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Purayil GP, Saeed EE, Mathai AM, El-Tarabily KA, AbuQamar SF. A high-quality genome assembly and annotation of Thielaviopsis punctulata DSM102798. Sci Data 2024; 11:745. [PMID: 38982096 PMCID: PMC11233662 DOI: 10.1038/s41597-024-03458-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 05/31/2024] [Indexed: 07/11/2024] Open
Abstract
Black scorch disease (BSD), caused by the fungal pathogen Thielaviopsis punctulata (Tp) DSM102798, poses a significant threat to date palm cultivation in the United Arab Emirates (UAE). In this study, Chicago and Hi-C libraries were prepared as input for the Dovetail HiRise pipeline to scaffold the genome of Tp DSM102798. We generated an assembly with a total length of 28.23 Mb comprising 1,256 scaffolds, and the assembly had a contig N50 of 18.56 kb, L50 of three, and a BUSCO completeness score of 98.6% for 758 orthologous genes. Annotation of this assembly produced 7,169 genes and 3,501 Gene Ontology (GO) terms. Compared to five other Thielaviopsis genomes, Tp DSM102798 exhibited the highest continuity with a cumulative size of 27.598 Mb for the first seven scaffolds, surpassing the assemblies of all examined strains. These findings offer a foundation for targeted strategies that enhance date palm resistance against BSD, and foster more sustainable and resilient agricultural systems.
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Affiliation(s)
- Gouthaman P Purayil
- Department of Biology, College of Science, United Arab Emirates University, Al Ain, 15551, United Arab Emirates
| | - Esam Eldin Saeed
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain, 15551, United Arab Emirates
| | - Archana M Mathai
- Department of Biology, College of Science, United Arab Emirates University, Al Ain, 15551, United Arab Emirates
| | - Khaled A El-Tarabily
- Department of Biology, College of Science, United Arab Emirates University, Al Ain, 15551, United Arab Emirates
| | - Synan F AbuQamar
- Department of Biology, College of Science, United Arab Emirates University, Al Ain, 15551, United Arab Emirates.
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2
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Sato M, Fukuda K, Kadota M, Makino-Itou H, Tatsumi K, Yamauchi S, Kuraku S. Chromosomal DNA sequences of the Pacific saury genome: versatile resources for fishery science and comparative biology. DNA Res 2024; 31:dsae004. [PMID: 38451834 PMCID: PMC11090075 DOI: 10.1093/dnares/dsae004] [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: 10/30/2023] [Revised: 12/19/2023] [Accepted: 01/26/2024] [Indexed: 03/09/2024] Open
Abstract
Pacific saury (Cololabis saira) is a commercially important small pelagic fish species in Asia. In this study, we conducted the first-ever whole genome sequencing of this species, with single molecule, real-time (SMRT) sequencing technology. The obtained high-fidelity (HiFi) long-read sequence data, which amount to ~30-folds of its haploid genome size that was measured with quantitative PCR (1.17 Gb), were assembled into contigs. Scaffolding with Hi-C reads yielded a whole genome assembly containing 24 chromosome-scale sequences, with a scaffold N50 length of 47.7 Mb. Screening of repetitive elements including telomeric repeats was performed to characterize possible factors that need to be resolved towards 'telomere-to-telomere' sequencing. The larger genome size than in medaka, a close relative in Beloniformes, is at least partly explained by larger repetitive element quantity, which is reflected in more abundant tRNAs, in the Pacific saury genome. Protein-coding regions were predicted using transcriptome data, which resulted in 22,274 components. Retrieval of Pacific saury homologs of aquaporin (AQP) genes known from other teleost fishes validated high completeness and continuity of the genome assembly. These resources are available at https://treethinkers.nig.ac.jp/saira/ and will assist various molecular-level studies in fishery science and comparative biology.
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Affiliation(s)
- Mana Sato
- Molecular Life History Laboratory, Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Kazuya Fukuda
- Laboratory of Reproductive Physiology of Aquatic Organisms, School of Marine Biosciences, Kitasato University, Sagamihara, Kanagawa, Japan
| | - Mitsutaka Kadota
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, Japan
| | - Hatsune Makino-Itou
- Molecular Life History Laboratory, Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Kaori Tatsumi
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, Japan
| | - Shinya Yamauchi
- Fukushima Marine Science Museum (Aquamarine Fukushima), Iwaki, Fukushima, Japan
| | - Shigehiro Kuraku
- Molecular Life History Laboratory, Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
- Department of Genetics, Sokendai (Graduate University for Advanced Studies), Mishima, Shizuoka, Japan
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3
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Yamaguchi K, Uno Y, Kadota M, Nishimura O, Nozu R, Murakumo K, Matsumoto R, Sato K, Kuraku S. Elasmobranch genome sequencing reveals evolutionary trends of vertebrate karyotype organization. Genome Res 2023; 33:1527-1540. [PMID: 37591668 PMCID: PMC10620051 DOI: 10.1101/gr.276840.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 07/31/2023] [Indexed: 08/19/2023]
Abstract
Genomic studies of vertebrate chromosome evolution have long been hindered by the scarcity of chromosome-scale DNA sequences of some key taxa. One of those limiting taxa has been the elasmobranchs (sharks and rays), which harbor species often with numerous chromosomes and enlarged genomes. Here, we report the chromosome-scale genome assembly for the zebra shark Stegostoma tigrinum, an endangered species that has a relatively small genome among sharks (3.71 Gb), as well as for the whale shark Rhincodon typus Our analysis using a male-female comparison identified an X Chromosome, the first genomically characterized shark sex chromosome. The X Chromosome harbors the Hox C cluster whose intact linkage has not been shown for an elasmobranch fish. The sequenced shark genomes show a gradualism of chromosome length with remarkable length-dependent characteristics-shorter chromosomes tend to have higher GC content, gene density, synonymous substitution rate, and simple tandem repeat content as well as smaller gene length and lower interspersed repeat content. We challenge the traditional binary classification of karyotypes as with and without so-called microchromosomes. Even without microchromosomes, the length-dependent characteristics persist widely in nonmammalian vertebrates. Our investigation of elasmobranch karyotypes underpins their unique characteristics and provides clues for understanding how vertebrate karyotypes accommodate intragenomic heterogeneity to realize a complex readout. It also paves the way to dissecting more genomes with variable sizes to be sequenced at high quality.
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Affiliation(s)
- Kazuaki Yamaguchi
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), 650-0047, Kobe, Japan
| | - Yoshinobu Uno
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), 650-0047, Kobe, Japan
| | - Mitsutaka Kadota
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), 650-0047, Kobe, Japan
| | - Osamu Nishimura
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), 650-0047, Kobe, Japan
| | - Ryo Nozu
- Okinawa Churashima Research Center, Okinawa Churashima Foundation, 905-0206, Okinawa, Japan
| | | | | | - Keiichi Sato
- Okinawa Churashima Research Center, Okinawa Churashima Foundation, 905-0206, Okinawa, Japan
- Okinawa Churaumi Aquarium, 905-0206, Okinawa, Japan
| | - Shigehiro Kuraku
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), 650-0047, Kobe, Japan;
- Molecular Life History Laboratory, Department of Genomics and Evolutionary Biology, National Institute of Genetics, 411-8540, Mishima, Japan
- Department of Genetics, Sokendai (Graduate University for Advanced Studies), 411-8540, Mishima, Japan
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4
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Ouchi S, Kajitani R, Itoh T. GreenHill: a de novo chromosome-level scaffolding and phasing tool using Hi-C. Genome Biol 2023; 24:162. [PMID: 37434204 DOI: 10.1186/s13059-023-03006-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 07/04/2023] [Indexed: 07/13/2023] Open
Abstract
Chromosome-level haplotype-resolved genome assembly is an important resource in molecular biology. However, current de novo haplotype assemblers require parental data or reference genomes and often fail to provide chromosome-level results. We present GreenHill, a novel scaffolding and phasing tool that considers various assemblers' contigs as input to reconstruct chromosome-level haplotypes using Hi-C without parental or reference data. Its unique functions include new error correction based on Hi-C contacts and the simultaneous use of Hi-C and long reads. Benchmarks reveal that GreenHill outperforms other approaches in contiguity and phasing accuracy, and the majority of chromosome arms are entirely phased.
