications, 9 Wenyuan Rd, Qixia District, 210003, Jiangsu, China
| | - Gyorgy Hutvagner
- School of Biomedical Engineering, University of Technology Sydney, 81 Broadway, Ultimo, 2007, NSW, Australia
| | - Wenjian Wang
- School of Computer and Information Technology, Shanxi University, Shanxi Road, 030006, Shanxi, China
| | - Jinyan Li
- Data Science Institute, University of Technology Sydney, 81 Broadway, Ultimo, 2007, NSW, Australia
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5
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Liu L, Megens HJ, Crooijmans RP, Bosse M, Huang Q, Sonsbeek GBV, Groenen MA, Madsen O. The Visayan warty pig (Sus cebifrons) genome provides insight into chromosome evolution and sensory adaptation in pigs. Mol Biol Evol 2022; 39:6596366. [PMID: 35642310 PMCID: PMC9178973 DOI: 10.1093/molbev/msac110] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
It is largely unknown how mammalian genomes evolve under rapid speciation and environmental adaptation. An excellent model for understanding fast evolution is provided by the genus Sus, which diverged relatively recently and lacks post-zygotic isolation. Here, we present a high-quality reference genome of the Visayan warty pig, which is specialized to a tropical island environment. Comparing the genome sequences and chromatin contact maps of the Visayan warty pig (Sus cebifrons) and domestic pig (Sus scrofa), we characterized the dynamics of chromosomal structure evolution during Sus speciation, revealing the similar chromosome conformation as the potential biological mechanism of frequent post-divergence hybridization among Suidae. We further investigated the different signatures of adaptive selection and domestication in Visayan warty pig and domestic pig with specific emphasize on the evolution of olfactory and gustatory genes, elucidating higher olfactory diversity in Visayan warty pig and positive and relaxed evolution of bitter and fat taste receptors, respectively, in domestic pig. Our comprehensive evolutionary and comparative genome analyses provide insight into the dynamics of genomes and how these change over relative short evolutionary times, as well as how these genomic differences encode for differences in the phenotypes.
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Affiliation(s)
- Langqing Liu
- Animal Breeding and Genomics, Wageningen University & Research, The Netherlands.,Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität Munich, Munich, Germany
| | - Hendrik-Jan Megens
- Animal Breeding and Genomics, Wageningen University & Research, The Netherlands
| | | | - Mirte Bosse
- Animal Breeding and Genomics, Wageningen University & Research, The Netherlands
| | - Qitong Huang
- Animal Breeding and Genomics, Wageningen University & Research, The Netherlands.,Center for Animal Genomics, Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | | | - Martien Am Groenen
- Animal Breeding and Genomics, Wageningen University & Research, The Netherlands
| | - Ole Madsen
- Animal Breeding and Genomics, Wageningen University & Research, The Netherlands
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6
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Pickett BD, Glass JR, Ridge PG, Kauwe JSK. De novo genome assembly of the marine teleost, bluefin trevally (Caranx melampygus). G3 (Bethesda) 2021; 11:jkab229. [PMID: 34568914 PMCID: PMC8473972 DOI: 10.1093/g3journal/jkab229] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 06/14/2021] [Indexed: 11/13/2022]
Abstract
The bluefin trevally, Caranx melampygus, also known as the bluefin kingfish or bluefin jack, is known for its remarkable, bright-blue fins. This marine teleost is a widely prized sportfish, but few resources have been devoted to the genomics and conservation of this species because it is not targeted by large-scale commercial fisheries. Population declines from recreational and artisanal overfishing have been observed in Hawai'i, USA, resulting in both an interest in aquaculture and concerns about the long-term conservation of this species. Most research to-date has been performed in Hawai'i, raising questions about the status of bluefin trevally populations across its Indo-Pacific range. Genomic resources allow for expanded research on stock status, genetic diversity, and population demography. We present a high quality, 711 Mb nuclear genome assembly of a Hawaiian bluefin trevally from noisy long-reads with a contig NG50 of 1.2 Mb and longest contig length of 8.9 Mb. As measured by single-copy orthologs, the assembly was 95% complete, and the genome is comprised of 16.9% repetitive elements. The assembly was annotated with 33.1 K protein-coding genes, 71.4% of which were assigned putative functions, using RNA-seq data from eight tissues from the same individual. This is the first whole-genome assembly published for the carangoid genus Caranx. Using this assembled genome, a multiple sequentially Markovian coalescent model was implemented to assess population demography. Estimates of effective population size suggest population expansion has occurred since the Late Pleistocene. This genome will be a valuable resource for comparative phylogenomic studies of carangoid fishes and will help elucidate demographic history and delineate stock structure for bluefin trevally populations throughout the Indo-Pacific.
