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Ichida H, Murata H, Hatakeyama S, Yamada A, Ohta A. Near-complete de novo assembly of Tricholoma bakamatsutake chromosomes revealed the structural divergence and differentiation of Tricholoma genomes. G3 (Bethesda) 2023; 13:jkad198. [PMID: 37659058 PMCID: PMC10627285 DOI: 10.1093/g3journal/jkad198] [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] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 08/08/2023] [Accepted: 08/14/2023] [Indexed: 09/05/2023]
Abstract
Tricholoma bakamatsutake, which is an edible ectomycorrhizal fungus associated with Fagaceae trees, may have diverged before the other species in Tricholoma section Caligata. We generated a highly contiguous whole-genome sequence for T. bakamatsutake SF-Tf05 isolated in an Oak (Quercus salicina) forest in Japan. The assembly of high-fidelity long reads, with a median read length of 12.3 kb, resulted in 13 chromosome-sized contigs comprising 142,068,211 bases with an average guanine and cytosine (GC) content of 43.94%. The 13 chromosomes were predicted to encode 11,060 genes. A contig (122,566 bases) presumably containing the whole circular mitochondrial genome was also recovered. The chromosome-wide comparison of T. bakamatsutake and Tricholoma matsutake (TMA_r1.0) indicated that the basic number of chromosomes (13) was conserved, but the structures of the corresponding chromosomes diverged, with multiple inversions and translocations. Gene conservation and cluster analyses revealed at least 3 phylogenetic clades in Tricholoma section Caligata. Specifically, all T. bakamatsutake strains belonged to the "bakamatsutake" clade, which is most proximal to the "caligatum" clade consisting of Tricholoma caligatum and Tricholoma fulvocastaneum. The constructed highly contiguous nearly telomere-to-telomere genome sequence of a T. bakamatsutake isolate will serve as a fundamental resource for future research on the evolution and differentiation of Tricholoma species.
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Affiliation(s)
- Hiroyuki Ichida
- Ion Beam Breeding Group, RIKEN Nishina Center for Accelerator-Based Science, Wako, Saitama 351-0198, Japan
| | - Hitoshi Murata
- Forestry and Forest Products Research Institute (FFPRI), Forest Research and Management Organization, Tsukuba, Ibaraki 305-8687, Japan
| | - Shin Hatakeyama
- Department of Regulatory Biology, Faculty of Science, Saitama University, Saitama, Saitama 338-8570, Japan
| | - Akiyoshi Yamada
- Faculty of Agriculture, Shinshu University, Minami-minowa, Nagano 399-4598, Japan
| | - Akira Ohta
- Kansai Research Center, FFPRI, Kyoto, Kyoto 612-0855, Japan
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Miura O, Toyoda A, Sakurai T. Chromosome-Scale Genome Assembly of the Freshwater Snail Semisulcospira habei from the Lake Biwa Drainage System. Genome Biol Evol 2023; 15:evad208. [PMID: 38014863 PMCID: PMC10683039 DOI: 10.1093/gbe/evad208] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/09/2023] [Indexed: 11/29/2023] Open
Abstract
Semisulcospira habei is a freshwater snail species endemic to the Lake Biwa drainage and belongs to a species group radiated within the lake system. We report the chromosome-scale genome assembly of S. habei, including eight megascaffolds larger than 150 Mb. The genome assembly size is about 2.0 Gb with an N50 of 237 Mb. There are 41,547 protein-coding genes modeled by ab initio gene prediction based on the transcriptome data set, and the BUSCO completeness of the annotated genes was 92.2%. The repeat elements comprise approximately 76% of the genome assembly. The Hi-C contact map showed seven well-resolved scaffolds that correspond to the basic haploid chromosome number of S. habei inferred from the preceding karyotypic study, while it also exhibited one scaffold with a complicated mosaic pattern that is likely to represent the complex of multiple supernumerary chromosomes. The genome assembly reported here represents a high-quality genome resource in disentangling the genomic background of the adaptive radiation of Semisulcospira and also facilitates evolutionary studies in the superfamily Cerithioidea.