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Affiliation(s)
- Shun Ouchi
- School of Life Science and Technology, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-Ku, Tokyo, 152-8550, Japan
| | - Rei Kajitani
- School of Life Science and Technology, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-Ku, Tokyo, 152-8550, Japan
| | - Takehiko Itoh
- School of Life Science and Technology, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-Ku, Tokyo, 152-8550, Japan.
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Fukuda K, Shimi T, Shimura C, Ono T, Suzuki T, Onoue K, Okayama S, Miura H, Hiratani I, Ikeda K, Okada Y, Dohmae N, Yonemura S, Inoue A, Kimura H, Shinkai Y. Epigenetic plasticity safeguards heterochromatin configuration in mammals. Nucleic Acids Res 2023; 51:6190-6207. [PMID: 37178005 PMCID: PMC10325917 DOI: 10.1093/nar/gkad387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 04/13/2023] [Accepted: 05/02/2023] [Indexed: 05/15/2023] Open
Abstract
Heterochromatin is a key architectural feature of eukaryotic chromosomes critical for cell type-specific gene expression and genome stability. In the mammalian nucleus, heterochromatin segregates from transcriptionally active genomic regions and exists in large, condensed, and inactive nuclear compartments. However, the mechanisms underlying the spatial organization of heterochromatin need to be better understood. Histone H3 lysine 9 trimethylation (H3K9me3) and lysine 27 trimethylation (H3K27me3) are two major epigenetic modifications that enrich constitutive and facultative heterochromatin, respectively. Mammals have at least five H3K9 methyltransferases (SUV39H1, SUV39H2, SETDB1, G9a and GLP) and two H3K27 methyltransferases (EZH1 and EZH2). In this study, we addressed the role of H3K9 and H3K27 methylation in heterochromatin organization using a combination of mutant cells for five H3K9 methyltransferases and an EZH1/2 dual inhibitor, DS3201. We showed that H3K27me3, which is normally segregated from H3K9me3, was redistributed to regions targeted by H3K9me3 after the loss of H3K9 methylation and that the loss of both H3K9 and H3K27 methylation resulted in impaired condensation and spatial organization of heterochromatin. Our data demonstrate that the H3K27me3 pathway safeguards heterochromatin organization after the loss of H3K9 methylation in mammalian cells.
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Affiliation(s)
- Kei Fukuda
- Cellular Memory Laboratory, RIKEN Cluster for Pioneering Research, Wako351-0198, Japan
- School of Biosciences, The University of Melbourne, Royal Parade, 3010 Parkville, Australia
| | - Takeshi Shimi
- World Research Hub Initiative, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Chikako Shimura
- Cellular Memory Laboratory, RIKEN Cluster for Pioneering Research, Wako351-0198, Japan
| | - Takao Ono
- Chromosome Dynamics Laboratory, RIKEN Cluster for Pioneering Research, Wako 351-0198, Japan
| | - Takehiro Suzuki
- Biomolecular Characterization Unit, Technology Platform Division, RIKEN Center for Sustainable Resource Science, Wako 351-0198, Japan
| | - Kenta Onoue
- Laboratory for Ultrastructural Research, RIKEN Center for Biosystems Dynamics Research, Kobe650-0047, Japan
| | - Satoko Okayama
- Laboratory for Ultrastructural Research, RIKEN Center for Biosystems Dynamics Research, Kobe650-0047, Japan
| | - Hisashi Miura
- Laboratory for Developmental Epigenetics, RIKEN Center for Biosystems Dynamics Research, Kobe650-0047, Japan
| | - Ichiro Hiratani
- Laboratory for Developmental Epigenetics, RIKEN Center for Biosystems Dynamics Research, Kobe650-0047, Japan
| | - Kazuho Ikeda
- Department of Cell Biology, Graduate School of Medicine, The University of Tokyo, Tokyo113-0033, Japan
| | - Yasushi Okada
- Department of Cell Biology, Graduate School of Medicine, The University of Tokyo, Tokyo113-0033, Japan
- Universal Biology Institute (UBI) and International Research Center for Neurointelligence (WPI-IRCN), The University of Tokyo, Tokyo113-0033, Japan
- Laboratory for Cell Polarity Regulation, RIKEN Center for Biosystems Dynamics Research (BDR), Osaka565-0874, Japan
- Department of Physics, Graduate School of Science, The University of Tokyo, Tokyo113-0033, Japan
| | - Naoshi Dohmae
- Biomolecular Characterization Unit, Technology Platform Division, RIKEN Center for Sustainable Resource Science, Wako 351-0198, Japan
| | - Shigenobu Yonemura
- Laboratory for Ultrastructural Research, RIKEN Center for Biosystems Dynamics Research, Kobe650-0047, Japan
- Department of Cell Biology, Tokushima University Graduate School of Medicine, Tokushima770-8503, Japan
| | - Azusa Inoue
- Laboratory for Epigenome Inheritance, RIKEN Center for Integrative Medical Sciences, Yokohama230-0045, Japan
- Tokyo Metropolitan University, Hachioji192-0397, Japan
| | - Hiroshi Kimura
- World Research Hub Initiative, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama226-8501, Japan
| | - Yoichi Shinkai
- Cellular Memory Laboratory, RIKEN Cluster for Pioneering Research, Wako351-0198, Japan
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6
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A global high-density chromatin interaction network reveals functional long-range and trans-chromosomal relationships. Genome Biol 2022; 23:238. [PMID: 36352464 PMCID: PMC9647974 DOI: 10.1186/s13059-022-02790-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 10/10/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Chromatin contacts are essential for gene-expression regulation; however, obtaining a high-resolution genome-wide chromatin contact map is still prohibitively expensive owing to large genome sizes and the quadratic scale of pairwise data. Chromosome conformation capture (3C)-based methods such as Hi-C have been extensively used to obtain chromatin contacts. However, since the sparsity of these maps increases with an increase in genomic distance between contacts, long-range or trans-chromatin contacts are especially challenging to sample. RESULTS Here, we create a high-density reference genome-wide chromatin contact map using a meta-analytic approach. We integrate 3600 human, 6700 mouse, and 500 fly Hi-C experiments to create species-specific meta-Hi-C chromatin contact maps with 304 billion, 193 billion, and 19 billion contacts in respective species. We validate that meta-Hi-C contact maps are uniquely powered to capture functional chromatin contacts in both cis and trans. We find that while individual dataset Hi-C networks are largely unable to predict any long-range coexpression (median 0.54 AUC), meta-Hi-C networks perform comparably in both cis and trans (0.65 AUC vs 0.64 AUC). Similarly, for long-range expression quantitative trait loci (eQTL), meta-Hi-C contacts outperform all individual Hi-C experiments, providing an improvement over the conventionally used linear genomic distance-based association. Assessing between species, we find patterns of chromatin contact conservation in both cis and trans and strong associations with coexpression even in species for which Hi-C data is lacking. CONCLUSIONS We have generated an integrated chromatin interaction network which complements a large number of methodological and analytic approaches focused on improved specificity or interpretation. This high-depth "super-experiment" is surprisingly powerful in capturing long-range functional relationships of chromatin interactions, which are now able to predict coexpression, eQTLs, and cross-species relationships. The meta-Hi-C networks are available at https://labshare.cshl.edu/shares/gillislab/resource/HiC/ .
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Nishimura O, Rozewicki J, Yamaguchi K, Tatsumi K, Ohishi Y, Ohta T, Yagura M, Niwa T, Tanegashima C, Teramura A, Hirase S, Kawaguchi A, Tan M, D'Aniello S, Castro F, Machado A, Koyanagi M, Terakita A, Misawa R, Horie M, Kawasaki J, Asahida T, Yamaguchi A, Murakumo K, Matsumoto R, Irisarri I, Miyamoto N, Toyoda A, Tanaka S, Sakamoto T, Semba Y, Yamauchi S, Yamada K, Nishida K, Kiyatake I, Sato K, Hyodo S, Kadota M, Uno Y, Kuraku S. Squalomix: shark and ray genome analysis consortium and its data sharing platform. F1000Res 2022; 11:1077. [PMID: 36262334 PMCID: PMC9561540 DOI: 10.12688/f1000research.123591.1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/31/2022] [Indexed: 01/13/2023] Open
Abstract
The taxon Elasmobranchii (sharks and rays) contains one of the long-established evolutionary lineages of vertebrates with a tantalizing collection of species occupying critical aquatic habitats. To overcome the current limitation in molecular resources, we launched the Squalomix Consortium in 2020 to promote a genome-wide array of molecular approaches, specifically targeting shark and ray species. Among the various bottlenecks in working with elasmobranchs are their elusiveness and low fecundity as well as the large and highly repetitive genomes. Their peculiar body fluid composition has also hindered the establishment of methods to perform routine cell culturing required for their karyotyping. In the Squalomix consortium, these obstacles are expected to be solved through a combination of in-house cytological techniques including karyotyping of cultured cells, chromatin preparation for Hi-C data acquisition, and high fidelity long-read sequencing. The resources and products obtained in this consortium, including genome and transcriptome sequences, a genome browser powered by JBrowse2 to visualize sequence alignments, and comprehensive matrices of gene expression profiles for selected species are accessible through https://github.com/Squalomix/info.