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Affiliation(s)
- Brandon D Pickett
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Jessica R Glass
- South African Institute for Aquatic Biodiversity, Makhanda 6139, South Africa
- College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Fairbanks, AK 99775, USA
| | - Perry G Ridge
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - John S K Kauwe
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
- University President's Office, Brigham Young University-Hawai'i, Laie, HI 96762, U SA
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7
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Field MA, Rosen BD, Dudchenko O, Chan EKF, Minoche AE, Edwards RJ, Barton K, Lyons RJ, Tuipulotu DE, Hayes VM, D. Omer A, Colaric Z, Keilwagen J, Skvortsova K, Bogdanovic O, Smith MA, Aiden EL, Smith TPL, Zammit RA, Ballard JWO. Canfam_GSD: De novo chromosome-length genome assembly of the German Shepherd Dog (Canis lupus familiaris) using a combination of long reads, optical mapping, and Hi-C. Gigascience 2020; 9:giaa027. [PMID: 32236524 PMCID: PMC7111595 DOI: 10.1093/gigascience/giaa027] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [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: 10/21/2019] [Revised: 01/29/2020] [Accepted: 02/20/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The German Shepherd Dog (GSD) is one of the most common breeds on earth and has been bred for its utility and intelligence. It is often first choice for police and military work, as well as protection, disability assistance, and search-and-rescue. Yet, GSDs are well known to be susceptible to a range of genetic diseases that can interfere with their training. Such diseases are of particular concern when they occur later in life, and fully trained animals are not able to continue their duties. FINDINGS Here, we provide the draft genome sequence of a healthy German Shepherd female as a reference for future disease and evolutionary studies. We generated this improved canid reference genome (CanFam_GSD) utilizing a combination of Pacific Bioscience, Oxford Nanopore, 10X Genomics, Bionano, and Hi-C technologies. The GSD assembly is ∼80 times as contiguous as the current canid reference genome (20.9 vs 0.267 Mb contig N50), containing far fewer gaps (306 vs 23,876) and fewer scaffolds (429 vs 3,310) than the current canid reference genome CanFamv3.1. Two chromosomes (4 and 35) are assembled into single scaffolds with no gaps. BUSCO analyses of the genome assembly results show that 93.0% of the conserved single-copy genes are complete in the GSD assembly compared with 92.2% for CanFam v3.1. Homology-based gene annotation increases this value to ∼99%. Detailed examination of the evolutionarily important pancreatic amylase region reveals that there are most likely 7 copies of the gene, indicative of a duplication of 4 ancestral copies and the disruption of 1 copy. CONCLUSIONS GSD genome assembly and annotation were produced with major improvement in completeness, continuity, and quality over the existing canid reference. This resource will enable further research related to canine diseases, the evolutionary relationships of canids, and other aspects of canid biology.
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Affiliation(s)
- Matt A Field
- Centre for Tropical Bioinformatics and Molecular Biology, Australian Institute of Tropical Health and Medicine, James Cook University, Smithfield Road, Cairns, QLD 4878, Australia
- John Curtin School of Medical Research, Australian National University, Garran Rd, Canberra, ACT 2600, Australia
| | - Benjamin D Rosen
- Animal Genomics and Improvement Laboratory, Agricultural Research Service USDA, Baltimore Ave, Beltsville, MD 20705, USA
| | - Olga Dudchenko
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Baylor Plaza, Houston, TX 77030, USA
- Department of Computer Science, Rice University, Main St, Houston, TX 77005, USA
- Center for Theoretical and Biological Physics, Rice University, Main St, Houston, TX 77005, USA
| | - Eva K F Chan
- Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010, Australia
- Faculty of Medicine, UNSW Sydney, High St, Kensington, NSW 2052, Australia
| | - Andre E Minoche
- Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010, Australia
- St Vincent’s Clinical School, University of New South Wales Sydney, Victoria Street, Darlinghurst NSW 2010, Australia
| | - Richard J Edwards