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Affiliation(s)
- Osamu Miura
- Faculty of Agriculture and Marine Science, Kochi University, Nankoku, Kochi, Japan
| | - Atsushi Toyoda
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Tetsuya Sakurai
- Faculty of Agriculture and Marine Science, Kochi University, Nankoku, Kochi, Japan
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Herrera M, Ravasi T, Laudet V. Anemonefishes: A model system for evolutionary genomics. F1000Res 2023; 12:204. [PMID: 37928172 PMCID: PMC10624958 DOI: 10.12688/f1000research.130752.2] [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] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/20/2023] [Indexed: 11/07/2023] Open
Abstract
Anemonefishes are an iconic group of coral reef fish particularly known for their mutualistic relationship with sea anemones. This mutualism is especially intriguing as it likely prompted the rapid diversification of anemonefish. Understanding the genomic architecture underlying this process has indeed become one of the holy grails of evolutionary research in these fishes. Recently, anemonefishes have also been used as a model system to study the molecular basis of highly complex traits such as color patterning, social sex change, larval dispersal and life span. Extensive genomic resources including several high-quality reference genomes, a linkage map, and various genetic tools have indeed enabled the identification of genomic features controlling some of these fascinating attributes, but also provided insights into the molecular mechanisms underlying adaptive responses to changing environments. Here, we review the latest findings and new avenues of research that have led to this group of fish being regarded as a model for evolutionary genomics.
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Affiliation(s)
- Marcela Herrera
- Marine Eco-Evo-Devo Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa, 904-0495, Japan
| | - Timothy Ravasi
- Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa, 904-0495, Japan
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, 4811, Australia
| | - Vincent Laudet
- Marine Eco-Evo-Devo Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa, 904-0495, Japan
- Marine Research Station, Institute of Cellular and Organismic Biology (ICOB), Academia Sinica, 23-10, Dah-Uen Rd, Jiau Shi I-Lan 262, Taiwan
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Moore B, Herrera M, Gairin E, Li C, Miura S, Jolly J, Mercader M, Izumiyama M, Kawai E, Ravasi T, Laudet V, Ryu T. The chromosome-scale genome assembly of the yellowtail clownfish Amphiprion clarkii provides insights into the melanic pigmentation of anemonefish. G3 (Bethesda) 2023; 13:6982751. [PMID: 36626199 PMCID: PMC9997566 DOI: 10.1093/g3journal/jkad002] [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: 08/25/2022] [Revised: 11/25/2022] [Accepted: 12/12/2022] [Indexed: 01/11/2023]
Abstract
Anemonefish are an emerging group of model organisms for studying genetic, ecological, evolutionary, and developmental traits of coral reef fish. The yellowtail clownfish Amphiprion clarkii possesses species-specific characteristics such as inter-species co-habitation, high intra-species color variation, no anemone specificity, and a broad geographic distribution, that can increase our understanding of anemonefish evolutionary history, behavioral strategies, fish-anemone symbiosis, and color pattern evolution. Despite its position as an emerging model species, the genome of A. clarkii is yet to be published. Using PacBio long-read sequencing and Hi-C chromatin capture technology, we generated a high-quality chromosome-scale genome assembly initially comprised of 1,840 contigs with an N50 of 1,203,211 bp. These contigs were successfully anchored into 24 chromosomes of 843,582,782 bp and annotated with 25,050 protein-coding genes encompassing 97.0% of conserved actinopterygian genes, making the quality and completeness of this genome the highest among all published anemonefish genomes to date. Transcriptomic analysis identified tissue-specific gene expression patterns, with the brain and optic lobe having the largest number of expressed genes. Further analyses revealed higher copy numbers of erbb3b (a gene involved in melanocyte development) in A. clarkii compared with other anemonefish, thus suggesting a possible link between erbb3b and the natural melanism polymorphism observed in A. clarkii. The publication of this high-quality genome, along with A. clarkii's many unique traits, position this species as an ideal model organism for addressing scientific questions across a range of disciplines.
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Affiliation(s)
- Billy Moore
- Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Marcela Herrera
- Marine Eco-Evo-Devo Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Emma Gairin
- Marine Eco-Evo-Devo Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Chengze Li
- Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Saori Miura
- Marine Eco-Evo-Devo Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Jeffrey Jolly
- Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Manon Mercader
- Marine Eco-Evo-Devo Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Michael Izumiyama
- Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Erina Kawai
- Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Timothy Ravasi
- Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan.,Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811, Australia
| | - Vincent Laudet
- Marine Eco-Evo-Devo Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan.,Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, I-Lan 262, Taiwan
| | - Taewoo Ryu
- Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
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Eleftheriou E, Aury JM, Vacherie B, Istace B, Belser C, Noel B, Moret Y, Rigaud T, Berro F, Gasparian S, Labadie-Bretheau K, Lefebvre T, Madoui MA. Chromosome-scale assembly of the yellow mealworm genome. Open Res Eur 2022; 1:94. [PMID: 37645128 PMCID: PMC10445852 DOI: 10.12688/openreseurope.13987.2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 08/30/2022] [Indexed: 03/12/2024]
Abstract
Background: The yellow mealworm beetle, Tenebrio molitor, is a promising alternative protein source for animal and human nutrition and its farming involves relatively low environmental costs. For these reasons, its industrial scale production started this century. However, to optimize and breed sustainable new T. molitor lines, the access to its genome remains essential. Methods: By combining Oxford Nanopore and Illumina Hi-C data, we constructed a high-quality chromosome-scale assembly of T. molitor. Then, we combined RNA-seq data and available coleoptera proteomes for gene prediction with GMOVE. Results: We produced a high-quality genome with a N50 = 21.9Mb with a completeness of 99.5% and predicted 21,435 genes with a median size of 1,780 bp. Gene orthology between T. molitor and Tribolium castaneum showed a highly conserved synteny between the two coleoptera and paralogs search revealed an expansion of histones in the T. molitor genome. Conclusions: The present genome will greatly help fundamental and applied research such as genetic breeding and will contribute to the sustainable production of the yellow mealworm.