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Affiliation(s)
- Osamu Nishimura
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, 657-0024, Japan
| | - John Rozewicki
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, 657-0024, Japan
| | - Kazuaki Yamaguchi
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, 657-0024, Japan
| | - Kaori Tatsumi
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, 657-0024, Japan
| | - Yuta Ohishi
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, 657-0024, Japan
| | - Tazro Ohta
- Joint Support-Center for Data Science Research, Database Center for Life Science, Mishima, Shizuoka, 411-8540, Japan
| | - Masaru Yagura
- Molecular Life History Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Taiki Niwa
- Molecular Life History Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan,Department of Genetics, Sokendai (Graduate University for Advanced Studies), Mishima, Shizuoka, Japan
| | - Chiharu Tanegashima
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, 657-0024, Japan
| | - Akinori Teramura
- Fisheries Laboratory, Graduate School of Agricultural and Life Sciences, University of Tokyo, Hamamatsu, Shizuoka, 431-0214, Japan
| | - Shotaro Hirase
- Fisheries Laboratory, Graduate School of Agricultural and Life Sciences, University of Tokyo, Hamamatsu, Shizuoka, 431-0214, Japan
| | - Akane Kawaguchi
- Molecular Life History Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Milton Tan
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, Illinois, USA
| | - Salvatore D'Aniello
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, Napoli, Italy
| | - Filipe Castro
- Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal,Faculty of Sciences, University of Porto, Porto, Portugal
| | - André Machado
- Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
| | - Mitsumasa Koyanagi
- Department of Biology, Graduate School of Science, Osaka Metropolitan University, Osaka, Osaka, Japan
| | - Akihisa Terakita
- Department of Biology, Graduate School of Science, Osaka Metropolitan University, Osaka, Osaka, Japan
| | - Ryo Misawa
- Japan Fisheries Research and Education Agency, Hachinohe, Aomori, Japan
| | - Masayuki Horie
- Graduate School of Veterinary Science, Osaka Metropolitan University, Izumisano, Osaka, Japan
| | - Junna Kawasaki
- Waseda Research Institute for Science and Engineering, Waseda University, Tokyo, Japan
| | - Takashi Asahida
- School of Marine Biosciences, Kitasato University, Sagamihara, Kanagawa, Japan
| | - Atsuko Yamaguchi
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Nagasaki, Nagasaki, Japan
| | | | | | - Iker Irisarri
- Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change (LIB), Museum of Nature-Zoology, Hamburg, 20146, Germany
| | - Norio Miyamoto
- X-STAR, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Kanagawa, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Sho Tanaka
- School of Marine Science and Technology, Tokai University, Shizuoka, Shizuoka, Japan
| | - Tatsuya Sakamoto
- Ushimado Marine Institute, Graduate School of Natural Science and Technology, Okayama University, Setouchi, Japan., Okayama, Japan
| | - Yasuko Semba
- Highly Migratory Resources Division, Fisheries Resources Institute, Japan Fisheries Research and Education Agency, Shizuoka, Shizuoka, Japan
| | | | - Kazuyuki Yamada
- Marine Science Museum, Tokai University, Shizuoka, Shizuoka, Japan
| | | | | | - Keiichi Sato
- Okinawa Churaumi Aquarium, Motobu, Okinawa, Japan
| | - Susumu Hyodo
- Laboratory of Physiology, Atmosphere and Ocean Research Institute, University of Tokyo,, Kashiwa, Chiba, Japan
| | - Mitsutaka Kadota
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, 657-0024, Japan
| | - Yoshinobu Uno
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Tokyo, Japan
| | - Shigehiro Kuraku
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, 657-0024, Japan,Molecular Life History Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan,Department of Genetics, Sokendai (Graduate University for Advanced Studies), Mishima, Shizuoka, Japan,
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8
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Menon VK, Okhuysen PC, Chappell CL, Mahmoud M, Mahmoud M, Meng Q, Doddapaneni H, Vee V, Han Y, Salvi S, Bhamidipati S, Kottapalli K, Weissenberger G, Shen H, Ross MC, Hoffman KL, Cregeen SJ, Muzny DM, Metcalf GA, Gibbs RA, Petrosino JF, Sedlazeck FJ. Fully resolved assembly of Cryptosporidium parvum. Gigascience 2022; 11:6528769. [PMID: 35166336 PMCID: PMC8848321 DOI: 10.1093/gigascience/giac010] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 12/07/2021] [Accepted: 01/20/2022] [Indexed: 11/17/2022] Open
Abstract
Background Cryptosporidium parvum is an apicomplexan parasite commonly found across many host species with a global infection prevalence in human populations of 7.6%. Understanding its diversity and genomic makeup can help in fighting established infections and prohibiting further transmission. The basis of every genomic study is a high-quality reference genome that has continuity and completeness, thus enabling comprehensive comparative studies. Findings Here, we provide a highly accurate and complete reference genome of Cryptosporidium parvum. The assembly is based on Oxford Nanopore reads and was improved using Illumina reads for error correction. We also outline how to evaluate and choose from different assembly methods based on 2 main approaches that can be applied to other Cryptosporidium species. The assembly encompasses 8 chromosomes and includes 13 telomeres that were resolved. Overall, the assembly shows a high completion rate with 98.4% single-copy BUSCO genes. Conclusions This high-quality reference genome of a zoonotic IIaA17G2R1 C. parvum subtype isolate provides the basis for subsequent comparative genomic studies across the Cryptosporidium clade. This will enable improved understanding of diversity, functional, and association studies.
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Affiliation(s)
- Vipin K Menon
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Pablo C Okhuysen
- Department of Infectious Diseases, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Cynthia L Chappell
- Center for Infectious Diseases, The University of Texas School of Public Health, Houston, TX 77030, USA
| | - Medhat Mahmoud
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Medhat Mahmoud
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Qingchang Meng
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Harsha Doddapaneni
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Vanesa Vee
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yi Han
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sejal Salvi
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sravya Bhamidipati
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kavya Kottapalli
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - George Weissenberger
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hua Shen
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Matthew C Ross
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Kristi L Hoffman
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Sara Javornik Cregeen
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ginger A Metcalf
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Joseph F Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
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9
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Hada M, Miura H, Tanigawa A, Matoba S, Inoue K, Ogonuki N, Hirose M, Watanabe N, Nakato R, Fujiki K, Hasegawa A, Sakashita A, Okae H, Miura K, Shikata D, Arima T, Shirahige K, Hiratani I, Ogura A. Highly rigid H3.1/H3.2-H3K9me3 domains set a barrier for cell fate reprogramming in trophoblast stem cells. Genes Dev 2022; 36:84-102. [PMID: 34992147 PMCID: PMC8763053 DOI: 10.1101/gad.348782.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 12/21/2021] [Indexed: 01/22/2023]
Abstract
Here, Hada et al. comprehensively analyzed epigenomic features of mouse trophoblast stem cells (TSCs). They used genome-wide, high-throughput analyses to show that the TSC genome contains large-scale (>1-Mb) rigid heterochromatin architectures that have a high degree of histone H3.1/3.2–H3K9me3 accumulation, termed TSC-defined highly heterochromatinized domains (THDs), and are uniquely developed in placental lineage cells that serve to protect them from fate reprogramming to stably maintain placental function. The placenta is a highly evolved, specialized organ in mammals. It differs from other organs in that it functions only for fetal maintenance during gestation. Therefore, there must be intrinsic mechanisms that guarantee its unique functions. To address this question, we comprehensively analyzed epigenomic features of mouse trophoblast stem cells (TSCs). Our genome-wide, high-throughput analyses revealed that the TSC genome contains large-scale (>1-Mb) rigid heterochromatin architectures with a high degree of histone H3.1/3.2–H3K9me3 accumulation, which we termed TSC-defined highly heterochromatinized domains (THDs). Importantly, depletion of THDs by knockdown of CAF1, an H3.1/3.2 chaperone, resulted in down-regulation of TSC markers, such as Cdx2 and Elf5, and up-regulation of the pluripotent marker Oct3/4, indicating that THDs maintain the trophoblastic nature of TSCs. Furthermore, our nuclear transfer technique revealed that THDs are highly resistant to genomic reprogramming. However, when H3K9me3 was removed, the TSC genome was fully reprogrammed, giving rise to the first TSC cloned offspring. Interestingly, THD-like domains are also present in mouse and human placental cells in vivo, but not in other cell types. Thus, THDs are genomic architectures uniquely developed in placental lineage cells, which serve to protect them from fate reprogramming to stably maintain placental function.