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, High St, Kensington, NSW 2052, Australia
| | - Kirston Barton
- Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010, Australia
- Faculty of Medicine, UNSW Sydney, High St, Kensington, NSW 2052, Australia
| | - Ruth J Lyons
- Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010, Australia
| | - Daniel Enosi Tuipulotu
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, High St, Kensington, NSW 2052, Australia
| | - Vanessa M Hayes
- Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010, Australia
- Faculty of Medicine, UNSW Sydney, High St, Kensington, NSW 2052, Australia
- Central Clinical School, University of Sydney, Parramatta Road, Camperdown, NSW 2050, Australia
| | - Arina D. Omer
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Baylor Plaza, Houston, TX 77030, USA
- Department of Computer Science, Rice University, Main St, Houston, TX 77005, USA
| | - Zane Colaric
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Baylor Plaza, Houston, TX 77030, USA
- Department of Computer Science, Rice University, Main St, Houston, TX 77005, USA
| | - Jens Keilwagen
- Julius Kühn-Institut, Erwin-Baur-Str. 27, 06484 Quedlinburg, Germany
| | - Ksenia Skvortsova
- Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010, Australia
| | - Ozren Bogdanovic
- Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010, Australia
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, High St, Kensington, NSW 2052, Australia
| | - Martin A Smith
- Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010, Australia
- Faculty of Medicine, UNSW Sydney, High St, Kensington, NSW 2052, Australia
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Baylor Plaza, Houston, TX 77030, USA
- Department of Computer Science, Rice University, Main St, Houston, TX 77005, USA
- Center for Theoretical and Biological Physics, Rice University, Main St, Houston, TX 77005, USA
- Broad Institute of MIT and Harvard, Main St, Cambridge, MA 02142, USA
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, ShanghaiTech University, Huaxia Middle Rd, Pudong 201210, China
| | - Timothy P L Smith
- US Meat Animal Research Center, Agricultural Research Service USDA, Rd 313, Clay Center, NE 68933, USA
| | - Robert A Zammit
- Vineyard Veterinary Hospital, Windsor Rd, Vineyard, NSW 2765, Australia
| | - J William O Ballard
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, High St, Kensington, NSW 2052, Australia
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8
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Martinez-Viaud KA, Lawley CT, Vergara MM, Ben-Zvi G, Biniashvili T, Baruch K, St. Leger J, Le J, Natarajan A, Rivera M, Guillergan M, Jaeger E, Steffy B, Zimin A. New de novo assembly of the Atlantic bottlenose dolphin (Tursiops truncatus) improves genome completeness and provides haplotype phasing. Gigascience 2019; 8:giy168. [PMID: 30698692 PMCID: PMC6443575 DOI: 10.1093/gigascience/giy168] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 11/14/2018] [Accepted: 12/23/2018] [Indexed: 01/06/2023] Open
Abstract
High-quality genomes are essential to resolve challenges in breeding, comparative biology, medicine, and conservation planning. New library preparation techniques along with better assembly algorithms result in continued improvements in assemblies for non-model organisms, moving them toward reference-quality genomes. We report on the latest genome assembly of the Atlantic bottlenose dolphin, leveraging Illumina sequencing data coupled with a combination of several library preparation techniques. These include Linked-Reads (Chromium, 10x Genomics), mate pairs (MP), long insert paired ends, and standard paired end. Data were assembled with the commercial DeNovoMAGIC assembly software, resulting in two assemblies, a traditional "haploid" assembly (Tur_tru_Illumina_hap_v1) that is a mosaic of the two parental haplotypes and a phased assembly (Tur_tru_Illumina_phased_v1) where each scaffold has sequence from a single homologous chromosome. We show that Tur_tru_Illumina_hap_v1 is more complete and more accurate compared to the current best reference based on the amount and composition of sequence, the consistency of the MP alignments to the assembled scaffolds, and on the analysis of conserved single-copy mammalian orthologs. The phased de novo assembly Tur_tru_Illumina_phased_v1 is the first publicly available for this species and provides the community with novel and accurate ways to explore the heterozygous nature of the dolphin genome.