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Affiliation(s)
- Evangelia Eleftheriou
- Génomique Métabolique, Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Univ Evry, Université Paris-Saclay, Université Paris-Saclay, Evry, 91057, France
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Univ Evry, Université Paris-Saclay, Université Paris-Saclay, Evry, 91057, France
| | - Benoît Vacherie
- Genoscope, Institut de biologie François Jacob, CEA, Université Paris‐Saclay, Evry, 91057, France
| | - Benjamin Istace
- Génomique Métabolique, Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Univ Evry, Université Paris-Saclay, Université Paris-Saclay, Evry, 91057, France
| | - Caroline Belser
- Génomique Métabolique, Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Univ Evry, Université Paris-Saclay, Université Paris-Saclay, Evry, 91057, France
| | - Benjamin Noel
- Génomique Métabolique, Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Univ Evry, Université Paris-Saclay, Université Paris-Saclay, Evry, 91057, France
| | - Yannick Moret
- Équipe Écologie Évolutive, UMR CNRS 6282 BioGéoSciences, Université de Bourgogne Franche-Comté, Dijon, 21000, France
| | - Thierry Rigaud
- Équipe Écologie Évolutive, UMR CNRS 6282 BioGéoSciences, Université de Bourgogne Franche-Comté, Dijon, 21000, France
| | | | | | - Karine Labadie-Bretheau
- Genoscope, Institut de biologie François Jacob, CEA, Université Paris‐Saclay, Evry, 91057, France
| | | | - Mohammed-Amin Madoui
- Génomique Métabolique, Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Univ Evry, Université Paris-Saclay, Université Paris-Saclay, Evry, 91057, France
- Équipe Écologie Évolutive, UMR CNRS 6282 BioGéoSciences, Université de Bourgogne Franche-Comté, Dijon, 21000, France
- Service d’Etude des Prions et des Infections Atypiques (SEPIA), Institut François Jacob, Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA), Université Paris Saclay, Fontenay-aux-Roses, France
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6
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Eleftheriou E, Aury JM, Vacherie B, Istace B, Belser C, Noel B, Moret Y, Rigaud T, Berro F, Gasparian S, Labadie-Bretheau K, Lefebvre T, Madoui MA. Chromosome-scale assembly of the yellow mealworm genome. Open Res Eur 2022; 1:94. [PMID: 37645128 PMCID: PMC10445852 DOI: 10.12688/openreseurope.13987.3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 08/30/2022] [Indexed: 08/31/2023]
Abstract
Background: The yellow mealworm beetle, Tenebrio molitor, is a promising alternative protein source for animal and human nutrition and its farming involves relatively low environmental costs. For these reasons, its industrial scale production started this century. However, to optimize and breed sustainable new T. molitor lines, the access to its genome remains essential. Methods: By combining Oxford Nanopore and Illumina Hi-C data, we constructed a high-quality chromosome-scale assembly of T. molitor. Then, we combined RNA-seq data and available coleoptera proteomes for gene prediction with GMOVE. Results: We produced a high-quality genome with a N50 = 21.9Mb with a completeness of 99.5% and predicted 21,435 genes with a median size of 1,780 bp. Gene orthology between T. molitor and Tribolium castaneum showed a highly conserved synteny between the two coleoptera and paralogs search revealed an expansion of histones in the T. molitor genome. Conclusions: The present genome will greatly help fundamental and applied research such as genetic breeding and will contribute to the sustainable production of the yellow mealworm.