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Affiliation(s)
- Masashi Hada
- Bioresource Engineering Division, Bioresource Center, RIKEN, Tsukuba, Ibaraki 305-0074, Japan.,Institute of Quantitative Biosciences, The University of Tokyo, Tokyo 113-0032, Japan
| | - Hisashi Miura
- Laboratory for Developmental Epigenetics, RIKEN Center for Developmental Biology, Center for Biosystems Dynamics Research, Kobe 650-0047, Japan
| | - Akie Tanigawa
- Laboratory for Developmental Epigenetics, RIKEN Center for Developmental Biology, Center for Biosystems Dynamics Research, Kobe 650-0047, Japan
| | - Shogo Matoba
- Bioresource Engineering Division, Bioresource Center, RIKEN, Tsukuba, Ibaraki 305-0074, Japan.,Cooperative Division of Veterinary Sciences, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Kimiko Inoue
- Bioresource Engineering Division, Bioresource Center, RIKEN, Tsukuba, Ibaraki 305-0074, Japan.,Graduate school of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
| | - Narumi Ogonuki
- Bioresource Engineering Division, Bioresource Center, RIKEN, Tsukuba, Ibaraki 305-0074, Japan
| | - Michiko Hirose
- Bioresource Engineering Division, Bioresource Center, RIKEN, Tsukuba, Ibaraki 305-0074, Japan
| | - Naomi Watanabe
- Bioresource Engineering Division, Bioresource Center, RIKEN, Tsukuba, Ibaraki 305-0074, Japan
| | - Ryuichiro Nakato
- Institute of Quantitative Biosciences, The University of Tokyo, Tokyo 113-0032, Japan
| | - Katsunori Fujiki
- Institute of Quantitative Biosciences, The University of Tokyo, Tokyo 113-0032, Japan
| | - Ayumi Hasegawa
- Bioresource Engineering Division, Bioresource Center, RIKEN, Tsukuba, Ibaraki 305-0074, Japan
| | - Akihiko Sakashita
- Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Hiroaki Okae
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, Aoba-ku, Sendai 980-8575, Japan
| | - Kento Miura
- Bioresource Engineering Division, Bioresource Center, RIKEN, Tsukuba, Ibaraki 305-0074, Japan.,Department of Disease Model, Research Institute of Radiation Biology and Medicine, Hiroshima University, Hiroshima 734-8553, Japan
| | - Daiki Shikata
- Bioresource Engineering Division, Bioresource Center, RIKEN, Tsukuba, Ibaraki 305-0074, Japan
| | - Takahiro Arima
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, Aoba-ku, Sendai 980-8575, Japan
| | - Katsuhiko Shirahige
- Institute of Quantitative Biosciences, The University of Tokyo, Tokyo 113-0032, Japan
| | - Ichiro Hiratani
- Laboratory for Developmental Epigenetics, RIKEN Center for Developmental Biology, Center for Biosystems Dynamics Research, Kobe 650-0047, Japan.,RIKEN Cluster for Pioneering Research, Hirosawa, Wako, Saitama 351-0198, Japan
| | - Atsuo Ogura
- Bioresource Engineering Division, Bioresource Center, RIKEN, Tsukuba, Ibaraki 305-0074, Japan.,Graduate school of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan.,RIKEN Cluster for Pioneering Research, Hirosawa, Wako, Saitama 351-0198, Japan
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10
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Zhou XJ, Li JT, Wang HL, Han JW, Zhang K, Dong SW, Zhang YZ, Ya HY, Cheng YW, Sun SS. The chromosome-scale genome assembly, annotation and evolution of Rhododendron henanense subsp. lingbaoense. Mol Ecol Resour 2021; 22:988-1001. [PMID: 34652864 DOI: 10.1111/1755-0998.13529] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 10/10/2021] [Accepted: 10/11/2021] [Indexed: 01/21/2023]
Abstract
Rhododendron henanense subsp. lingbaoense (hereafter referred to as R. henanense) is an endemic species naturally distributed in the Henan province, China, with high horticultural, ornamental and medicinal value. Herein, we report a de novo genome assembly for R. henanense using a combination of PacBio long read and Illumina short read sequencing technologies. In total, we assembled 634.07 Mb with a contig N50 of 2.5 Mb, representing ~96.93% of the estimated genome size. By applying Hi-C data, 13 pseudochromosomes of R. henanense genome were assembled, covering ~98.21% of the genome assembly. The genome was composed of ~65.76% repetitive sequences and 31,098 protein-coding genes, 88.77% of which could be functionally annotated. Rhododendron henanense displayed a high level of synteny with other Rhododendron species from the Hymenanthes subgenus. Our data also suggests that R. henanense genes related to stress responses have undergone expansion, which may underly the unique abiotic and biotic stress resistance of the species. This alpine Rhododendron chromosome-scale genome assembly provides fundamental molecular resources for germplasm conservation, breeding efforts, evolutionary studies, and elucidating the unique biological characteristics of R. henanense.
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Affiliation(s)
- Xiao-Jun Zhou
- Life Science College, Luoyang Normal University, Luoyang, China
| | - Jian-Tao Li
- Wuhan Frasergen Bioinformatics Co., Ltd., Wuhan, China
| | - Hai-Liang Wang
- Henan Xiaoqinling National Nature Reserve Management Bureau, Sanmenxia, China
| | - Jun-Wang Han
- Henan Xiaoqinling National Nature Reserve Management Bureau, Sanmenxia, China
| | - Kai Zhang
- Henan Xiaoqinling National Nature Reserve Management Bureau, Sanmenxia, China
| | - Shuai-Wei Dong
- Henan Xiaoqinling National Nature Reserve Management Bureau, Sanmenxia, China
| | - Yan-Zhao Zhang
- Life Science College, Luoyang Normal University, Luoyang, China
| | - Hui-Yuan Ya
- Life Science College, Luoyang Normal University, Luoyang, China
| | - Yan-Wei Cheng
- Life Science College, Luoyang Normal University, Luoyang, China
| | - Shan-Shan Sun
- Life Science College, Luoyang Normal University, Luoyang, China
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11
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DeMaere MZ, Darling AE. qc3C: Reference-free quality control for Hi-C sequencing data. PLoS Comput Biol 2021; 17:e1008839. [PMID: 34634030 PMCID: PMC8530316 DOI: 10.1371/journal.pcbi.1008839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 10/21/2021] [Accepted: 09/16/2021] [Indexed: 11/19/2022] Open
Abstract
Hi-C is a sample preparation method that enables high-throughput sequencing to capture genome-wide spatial interactions between DNA molecules. The technique has been successfully applied to solve challenging problems such as 3D structural analysis of chromatin, scaffolding of large genome assemblies and more recently the accurate resolution of metagenome-assembled genomes (MAGs). Despite continued refinements, however, preparing a Hi-C library remains a complex laboratory protocol. To avoid costly failures and maximise the odds of successful outcomes, diligent quality management is recommended. Current wet-lab methods provide only a crude assay of Hi-C library quality, while key post-sequencing quality indicators used have—thus far—relied upon reference-based read-mapping. When a reference is accessible, this reliance introduces a concern for quality, where an incomplete or inexact reference skews the resulting quality indicators. We propose a new, reference-free approach that infers the total fraction of read-pairs that are a product of proximity ligation. This quantification of Hi-C library quality requires only a modest amount of sequencing data and is independent of other application-specific criteria. The algorithm builds upon the observation that proximity ligation events are likely to create k-mers that would not naturally occur in the sample. Our software tool (qc3C) is to our knowledge the first to implement a reference-free Hi-C QC tool, and also provides reference-based QC, enabling Hi-C to be more easily applied to non-model organisms and environmental samples. We characterise the accuracy of the new algorithm on simulated and real datasets and compare it to reference-based methods. The Hi-C sequencing technique offers the potential for significant scientific insight about the spatial arrangement of DNA, however achieving such outcomes is highly dependent on the quality of the resulting sequencing library. Unlike conventional next-gen sequencing, only a fraction of a given Hi-C library contains this useful spatial information (the signal) with the remainder being effectively noise. As Hi-C remains a challenging laboratory technique, signal strength of resulting libraries can vary greatly. As a quality metric, the quantification a library’s signal content is an essential asset in any quality mitigation strategy. Quality assessment of Hi-C data has until now relied on access to a (ideally refined) reference sequence, by which indirect indicators of quality are determined. Here we describe qc3C, a software tool capable of the direct, reference-free estimation of the signal content of a Hi-C library. In doing so, not only can researchers make informed decisions on how to progress based on library information content, but eliminating the reference also enables Hi-C quality management for non-model organism and metagenomics researchers.