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Affiliation(s)
| | - Cindy Taylor Lawley
- GinkgoFish LLC, 204 West Spear St, Carson City, NV 89703
- Ocean Discovery Institute, 4255 Thorn St., San Diego, CA 92105 USA
| | | | - Gil Ben-Zvi
- NRGene, 5 Golda Meir St., Ness-Ziona 7403649, Israel
| | | | - Kobi Baruch
- NRGene, 5 Golda Meir St., Ness-Ziona 7403649, Israel
| | - Judy St. Leger
- SeaWorld San Diego, 500 Sea World Dr., San Diego, CA 92109, USA
| | - Jennie Le
- Illumina, Inc., 5200 Illumina Way, San Diego, CA 92122, USA
| | | | - Marlem Rivera
- Illumina, Inc., 5200 Illumina Way, San Diego, CA 92122, USA
- Ocean Discovery Institute, 4255 Thorn St., San Diego, CA 92105 USA
| | | | - Erich Jaeger
- Illumina, Inc., 5200 Illumina Way, San Diego, CA 92122, USA
| | - Brian Steffy
- Illumina, Inc., 5200 Illumina Way, San Diego, CA 92122, USA
| | - Aleksey Zimin
- Johns Hopkins University, Welch Library of Medicine, Ste 105, 1900 E. Monument St., Baltimore, MD 21205, USA
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9
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Xu CQ, Liu H, Zhou SS, Zhang DX, Zhao W, Wang S, Chen F, Sun YQ, Nie S, Jia KH, Jiao SQ, Zhang RG, Yun QZ, Guan W, Wang X, Gao Q, Bennetzen JL, Maghuly F, Porth I, Van de Peer Y, Wang XR, Ma Y, Mao JF. Genome sequence of Malania oleifera, a tree with great value for nervonic acid production. Gigascience 2019; 8:giy164. [PMID: 30689848 PMCID: PMC6377399 DOI: 10.1093/gigascience/giy164] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Revised: 11/12/2018] [Accepted: 12/17/2018] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Malania oleifera, a member of the Olacaceae family, is an IUCN red listed tree, endemic and restricted to the Karst region of southwest China. This tree's seed is valued for its high content of precious fatty acids (especially nervonic acid). However, studies on its genetic makeup and fatty acid biogenesis are severely hampered by a lack of molecular and genetic tools. FINDINGS We generated 51 Gb and 135 Gb of raw DNA sequences, using Pacific Biosciences (PacBio) single-molecule real-time and 10× Genomics sequencing, respectively. A final genome assembly, with a scaffold N50 size of 4.65 Mb and a total length of 1.51 Gb, was obtained by primary assembly based on PacBio long reads plus scaffolding with 10× Genomics reads. Identified repeats constituted ∼82% of the genome, and 24,064 protein-coding genes were predicted with high support. The genome has low heterozygosity and shows no evidence for recent whole genome duplication. Metabolic pathway genes relating to the accumulation of long-chain fatty acid were identified and studied in detail. CONCLUSIONS Here, we provide the first genome assembly and gene annotation for M. oleifera. The availability of these resources will be of great importance for conservation biology and for the functional genomics of nervonic acid biosynthesis.
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Affiliation(s)
- Chao-Qun Xu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, School of Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Hui Liu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, School of Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Shan-Shan Zhou
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, School of Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Dong-Xu Zhang
- College of Life Science, Datong University, Datong, Shanxi, 037009, China
| | - Wei Zhao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, School of Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Sihai Wang
- Yunnan Key Laboratory of Forest Plant Cultivation and Utilization, State Forestry Administration Key Laboratory of Yunnan Rare and Endangered Species Conservation and Propagation, Yunnan Academy of Forestry, Kunming, Yunnan, 650201, China
| | - Fu Chen
- The Camellia Institute, Yunnan Academy of Forestry, Guangnan, Yunnan, 663300, China
| | - Yan-Qiang Sun
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, School of Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Shuai Nie
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, School of Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Kai-Hua Jia
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, School of Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Si-Qian Jiao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, School of Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Ren-Gang Zhang
- Beijing Ori-Gene Science and Technology Co. Ltd, Beijing, 102206, China
| | - Quan-Zheng Yun
- Beijing Ori-Gene Science and Technology Co. Ltd, Beijing, 102206, China
| | - Wenbin Guan
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, School of Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Xuewen Wang
- The Camellia Institute, Yunnan Academy of Forestry, Guangnan, Yunnan, 663300, China
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Qiong Gao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, School of Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Jeffrey L Bennetzen
- The Camellia Institute, Yunnan Academy of Forestry, Guangnan, Yunnan, 663300, China
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Fatemeh Maghuly
- Plant Biotechnology Unit (PBU), Dept. Biotechnology, BOKU-VIBT, University of Natural Resources and Life Sciences, Muthgasse 18, Vienna 1190, Austria
| | - Ilga Porth
- Département des sciences du bois et de la forêt, 1030, Avenue de la Médecine, Université Laval, Québec (Québec) G1V 0A6, Canada
- Institute for System and Integrated Biology, Pavillon Charles-Eugène-Marchand, 1030, Avenue de la Médecine, Université Laval, Québec (Québec) G1V 0A6, Canada
- Centre d'Étude de la Forêt, 1030, Avenue de la Médecine, Université Laval, Québec (Québec) G1V 0A6, Canada
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent 9052, Belgium
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology Genetics, University of Pretoria, Private bag X20, Pretoria 0028, South Africa
| | - Xiao-Ru Wang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, School of Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- Department of Ecology and Environmental Science, UPSC, Umeå University, Umeå SE-901 87, Sweden
| | - Yongpeng Ma
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Population, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Jian-Feng Mao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, School of Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
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