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Affiliation(s)
- Evangelia Eleftheriou
- Génomique Métabolique, Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Univ Evry, Université Paris-Saclay, Université Paris-Saclay, Evry, 91057, France
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Univ Evry, Université Paris-Saclay, Université Paris-Saclay, Evry, 91057, France
| | - Benoît Vacherie
- Genoscope, Institut de biologie François Jacob, CEA, Université Paris‐Saclay, Evry, 91057, France
| | - Benjamin Istace
- Génomique Métabolique, Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Univ Evry, Université Paris-Saclay, Université Paris-Saclay, Evry, 91057, France
| | - Caroline Belser
- Génomique Métabolique, Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Univ Evry, Université Paris-Saclay, Université Paris-Saclay, Evry, 91057, France
| | - Benjamin Noel
- Génomique Métabolique, Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Univ Evry, Université Paris-Saclay, Université Paris-Saclay, Evry, 91057, France
| | - Yannick Moret
- Équipe Écologie Évolutive, UMR CNRS 6282 BioGéoSciences, Université de Bourgogne Franche-Comté, Dijon, 21000, France
| | - Thierry Rigaud
- Équipe Écologie Évolutive, UMR CNRS 6282 BioGéoSciences, Université de Bourgogne Franche-Comté, Dijon, 21000, France
| | | | | | - Karine Labadie-Bretheau
- Genoscope, Institut de biologie François Jacob, CEA, Université Paris‐Saclay, Evry, 91057, France
| | | | - Mohammed-Amin Madoui
- Génomique Métabolique, Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Univ Evry, Université Paris-Saclay, Université Paris-Saclay, Evry, 91057, France
- Équipe Écologie Évolutive, UMR CNRS 6282 BioGéoSciences, Université de Bourgogne Franche-Comté, Dijon, 21000, France
- Service d’Etude des Prions et des Infections Atypiques (SEPIA), Institut François Jacob, Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA), Université Paris Saclay, Fontenay-aux-Roses, France
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7
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Ryu T, Herrera M, Moore B, Izumiyama M, Kawai E, Laudet V, Ravasi T. A chromosome-scale genome assembly of the false clownfish, Amphiprion ocellaris. G3 (Bethesda) 2022; 12:6555996. [PMID: 35353192 PMCID: PMC9073690 DOI: 10.1093/g3journal/jkac074] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/24/2022] [Indexed: 04/13/2023]
Abstract
The false clownfish Amphiprion ocellaris is a popular fish species and an emerging model organism for studying the ecology, evolution, adaptation, and developmental biology of reef fishes. Despite this, high-quality genomic resources for this species are scarce, hindering advanced genomic analyses. Leveraging the power of PacBio long-read sequencing and Hi-C chromosome conformation capture techniques, we constructed a high-quality chromosome-scale genome assembly for the clownfish A. ocellaris. The initial genome assembly comprised of 1,551 contigs of 861.42 Mb, with an N50 of 863.85 kb. Hi-C scaffolding of the genome resulted in 24 chromosomes containing 856.61 Mb. The genome was annotated with 26,797 protein-coding genes and had 96.62% completeness of conserved actinopterygian genes, making this genome the most complete and high quality among published anemonefish genomes. Transcriptomic analysis identified tissue-specific gene expression patterns, with the brain and optic lobe having the largest number of expressed genes. Further, comparative genomic analysis revealed 91 genome elements conserved only in A. ocellaris and its sister species Amphiprion percula, and not in other anemonefish species. These elements are close to genes that are involved in various nervous system functions and exhibited distinct expression patterns in brain tissue, potentially highlighting the genetic toolkits involved in lineage-specific divergence and behaviors of the clownfish branch. Overall, our study provides the highest quality A. ocellaris genome assembly and annotation to date, whilst also providing a valuable resource for understanding the ecology and evolution of reef fishes.
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Affiliation(s)
- Taewoo Ryu
- Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495 Japan
- Corresponding author: Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495 Japan. ; *Corresponding author: Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495 Japan.
| | - Marcela Herrera
- Marine Eco-Evo-Devo Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495 Japan
| | - Billy Moore
- Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495 Japan
| | - Michael Izumiyama
- Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495 Japan
| | - Erina Kawai
- Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495 Japan
| | - Vincent Laudet
- Marine Eco-Evo-Devo Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495 Japan
- Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, I‐Lan, Taiwan
| | - Timothy Ravasi
- Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495 Japan
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811, Australia
- Corresponding author: Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495 Japan. ; *Corresponding author: Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495 Japan.