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Affiliation(s)
- Matthew Z. DeMaere
- The iThree Institute, University of Technology Sydney, Ultimo, NSW, Australia
- * E-mail:
| | - Aaron E. Darling
- The iThree Institute, University of Technology Sydney, Ultimo, NSW, Australia
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12
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Freire R, Weisweiler M, Guerreiro R, Baig N, Hüttel B, Obeng-Hinneh E, Renner J, Hartje S, Muders K, Truberg B, Rosen A, Prigge V, Bruckmüller J, Lübeck J, Stich B. Chromosome-scale reference genome assembly of a diploid potato clone derived from an elite variety. G3-GENES GENOMES GENETICS 2021; 11:6371871. [PMID: 34534288 PMCID: PMC8664475 DOI: 10.1093/g3journal/jkab330] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 09/08/2021] [Indexed: 01/27/2023]
Abstract
Potato (Solanum tuberosum L.) is one of the most important crops with a worldwide production of 370 million metric tons. The objectives of this study were (1) to create a high-quality consensus sequence across the two haplotypes of a diploid clone derived from a tetraploid elite variety and assess the sequence divergence from the available potato genome assemblies, as well as among the two haplotypes; (2) to evaluate the new assembly’s usefulness for various genomic methods; and (3) to assess the performance of phasing in diploid and tetraploid clones, using linked-read sequencing technology. We used PacBio long reads coupled with 10x Genomics reads and proximity ligation scaffolding to create the dAg1_v1.0 reference genome sequence. With a final assembly size of 812 Mb, where 750 Mb are anchored to 12 chromosomes, our assembly is larger than other available potato reference sequences and high proportions of properly paired reads were observed for clones unrelated by pedigree to dAg1. Comparisons of the new dAg1_v1.0 sequence to other potato genome sequences point out the high divergence between the different potato varieties and illustrate the potential of using dAg1_v1.0 sequence in breeding applications.
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Affiliation(s)
- Ruth Freire
- Institute for Quantitative Genetics and Genomics of Plants, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Marius Weisweiler
- Institute for Quantitative Genetics and Genomics of Plants, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Ricardo Guerreiro
- Institute for Quantitative Genetics and Genomics of Plants, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Nadia Baig
- Institute for Quantitative Genetics and Genomics of Plants, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Bruno Hüttel
- Max Planck-Genome-centre Cologne, Max Planck Institute for Plant Breeding, Carl-von-Linne-Weg 10, 50829 Köln, Germany
| | - Evelyn Obeng-Hinneh
- Böhm-Nordkartoffel Agrarproduktion GmbH & Co. OHG, Strehlow 19, 17111 Hohenmocker, Germany
| | - Juliane Renner
- Böhm-Nordkartoffel Agrarproduktion GmbH & Co. OHG, Strehlow 19, 17111 Hohenmocker, Germany
| | - Stefanie Hartje
- Böhm-Nordkartoffel Agrarproduktion GmbH & Co. OHG, Strehlow 19, 17111 Hohenmocker, Germany
| | - Katja Muders
- Nordring- Kartoffelzucht- und Vermehrungs- GmbH, Parkweg 4, 18190 Sanitz, Germany
| | - Bernd Truberg
- Nordring- Kartoffelzucht- und Vermehrungs- GmbH, Parkweg 4, 18190 Sanitz, Germany
| | - Arne Rosen
- Nordring- Kartoffelzucht- und Vermehrungs- GmbH, Parkweg 4, 18190 Sanitz, Germany
| | - Vanessa Prigge
- SaKa Pflanzenzucht GmbH & Co. KG, Zuchtstation Windeby, Eichenallee 9, 24340 Windeby, Germany
| | | | - Jens Lübeck
- Solana Research GmbH, Eichenallee 9, 24340 Windeby, Germany
| | - Benjamin Stich
- Institute for Quantitative Genetics and Genomics of Plants, Universitätsstraße 1, 40225 Düsseldorf, Germany.,Cluster of Excellence on Plant Sciences, From Complex Traits towards Synthetic Modules, Universitätsstraße 1, 40225 Düsseldorf, Germany
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13
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Yamaguchi K, Kadota M, Nishimura O, Ohishi Y, Naito Y, Kuraku S. Technical considerations in Hi-C scaffolding and evaluation of chromosome-scale genome assemblies. Mol Ecol 2021; 30:5923-5934. [PMID: 34432923 PMCID: PMC9292758 DOI: 10.1111/mec.16146] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 07/28/2021] [Accepted: 08/18/2021] [Indexed: 12/15/2022]
Abstract
The recent development of ecological studies has been fueled by the introduction of massive information based on chromosome‐scale genome sequences, even for species for which genetic linkage is not accessible. This was enabled mainly by the application of Hi‐C, a method for genome‐wide chromosome conformation capture that was originally developed for investigating the long‐range interaction of chromatins. Performing genomic scaffolding using Hi‐C data is highly resource‐demanding and employs elaborate laboratory steps for sample preparation. It starts with building a primary genome sequence assembly as an input, which is followed by computation for genome scaffolding using Hi‐C data, requiring careful validation. This article presents technical considerations for obtaining optimal Hi‐C scaffolding results and provides a test case of its application to a reptile species, the Madagascar ground gecko (Paroedura picta). Among the metrics that are frequently used for evaluating scaffolding results, we investigate the validity of the completeness assessment of chromosome‐scale genome assemblies using single‐copy reference orthologues.
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Affiliation(s)
- Kazuaki Yamaguchi
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Mitsutaka Kadota
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Osamu Nishimura
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Yuta Ohishi
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Yuki Naito
- Database Center for Life Science (DBCLS), Mishima, Japan
| | - Shigehiro Kuraku
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan.,Molecular Life History Laboratory, National Institute of Genetics, Mishima, Japan.,Department of Genetics, Sokendai (Graduate University for Advanced Studies), Mishima, Japan
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14
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Hajirnis N, Mishra RK. Homeotic Genes: Clustering, Modularity, and Diversity. Front Cell Dev Biol 2021; 9:718308. [PMID: 34458272 PMCID: PMC8386295 DOI: 10.3389/fcell.2021.718308] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 07/22/2021] [Indexed: 11/13/2022] Open
Abstract
Hox genes code for transcription factors and are evolutionarily conserved. They regulate a plethora of downstream targets to define the anterior-posterior (AP) body axis of a developing bilaterian embryo. Early work suggested a possible role of clustering and ordering of Hox to regulate their expression in a spatially restricted manner along the AP axis. However, the recent availability of many genome assemblies for different organisms uncovered several examples that defy this constraint. With recent advancements in genomics, the current review discusses the arrangement of Hox in various organisms. Further, we revisit their discovery and regulation in Drosophila melanogaster. We also review their regulation in different arthropods and vertebrates, with a significant focus on Hox expression in the crustacean Parahyale hawaiensis. It is noteworthy that subtle changes in the levels of Hox gene expression can contribute to the development of novel features in an organism. We, therefore, delve into the distinct regulation of these genes during primary axis formation, segment identity, and extra-embryonic roles such as in the formation of hair follicles or misregulation leading to cancer. Toward the end of each section, we emphasize the possibilities of several experiments involving various organisms, owing to the advancements in the field of genomics and CRISPR-based genome engineering. Overall, we present a holistic view of the functioning of Hox in the animal world.