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Wang Z, Rouard M, Biswas MK, Droc G, Cui D, Roux N, Baurens FC, Ge XJ, Schwarzacher T, Heslop-Harrison P(JS, Liu Q. A chromosome-level reference genome of Ensete glaucum gives insight into diversity and chromosomal and repetitive sequence evolution in the Musaceae. Gigascience 2022; 11:6576245. [PMID: 35488861 PMCID: PMC9055855 DOI: 10.1093/gigascience/giac027] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 01/26/2022] [Accepted: 02/22/2022] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Ensete glaucum (2n = 2x = 18) is a giant herbaceous monocotyledonous plant in the small Musaceae family along with banana (Musa). A high-quality reference genome sequence assembly of E. glaucum is a resource for functional and evolutionary studies of Ensete, Musaceae, and the Zingiberales. FINDINGS Using Oxford Nanopore Technologies, chromosome conformation capture (Hi-C), Illumina and RNA survey sequence, supported by molecular cytogenetics, we report a high-quality 481.5 Mb genome assembly with 9 pseudo-chromosomes and 36,836 genes. A total of 55% of the genome is composed of repetitive sequences with predominantly LTR-retroelements (37%) and DNA transposons (7%). The single 5S ribosomal DNA locus had an exceptionally long monomer length of 1,056 bp, more than twice that of the monomers at multiple loci in Musa. A tandemly repeated satellite (1.1% of the genome, with no similar sequence in Musa) was present around all centromeres, together with a few copies of a long interspersed nuclear element (LINE) retroelement. The assembly enabled us to characterize in detail the chromosomal rearrangements occurring between E. glaucum and the x = 11 species of Musa. One E. glaucum chromosome has the same gene content as Musa acuminata, while others show multiple, complex, but clearly defined evolutionary rearrangements in the change between x= 9 and 11. CONCLUSIONS The advance towards a Musaceae pangenome including E. glaucum, tolerant of extreme environments, makes a complete set of gene alleles, copy number variation, and a reference for structural variation available for crop breeding and understanding environmental responses. The chromosome-scale genome assembly shows the nature of chromosomal fusion and translocation events during speciation, and features of rapid repetitive DNA change in terms of copy number, sequence, and genomic location, critical to understanding its role in diversity and evolution.
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Affiliation(s)
- Ziwei Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510650, China,College of Life Sciences, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Mathieu Rouard
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France,French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Alliance Bioversity and CIAT, CIRAD, INRAE, IRD, F-34398 Montpellier, France
| | - Manosh Kumar Biswas
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Gaetan Droc
- French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Alliance Bioversity and CIAT, CIRAD, INRAE, IRD, F-34398 Montpellier, France,CIRAD, UMR AGAP Institut, F-34398 Montpellier, France,UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
| | - Dongli Cui
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510650, China,College of Life Sciences, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Nicolas Roux
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France
| | - Franc-Christophe Baurens
- CIRAD, UMR AGAP Institut, F-34398 Montpellier, France,UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
| | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Trude Schwarzacher
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China,Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Pat (J S) Heslop-Harrison
- Correspondence address. Qing Liu. Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China. Pat Heslop-Harrison. Department of Genetics and Genome Biology, University of Leicester, Leicester, LE 7RH, UK Qing Liu. Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China E-mail:
| | - Qing Liu
- Correspondence address. Pat Heslop-Harrison. Department of Genetics and Genome Biology, University of Leicester, Leicester, LE 7RH, UK. E-mail:
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9
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Wu JQ, Song L, Ding Y, Dong C, Hasan M, Park RF. A Chromosome-Scale Assembly of the Wheat Leaf Rust Pathogen Puccinia triticina Provides Insights Into Structural Variations and Genetic Relationships With Haplotype Resolution. Front Microbiol 2021; 12:704253. [PMID: 34394053 PMCID: PMC8358450 DOI: 10.3389/fmicb.2021.704253] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 07/12/2021] [Indexed: 11/24/2022] Open
Abstract
Despite the global economic importance of the wheat leaf rust pathogen Puccinia triticina (Pt), genomic resources for Pt are limited and chromosome-level assemblies of Pt are lacking. Here, we present a complete haplotype-resolved genome assembly at a chromosome-scale for Pt using the Australian pathotype 64-(6),(7),(10),11 (Pt64; North American race LBBQB) built upon the newly developed technologies of PacBio and Hi-C sequencing. PacBio reads with ∼200-fold coverage (29.8 Gb data) were assembled by Falcon and Falcon-unzip and subsequently scaffolded with Hi-C data using Falcon-phase and Proximo. This approach allowed us to construct 18 chromosome pseudomolecules ranging from 3.5 to 12.3 Mb in size for each haplotype of the dikaryotic genome of Pt64. Each haplotype had a total length of ∼147 Mb, scaffold N50 of ∼9.4 Mb, and was ∼93% complete for BUSCOs. Each haplotype had ∼29,800 predicted genes, of which ∼2,000 were predicted as secreted proteins (SPs). The investigation of structural variants (SVs) between haplotypes A and B revealed that 10% of the total genome was spanned by SVs, highlighting variations previously undetected by short-read based assemblies. For the first time, the mating type (MAT) genes on each haplotype of Pt64 were identified, which showed that MAT loci a and b are located on two chromosomes (chromosomes 7 and 14), representing a tetrapolar type. Furthermore, the Pt64 assembly enabled haplotype-based evolutionary analyses for 21 Australian Pt isolates, which highlighted the importance of a haplotype resolved reference when inferring genetic relationships using whole genome SNPs. This Pt64 assembly at chromosome-scale with full phase information provides an invaluable resource for genomic and evolutionary research, which will accelerate the understanding of molecular mechanisms underlying Pt-wheat interactions and facilitate the development of durable resistance to leaf rust in wheat and sustainable control of rust disease.