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Affiliation(s)
- Nikhil Hajirnis
- CSIR – Centre for Cellular and Molecular Biology (CCMB), Hyderabad, India
| | - Rakesh K. Mishra
- CSIR – Centre for Cellular and Molecular Biology (CCMB), Hyderabad, India
- AcSIR – Academy of Scientific and Innovative Research, Ghaziabad, India
- Tata Institute for Genetics and Society (TIGS), Bangalore, India
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15
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Ma L, Dong C, Song C, Wang X, Zheng X, Niu Y, Chen S, Feng W. De novo genome assembly of the potent medicinal plant Rehmannia glutinosa using nanopore technology. Comput Struct Biotechnol J 2021; 19:3954-3963. [PMID: 34377362 PMCID: PMC8318827 DOI: 10.1016/j.csbj.2021.07.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 06/30/2021] [Accepted: 07/06/2021] [Indexed: 01/16/2023] Open
Abstract
Rehmannia glutinosa is a potent medicinal plant with a significant importance in traditional Chinese medicine. Its root is enriched with various bioactive molecules mainly iridoids, possessing important pharmaceutical properties. However, the molecular biology and evolution of R. glutinosa have been largely unexplored. Here, we report a reference genome of R. glutinosa using Nanopore technology, Illumina and Hi-C sequencing. The assembly genome is 2.49 Gb long with a scaffold N50 length of 70 Mb and high heterozygosity (2%). Since R. glutinosa is an autotetraploid (4n = 56), the difference between each set of chromosomes is very small, and it is difficult to distinguish the two sets of chromosomes using Hi-C. Hence, only one set of the genome size was mounted to the chromosome level. Scaffolds covering 52.61% of the assembled genome were anchored on 14 pseudochromosomes. Over 67% of the genome consists of repetitive sequences dominated by Copia long terminal repeats and 48,475 protein-coding genes were predicted. Phylogenetic analysis corroborates the placement of R. glutinosa in the Orobanchaceae family. Our results indicated an independent and very recent whole genome duplication event that occurred 3.64 million year ago in the R. glutinosa lineage. Comparative genomics analysis demonstrated expansion of the UDP-dependent glycosyltransferases and terpene synthase gene families, known to be involved in terpenoid biosynthesis and diversification. Furthermore, the molecular biosynthetic pathway of iridoids has been clarified in this work. Collectively, the generated reference genome of R. glutinosa will facilitate discovery and development of important pharmacological compounds.
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Affiliation(s)
- Ligang Ma
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou 450046, China
- Co-construction Collaborative Innovation Center for Chinese Medicine and Respiratory Diseases by Henan & Education Ministry of P.R. China, Zhengzhou 450046, China
| | - Chengming Dong
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou 450046, China
- Co-construction Collaborative Innovation Center for Chinese Medicine and Respiratory Diseases by Henan & Education Ministry of P.R. China, Zhengzhou 450046, China
| | - Chi Song
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Xiaolan Wang
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou 450046, China
- Co-construction Collaborative Innovation Center for Chinese Medicine and Respiratory Diseases by Henan & Education Ministry of P.R. China, Zhengzhou 450046, China
| | - Xiaoke Zheng
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou 450046, China
- Co-construction Collaborative Innovation Center for Chinese Medicine and Respiratory Diseases by Henan & Education Ministry of P.R. China, Zhengzhou 450046, China
| | - Yan Niu
- Wuhan Benagen Tech Solutions Company Limited, Wuhan 430070, China
| | - Shilin Chen
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Weisheng Feng
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou 450046, China
- Co-construction Collaborative Innovation Center for Chinese Medicine and Respiratory Diseases by Henan & Education Ministry of P.R. China, Zhengzhou 450046, China
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16
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Jayakumar V, Nishimura O, Kadota M, Hirose N, Sano H, Murakawa Y, Yamamoto Y, Nakaya M, Tsukiyama T, Seita Y, Nakamura S, Kawai J, Sasaki E, Ema M, Kuraku S, Kawaji H, Sakakibara Y. Chromosomal-scale de novo genome assemblies of Cynomolgus Macaque and Common Marmoset. Sci Data 2021; 8:159. [PMID: 34183680 PMCID: PMC8239027 DOI: 10.1038/s41597-021-00935-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 04/29/2021] [Indexed: 01/18/2023] Open
Abstract
Cynomolgus macaque (Macaca fascicularis) and common marmoset (Callithrix jacchus) have been widely used in human biomedical research. Long-standing primate genome assemblies used the human genome as a reference for ordering and orienting the assembled fragments into chromosomes. Here we performed de novo genome assembly of these two species without any human genome-based bias observed in the genome assemblies released earlier. We assembled PacBio long reads, and the resultant contigs were scaffolded with Hi-C data, which were further refined based on Hi-C contact maps and alternate de novo assemblies. The assemblies achieved scaffold N50 lengths of 149 Mb and 137 Mb for cynomolgus macaque and common marmoset, respectively. The high fidelity of our assembly is also ascertained by BAC-end concordance in common marmoset. Our assembly of cynomolgus macaque outperformed all the available assemblies of this species in terms of contiguity. The chromosome-scale genome assemblies produced in this study are valuable resources for non-human primate models and provide an important baseline in human biomedical research.
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Affiliation(s)
- Vasanthan Jayakumar
- Department of Biosciences and Informatics, Keio University, Yokohama, Kanagawa, 223-8522, Japan
| | - Osamu Nishimura
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Minatojimaminami-machi 2-2-3, Kobe, Hyogo, 650-0047, Japan
| | - Mitsutaka Kadota
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Minatojimaminami-machi 2-2-3, Kobe, Hyogo, 650-0047, Japan
| | - Naoki Hirose
- RIKEN Center for Integrative Medical Science Preventive Medicine and Applied Genomics Unit, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
- Research Center for Genome & Medical Sciences, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, 156-8506, Japan
- Institute for the Advanced Study of Human Biology, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Hiromi Sano
- RIKEN Center for Integrative Medical Science Preventive Medicine and Applied Genomics Unit, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
- RIKEN Center for Integrative Medical Sciences RIKEN-IFOM Joint Laboratory for Cancer Genomics, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Yasuhiro Murakawa
- RIKEN Center for Integrative Medical Sciences RIKEN-IFOM Joint Laboratory for Cancer Genomics, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
- RIKEN Preventive Medicine and Diagnosis Innovation Program, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
- Institute for the Advanced Study of Human Biology, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
- Department of Medical Systems Genomics, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
- IFOM-the FIRC Institute of Molecular Oncology, Milan, Italy
| | - Yumiko Yamamoto
- RIKEN Center for Integrative Medical Sciences Laboratory for Comprehensive Genomic Analysis, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Masataka Nakaya
- Department of Stem Cells and Human Disease Models, Research Center for Animal Life Science, Shiga University of Medical Science, Shiga, 520-2192, Japan
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, 606-8501, Japan
| | - Tomoyuki Tsukiyama
- Department of Stem Cells and Human Disease Models, Research Center for Animal Life Science, Shiga University of Medical Science, Shiga, 520-2192, Japan
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, 606-8501, Japan
| | - Yasunari Seita
- Department of Stem Cells and Human Disease Models, Research Center for Animal Life Science, Shiga University of Medical Science, Shiga, 520-2192, Japan
| | - Shinichiro Nakamura
- Department of Stem Cells and Human Disease Models, Research Center for Animal Life Science, Shiga University of Medical Science, Shiga, 520-2192, Japan
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, 606-8501, Japan
| | - Jun Kawai
- RIKEN Preventive Medicine and Diagnosis Innovation Program, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Erika Sasaki
- Central Institute for Experimental Animals, Department of Marmoset Biology and Medicine, Central Institute for Experimental Animals, 3-25-12, Tonomachi, Kawasaki-ku, Kawasaki, 210-0821, Japan
| | - Masatsugu Ema
- Department of Stem Cells and Human Disease Models, Research Center for Animal Life Science, Shiga University of Medical Science, Shiga, 520-2192, Japan
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, 606-8501, Japan
| | - Shigehiro Kuraku
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Minatojimaminami-machi 2-2-3, Kobe, Hyogo, 650-0047, Japan
| | - Hideya Kawaji
- RIKEN Center for Integrative Medical Science Preventive Medicine and Applied Genomics Unit, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.
- Research Center for Genome & Medical Sciences, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, 156-8506, Japan.
- RIKEN Preventive Medicine and Diagnosis Innovation Program, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.
| | - Yasubumi Sakakibara
- Department of Biosciences and Informatics, Keio University, Yokohama, Kanagawa, 223-8522, Japan.
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17
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18
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Regulation of mammalian 3D genome organization and histone H3K9 dimethylation by H3K9 methyltransferases. Commun Biol 2021; 4:571. [PMID: 33986449 PMCID: PMC8119675 DOI: 10.1038/s42003-021-02089-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 04/08/2021] [Indexed: 01/15/2023] Open
Abstract
Histone H3 lysine 9 dimethylation (H3K9me2) is a highly conserved silencing epigenetic mark. Chromatin marked with H3K9me2 forms large domains in mammalian cells and overlaps well with lamina-associated domains and the B compartment defined by Hi-C. However, the role of H3K9me2 in 3-dimensional (3D) genome organization remains unclear. Here, we investigated genome-wide H3K9me2 distribution, transcriptome, and 3D genome organization in mouse embryonic stem cells following the inhibition or depletion of H3K9 methyltransferases (MTases): G9a, GLP, SETDB1, SUV39H1, and SUV39H2. We show that H3K9me2 is regulated by all five MTases; however, H3K9me2 and transcription in the A and B compartments are regulated by different MTases. H3K9me2 in the A compartments is primarily regulated by G9a/GLP and SETDB1, while H3K9me2 in the B compartments is regulated by all five MTases. Furthermore, decreased H3K9me2 correlates with changes to more active compartmental state that accompanied transcriptional activation. Thus, H3K9me2 contributes to inactive compartment setting.
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19
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Linard B, Ebersberger I, McGlynn SE, Glover N, Mochizuki T, Patricio M, Lecompte O, Nevers Y, Thomas PD, Gabaldón T, Sonnhammer E, Dessimoz C, Uchiyama I. Ten Years of Collaborative Progress in the Quest for Orthologs. Mol Biol Evol 2021; 38:3033-3045. [PMID: 33822172 PMCID: PMC8321534 DOI: 10.1093/molbev/msab098] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 02/07/2021] [Accepted: 04/01/2021] [Indexed: 12/19/2022] Open
Abstract
Accurate determination of the evolutionary relationships between genes is a foundational challenge in biology. Homology-evolutionary relatedness-is in many cases readily determined based on sequence similarity analysis. By contrast, whether or not two genes directly descended from a common ancestor by a speciation event (orthologs) or duplication event (paralogs) is more challenging, yet provides critical information on the history of a gene. Since 2009, this task has been the focus of the Quest for Orthologs (QFO) Consortium. The sixth QFO meeting took place in Okazaki, Japan in conjunction with the 67th National Institute for Basic Biology conference. Here, we report recent advances, applications, and oncoming challenges that were discussed during the conference. Steady progress has been made toward standardization and scalability of new and existing tools. A feature of the conference was the presentation of a panel of accessible tools for phylogenetic profiling and several developments to bring orthology beyond the gene unit-from domains to networks. This meeting brought into light several challenges to come: leveraging orthology computations to get the most of the incoming avalanche of genomic data, integrating orthology from domain to biological network levels, building better gene models, and adapting orthology approaches to the broad evolutionary and genomic diversity recognized in different forms of life and viruses.
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Affiliation(s)
- Benjamin Linard
- LIRMM, University of Montpellier, CNRS, Montpellier, France.,SPYGEN, Le Bourget-du-Lac, France
| | - Ingo Ebersberger
- Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt, Germany.,Senckenberg Biodiversity and Climate Research Centre (S-BIKF), Frankfurt, Germany.,LOEWE Center for Translational Biodiversity Genomics (TBG), Frankfurt, Germany
| | - Shawn E McGlynn
- Earth-Life Science Institute, Tokyo Institute of Technology, Meguro, Tokyo, Japan.,Blue Marble Space Institute of Science, Seattle, WA, USA
| | - Natasha Glover
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.,Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Tomohiro Mochizuki
- Earth-Life Science Institute, Tokyo Institute of Technology, Meguro, Tokyo, Japan
| | - Mateus Patricio
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Odile Lecompte
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Fédération de Médecine Translationnelle de Strasbourg, Strasbourg, France
| | - Yannis Nevers
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.,Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Paul D Thomas
- Division of Bioinformatics, Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
| | - Toni Gabaldón
- Barcelona Supercomputing Centre (BCS-CNS), Jordi Girona, Barcelona, Spain.,Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Erik Sonnhammer
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Christophe Dessimoz
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.,Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.,Department of Computer Science, University College London, London, United Kingdom.,Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Ikuo Uchiyama
- Department of Theoretical Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Aichi, Japan
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20
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Zheng J, Meinhardt LW, Goenaga R, Zhang D, Yin Y. The chromosome-level genome of dragon fruit reveals whole-genome duplication and chromosomal co-localization of betacyanin biosynthetic genes. HORTICULTURE RESEARCH 2021; 8:63. [PMID: 33750805 PMCID: PMC7943767 DOI: 10.1038/s41438-021-00501-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 01/19/2021] [Accepted: 01/20/2021] [Indexed: 05/05/2023]
Abstract
Dragon fruits are tropical fruits economically important for agricultural industries. As members of the family of Cactaceae, they have evolved to adapt to the arid environment. Here we report the draft genome of Hylocereus undatus, commercially known as the white-fleshed dragon fruit. The chromosomal level genome assembly contains 11 longest scaffolds corresponding to the 11 chromosomes of H. undatus. Genome annotation of H. undatus found ~29,000 protein-coding genes, similar to Carnegiea gigantea (saguaro). Whole-genome duplication (WGD) analysis revealed a WGD event in the last common ancestor of Cactaceae followed by extensive genome rearrangements. The divergence time between H. undatus and C. gigantea was estimated to be 9.18 MYA. Functional enrichment analysis of orthologous gene clusters (OGCs) in six Cactaceae plants found significantly enriched OGCs in drought resistance. Fruit flavor-related functions were overrepresented in OGCs that are significantly expanded in H. undatus. The H. undatus draft genome also enabled the discovery of carbohydrate and plant cell wall-related functional enrichment in dragon fruits treated with trypsin for a longer storage time. Lastly, genes of the betacyanin (a red-violet pigment and antioxidant with a very high concentration in dragon fruits) biosynthetic pathway were found to be co-localized on a 12 Mb region of one chromosome. The consequence may be a higher efficiency of betacyanin biosynthesis, which will need experimental validation in the future. The H. undatus draft genome will be a great resource to study various cactus plants.
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Affiliation(s)
- Jinfang Zheng
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska, Lincoln, NE, 68588, USA
| | | | - Ricardo Goenaga
- Tropical Agriculture Research Station, USDA-ARS, Puerto Rico, PR, USA
| | - Dapeng Zhang
- Sustainable Perennial Crops Lab, USDA-ARS, Beltsville, MD, USA.
| | - Yanbin Yin
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska, Lincoln, NE, 68588, USA.
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21
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Abstract
Generation of mature red blood cells, consisting mainly of hemoglobin, is a remarkable example of coordinated action of various signaling networks. Chromatin condensation is an essential step for terminal erythroid differentiation and subsequent nuclear expulsion in mammals. Here, we profiled 3D genome organization in the blood cells from ten species belonging to different vertebrate classes. Our analysis of contact maps revealed a striking absence of such 3D interaction patterns as loops or TADs in blood cells of all analyzed representatives. We also detect large-scale chromatin rearrangements in blood cells from mammals, birds, reptiles and amphibians: their contact maps display strong second diagonal pattern, representing an increased frequency of long-range contacts, unrelated to TADs or compartments. This pattern is completely atypical for interphase chromosome structure. We confirm that these principles of genome organization are conservative in vertebrate erythroid cells.