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Affiliation(s)
- Jing Qin Wu
- Plant Breeding Institute, School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, NSW, Australia
| | - Long Song
- Plant Breeding Institute, School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, NSW, Australia
| | - Yi Ding
- Plant Breeding Institute, School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, NSW, Australia
| | - Chongmei Dong
- Plant Breeding Institute, School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, NSW, Australia
| | - Mafruha Hasan
- Plant Breeding Institute, School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, NSW, Australia
| | - Robert F Park
- Plant Breeding Institute, School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, NSW, Australia
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10
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Nowak MD, Birkeland S, Mandáková T, Roy Choudhury R, Guo X, Gustafsson ALS, Gizaw A, Schrøder‐Nielsen A, Fracassetti M, Brysting AK, Rieseberg L, Slotte T, Parisod C, Lysak MA, Brochmann C. The genome of Draba nivalis shows signatures of adaptation to the extreme environmental stresses of the Arctic. Mol Ecol Resour 2021; 21:661-676. [PMID: 33058468 PMCID: PMC7983928 DOI: 10.1111/1755-0998.13280] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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: 04/01/2020] [Revised: 08/26/2020] [Accepted: 10/09/2020] [Indexed: 01/04/2023]
Abstract
The Arctic is one of the most extreme terrestrial environments on the planet. Here, we present the first chromosome-scale genome assembly of a plant adapted to the high Arctic, Draba nivalis (Brassicaceae), an attractive model species for studying plant adaptation to the stresses imposed by this harsh environment. We used an iterative scaffolding strategy with data from short-reads, single-molecule long reads, proximity ligation data, and a genetic map to produce a 302 Mb assembly that is highly contiguous with 91.6% assembled into eight chromosomes (the base chromosome number). To identify candidate genes and gene families that may have facilitated adaptation to Arctic environmental stresses, we performed comparative genomic analyses with nine non-Arctic Brassicaceae species. We show that the D. nivalis genome contains expanded suites of genes associated with drought and cold stress (e.g., related to the maintenance of oxidation-reduction homeostasis, meiosis, and signaling pathways). The expansions of gene families associated with these functions appear to be driven in part by the activity of transposable elements. Tests of positive selection identify suites of candidate genes associated with meiosis and photoperiodism, as well as cold, drought, and oxidative stress responses. Our results reveal a multifaceted landscape of stress adaptation in the D. nivalis genome, offering avenues for the continued development of this species as an Arctic model plant.
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Affiliation(s)
| | | | | | | | - Xinyi Guo
- CEITECMasaryk UniversityBrnoCzech Republic
| | | | - Abel Gizaw
- Natural History MuseumUniversity of OsloOsloNorway
| | | | - Marco Fracassetti
- Science for Life Laboratory and Department of EcologyEnvironment and Plant ScienceStockholm UniversityStockholmSweden
| | - Anne K. Brysting
- Centre for Ecological and Evolutionary SynthesisDepartment of BiosciencesUniversity of OsloOsloNorway
| | - Loren Rieseberg
- Department of BotanyThe University of British ColumbiaVancouverBCCanada
| | - Tanja Slotte
- Science for Life Laboratory and Department of EcologyEnvironment and Plant ScienceStockholm UniversityStockholmSweden
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11
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Linsmith G, Rombauts S, Montanari S, Deng CH, Celton JM, Guérif P, Liu C, Lohaus R, Zurn JD, Cestaro A, Bassil NV, Bakker LV, Schijlen E, Gardiner SE, Lespinasse Y, Durel CE, Velasco R, Neale DB, Chagné D, Van de Peer Y, Troggio M, Bianco L. Pseudo-chromosome-length genome assembly of a double haploid "Bartlett" pear (Pyrus communis L.). Gigascience 2019; 8:giz138. [PMID: 31816089 PMCID: PMC6901071 DOI: 10.1093/gigascience/giz138] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [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: 07/16/2019] [Revised: 10/18/2019] [Accepted: 10/30/2019] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND We report an improved assembly and scaffolding of the European pear (Pyrus communis L.) genome (referred to as BartlettDHv2.0), obtained using a combination of Pacific Biosciences RSII long-read sequencing, Bionano optical mapping, chromatin interaction capture (Hi-C), and genetic mapping. The sample selected for sequencing is a double haploid derived from the same "Bartlett" reference pear that was previously sequenced. Sequencing of di-haploid plants makes assembly more tractable in highly heterozygous species such as P. communis. FINDINGS A total of 496.9 Mb corresponding to 97% of the estimated genome size were assembled into 494 scaffolds. Hi-C data and a high-density genetic map allowed us to anchor and orient 87% of the sequence on the 17 pear chromosomes. Approximately 50% (247 Mb) of the genome consists of repetitive sequences. Gene annotation confirmed the presence of 37,445 protein-coding genes, which is 13% fewer than previously predicted. CONCLUSIONS We showed that the use of a doubled-haploid plant is an effective solution to the problems presented by high levels of heterozygosity and duplication for the generation of high-quality genome assemblies. We present a high-quality chromosome-scale assembly of the European pear Pyrus communis and demostrate its high degree of synteny with the genomes of Malus x Domestica and Pyrus x bretschneideri.
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Affiliation(s)
- Gareth Linsmith
- Center for Plant Systems Biology, VIB, Technologiepark 71, 9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Gent, Belgium
- Fondazione Edmund Mach, via E. Mach 1, 38010, San Michele all'Adige (TN), Italy
| | - Stephane Rombauts
- Center for Plant Systems Biology, VIB, Technologiepark 71, 9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Gent, Belgium
| | - Sara Montanari
- University of California Davis, Department of Plant Sciences, One Shields Ave, Davis, CA 95616, USA
| | - Cecilia H Deng
- The New Zealand Institute for Plant & Food Research Limited (PFR), Mt Albert Research Centre,120 Mt Albert Road, Sandringham, Auckland, 1025, New Zealand
| | - Jean-Marc Celton
- IRHS, INRA, Agrocampus-Ouest, Université d'Angers, SFR 4207 Quasav, 42 rue Georges Morel, F-49071 Beaucouzé, France
| | - Philippe Guérif
- IRHS, INRA, Agrocampus-Ouest, Université d'Angers, SFR 4207 Quasav, 42 rue Georges Morel, F-49071 Beaucouzé, France
| | - Chang Liu
- ZMBP, Allgemeine Genetik, Universität Tübingen, Auf der Morgenstelle 32, D-72076 Tübingen, Germany
| | - Rolf Lohaus
- Center for Plant Systems Biology, VIB, Technologiepark 71, 9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Gent, Belgium
| | - Jason D Zurn
- USDA-ARS National Clonal Germplasm Repository, 33447 Peoria Road, Corvallis, OR 97333, USA
| | - Alessandro Cestaro
- Fondazione Edmund Mach, via E. Mach 1, 38010, San Michele all'Adige (TN), Italy
| | - Nahla V Bassil
- USDA-ARS National Clonal Germplasm Repository, 33447 Peoria Road, Corvallis, OR 97333, USA
| | - Linda V Bakker
- Wageningen UR – Bioscience P.O. Box 16, 6700AA, Wageningen, The Netherlands
| | - Elio Schijlen
- Wageningen UR – Bioscience P.O. Box 16, 6700AA, Wageningen, The Netherlands
| | - Susan E Gardiner
- The New Zealand Institute for Plant & Food Research Limited (PFR), Palmerston North Research Centre, Palmerston North, New Zealand
| | - Yves Lespinasse
- IRHS, INRA, Agrocampus-Ouest, Université d'Angers, SFR 4207 Quasav, 42 rue Georges Morel, F-49071 Beaucouzé, France
| | - Charles-Eric Durel
- IRHS, INRA, Agrocampus-Ouest, Université d'Angers, SFR 4207 Quasav, 42 rue Georges Morel, F-49071 Beaucouzé, France
| | - Riccardo Velasco
- CREA Research Centre for Viticulture and Enology, Via XXVIII Aprile 26, 31015 Conegliano (TV), Italy
| | - David B Neale
- University of California Davis, Department of Plant Sciences, One Shields Ave, Davis, CA 95616, USA
| | - David Chagné
- The New Zealand Institute for Plant & Food Research Limited (PFR), Palmerston North Research Centre, Palmerston North, New Zealand
| | - Yves Van de Peer
- Center for Plant Systems Biology, VIB, Technologiepark 71, 9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Gent, Belgium
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Roper street, Pretoria 0028, South Africa
| | - Michela Troggio
- Fondazione Edmund Mach, via E. Mach 1, 38010, San Michele all'Adige (TN), Italy
| | - Luca Bianco
- Fondazione Edmund Mach, via E. Mach 1, 38010, San Michele all'Adige (TN), Italy
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12
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Li Q, Li H, Huang W, Xu Y, Zhou Q, Wang S, Ruan J, Huang S, Zhang Z. A chromosome-scale genome assembly of cucumber (Cucumis sativus L.). Gigascience 2019; 8:giz072. [PMID: 31216035 PMCID: PMC6582320 DOI: 10.1093/gigascience/giz072] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [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: 12/15/2018] [Revised: 03/13/2019] [Accepted: 05/23/2019] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Accurate and complete reference genome assemblies are fundamental for biological research. Cucumber is an important vegetable crop and model system for sex determination and vascular biology. Low-coverage Sanger sequences and high-coverage short Illumina sequences have been used to assemble draft cucumber genomes, but the incompleteness and low quality of these genomes limit their use in comparative genomics and genetic research. A high-quality and complete cucumber genome assembly is therefore essential. FINDINGS We assembled single-molecule real-time (SMRT) long reads to generate an improved cucumber reference genome. This version contains 174 contigs with a total length of 226.2 Mb and an N50 of 8.9 Mb, and provides 29.0 Mb more sequence data than previous versions. Using 10X Genomics and high-throughput chromosome conformation capture (Hi-C) data, 89 contigs (∼211.0 Mb) were directly linked into 7 pseudo-chromosome sequences. The newly assembled regions show much higher guanine-cytosine or adenine-thymine content than found previously, which is likely to have been inaccessible to Illumina sequencing. The new assembly contains 1,374 full-length long terminal retrotransposons and 1,078 novel genes including 239 tandemly duplicated genes. For example, we found 4 tandemly duplicated tyrosylprotein sulfotransferases, in contrast to the single copy of the gene found previously and in most other plants. CONCLUSION This high-quality genome presents novel features of the cucumber genome and will serve as a valuable resource for genetic research in cucumber and plant comparative genomics.