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22
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Abstract
The recent Coronavirus Disease 2019 pandemic has once again reminded us the importance of understanding infectious diseases. One important but understudied area in infectious disease research is the role of nuclear architecture or the physical arrangement of the genome in the nucleus in controlling gene regulation and pathogenicity. Recent advances in research methods, such as Genome-wide chromosome conformation capture using high-throughput sequencing (Hi-C), have allowed for easier analysis of nuclear architecture and chromosomal reorganization in both the infectious disease agents themselves as well as in their host cells. This review will discuss broadly on what is known about nuclear architecture in infectious disease, with an emphasis on chromosomal reorganization, and briefly discuss what steps are required next in the field. In this review, we examine the current state of nuclear architecture in infectious diseases with an emphasis on chromosomal reorganization. Nuclear architecture plays an important role in regulation of transcription for several pathogens, as well as inflammatory responses in their host. Recent advances in technologies such as Hi-C have allowed in-depth studies of chromosomal reorganization during infectious disease development and provided insights into transcription mechanisms and pathogenicity. In addition, it has been demonstrated that pathogens can also affect/utilize the hosts nuclear architecture. These areas are heavily understudied in pathogens, and we hope this review will provide a comprehensive review on the current state of nuclear architecture in infectious diseases and provide an additional avenue for eradication efforts.
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23
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Uno Y, Nozu R, Kiyatake I, Higashiguchi N, Sodeyama S, Murakumo K, Sato K, Kuraku S. Cell culture-based karyotyping of orectolobiform sharks for chromosome-scale genome analysis. Commun Biol 2020; 3:652. [PMID: 33159152 PMCID: PMC7648076 DOI: 10.1038/s42003-020-01373-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 10/12/2020] [Indexed: 11/09/2022] Open
Abstract
Karyotyping, traditionally performed using cytogenetic techniques, is indispensable for validating genome assemblies whose sequence lengths can be scaled up to chromosome sizes using modern methods. Karyotype reports of chondrichthyans are scarce because of the difficulty in cell culture. Here, we focused on carpet shark species and the culture conditions for fibroblasts and lymphocytes. The utility of the cultured cells enabled the high-fidelity characterization of their karyotypes, namely 2n = 102 for the whale shark (Rhincodon typus) and zebra shark (Stegostoma fasciatum), and 2n = 106 for the brownbanded bamboo shark (Chiloscyllium punctatum) and whitespotted bamboo shark (C. plagiosum). We identified heteromorphic XX/XY sex chromosomes for the two latter species and demonstrated the first-ever fluorescence in situ hybridization of shark chromosomes prepared from cultured cells. Our protocols are applicable to diverse chondrichthyan species and will deepen the understanding of early vertebrate evolution at the molecular level.
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Affiliation(s)
- Yoshinobu Uno
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan. .,Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan.
| | - Ryo Nozu
- Okinawa Churashima Research Center, Okinawa Churashima Foundation, Okinawa, Japan.,Okinawa Churaumi Aquarium, Okinawa, Japan
| | | | | | | | | | - Keiichi Sato
- Okinawa Churashima Research Center, Okinawa Churashima Foundation, Okinawa, Japan.,Okinawa Churaumi Aquarium, Okinawa, Japan
| | - Shigehiro Kuraku
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan
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Kadota M, Nishimura O, Miura H, Tanaka K, Hiratani I, Kuraku S. Multifaceted Hi-C benchmarking: what makes a difference in chromosome-scale genome scaffolding? Gigascience 2020; 9:5695848. [PMID: 31919520 PMCID: PMC6952475 DOI: 10.1093/gigascience/giz158] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 10/23/2019] [Accepted: 12/02/2019] [Indexed: 12/28/2022] Open
Abstract
Background Hi-C is derived from chromosome conformation capture (3C) and targets chromatin contacts on a genomic scale. This method has also been used frequently in scaffolding nucleotide sequences obtained by de novo genome sequencing and assembly, in which the number of resultant sequences rarely converges to the chromosome number. Despite its prevalent use, the sample preparation methods for Hi-C have not been intensively discussed, especially from the standpoint of genome scaffolding. Results To gain insight into the best practice of Hi-C scaffolding, we performed a multifaceted methodological comparison using vertebrate samples and optimized various factors during sample preparation, sequencing, and computation. As a result, we identified several key factors that helped improve Hi-C scaffolding, including the choice and preparation of tissues, library preparation conditions, the choice of restriction enzyme(s), and the choice of scaffolding program and its usage. Conclusions This study provides the first comparison of multiple sample preparation kits/protocols and computational programs for Hi-C scaffolding by an academic third party. We introduce a customized protocol designated “inexpensive and controllable Hi-C (iconHi-C) protocol,” which incorporates the optimal conditions identified in this study, and demonstrate this technique on chromosome-scale genome sequences of the Chinese softshell turtle Pelodiscus sinensis.
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Affiliation(s)
- Mitsutaka Kadota
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe 650-0047, Japan
| | - Osamu Nishimura
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe 650-0047, Japan
| | - Hisashi Miura
- Laboratory for Developmental Epigenetics, RIKEN BDR, Kobe 650-0047, Japan
| | - Kaori Tanaka
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe 650-0047, Japan
| | - Ichiro Hiratani
- Laboratory for Developmental Epigenetics, RIKEN BDR, Kobe 650-0047, Japan
| | - Shigehiro Kuraku
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe 650-0047, Japan
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Early vertebrate origin of CTCFL, a CTCF paralog, revealed by proximity-guided shark genome scaffolding. Sci Rep 2020; 10:14629. [PMID: 32884037 PMCID: PMC7471279 DOI: 10.1038/s41598-020-71602-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 08/17/2020] [Indexed: 11/08/2022] Open
Abstract
The nuclear protein CCCTC-binding factor (CTCF) contributes as an insulator to chromatin organization in diverse animals. The gene encoding this protein has a paralog which was first identified to be expressed exclusively in the testis in mammals and designated as CTCFL (also called BORIS). CTCFL orthologs were reported only among amniotes, and thus CTCFL was once thought to have arisen in the amniote lineage. In this study, we identified elasmobranch CTCFL orthologs, and investigated its origin with the aid of a shark genome assembly improved by proximity-guided scaffolding. Our analysis employing evolutionary interpretation of syntenic gene location suggested an earlier timing of the gene duplication between CTCF and CTCFL than previously thought, that is, around the common ancestor of extant vertebrates. Also, our transcriptomic sequencing revealed a biased expression of the catshark CTCFL in the testis, suggesting the origin of the tissue-specific localization in mammals more than 400 million years ago. To understand the historical process of the functional consolidation of the long-standing chromatin regulator CTCF, its additional paralogs remaining in some of the descendant lineages for spatially restricted transcript distribution should be taken into consideration.
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26
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Hojsgaard D. Apomixis Technology: Separating the Wheat from the Chaff. Genes (Basel) 2020; 11:E411. [PMID: 32290084 PMCID: PMC7231277 DOI: 10.3390/genes11040411] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 04/03/2020] [Accepted: 04/08/2020] [Indexed: 02/06/2023] Open
Abstract
Projections indicate that current plant breeding approaches will be unable to incorporate the global crop yields needed to deliver global food security. Apomixis is a disruptive innovation by which a plant produces clonal seeds capturing heterosis and gene combinations of elite phenotypes. Introducing apomixis into hybrid cultivars is a game-changing development in the current plant breeding paradigm that will accelerate the generation of high-yield cultivars. However, apomixis is a developmentally complex and genetically multifaceted trait. The central problem behind current constraints to apomixis breeding is that the genomic configuration and molecular mechanism that initiate apomixis and guide the formation of a clonal seed are still unknown. Today, not a single explanation about the origin of apomixis offer full empirical coverage, and synthesizing apomixis by manipulating individual genes has failed or produced little success. Overall evidence suggests apomixis arise from a still unknown single event molecular mechanism with multigenic effects. Disentangling the genomic basis and complex genetics behind the emergence of apomixis in plants will require the use of novel experimental approaches benefiting from Next Generation Sequencing technologies and targeting not only reproductive genes, but also the epigenetic and genomic configurations associated with reproductive phenotypes in homoploid sexual and apomictic carriers. A comprehensive picture of most regulatory changes guiding apomixis emergence will be central for successfully installing apomixis into the target species by exploiting genetic modification techniques.
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Affiliation(s)
- Diego Hojsgaard
- Department of Systematics, Biodiversity and Evolution of Plants, Albrecht-von-Haller Institute for Plant Sciences, Georg-August-University of Göttingen, Untere Karspüle 2, D-37073-1 Göttingen, Germany
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