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Affiliation(s)
- Qing Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12, Haidian District, Beijing 100081, China
| | - Hongbo Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12, Haidian District, Beijing 100081, China
| | - Wu Huang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12, Haidian District, Beijing 100081, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, No. 7, Pengfei Road, Dapeng District, Shenzhen 518124, China
| | - Yuanchao Xu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12, Haidian District, Beijing 100081, China
| | - Qian Zhou
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12, Haidian District, Beijing 100081, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, No. 7, Pengfei Road, Dapeng District, Shenzhen 518124, China
| | - Shenhao Wang
- College of Horticulture, Northwest A&F University, Yangling, Shanxi 712100, China
| | - Jue Ruan
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, No. 7, Pengfei Road, Dapeng District, Shenzhen 518124, China
| | - Sanwen Huang
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, No. 7, Pengfei Road, Dapeng District, Shenzhen 518124, China
| | - Zhonghua Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12, Haidian District, Beijing 100081, China
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13
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Lehmann R, Lightfoot DJ, Schunter C, Michell CT, Ohyanagi H, Mineta K, Foret S, Berumen ML, Miller DJ, Aranda M, Gojobori T, Munday PL, Ravasi T. Finding Nemo's Genes: A chromosome-scale reference assembly of the genome of the orange clownfish Amphiprion percula. Mol Ecol Resour 2018; 19:570-585. [PMID: 30203521 PMCID: PMC7379943 DOI: 10.1111/1755-0998.12939] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 07/31/2018] [Accepted: 08/08/2018] [Indexed: 11/29/2022]
Abstract
The iconic orange clownfish, Amphiprion percula, is a model organism for studying the ecology and evolution of reef fishes, including patterns of population connectivity, sex change, social organization, habitat selection and adaptation to climate change. Notably, the orange clownfish is the only reef fish for which a complete larval dispersal kernel has been established and was the first fish species for which it was demonstrated that antipredator responses of reef fishes could be impaired by ocean acidification. Despite its importance, molecular resources for this species remain scarce and until now it lacked a reference genome assembly. Here, we present a de novo chromosome-scale assembly of the genome of the orange clownfish Amphiprion percula. We utilized single-molecule real-time sequencing technology from Pacific Biosciences to produce an initial polished assembly comprised of 1,414 contigs, with a contig N50 length of 1.86 Mb. Using Hi-C-based chromatin contact maps, 98% of the genome assembly were placed into 24 chromosomes, resulting in a final assembly of 908.8 Mb in length with contig and scaffold N50s of 3.12 and 38.4 Mb, respectively. This makes it one of the most contiguous and complete fish genome assemblies currently available. The genome was annotated with 26,597 protein-coding genes and contains 96% of the core set of conserved actinopterygian orthologs. The availability of this reference genome assembly as a community resource will further strengthen the role of the orange clownfish as a model species for research on the ecology and evolution of reef fishes.
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Affiliation(s)
- Robert Lehmann
- KAUST Environmental Epigenetic Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Damien J Lightfoot
- KAUST Environmental Epigenetic Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Celia Schunter
- KAUST Environmental Epigenetic Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Craig T Michell
- Red Sea Research Center, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Hajime Ohyanagi
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Katsuhiko Mineta
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Sylvain Foret
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia.,Evolution, Ecology and Genetics, Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Michael L Berumen
- Red Sea Research Center, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - David J Miller
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
| | - Manuel Aranda
- Red Sea Research Center, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Takashi Gojobori
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Philip L Munday
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
| | - Timothy Ravasi
- KAUST Environmental Epigenetic Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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