1
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Park JE, Patnaik BB, Sang MK, Song DK, Jeong JY, Hong CE, Kim YT, Shin HJ, Ziwei L, Patnaik HH, Hwang HJ, Park SY, Kang SW, Ko JH, Lee JS, Park HS, Jo YH, Han YS, Lee YS. Transcriptome sequencing of the endangered land snail Karaftohelix adamsi from the Island Ulleung: De novo assembly, annotation, valuation of fitness genes and SSR markers. Genes Genomics 2024; 46:851-870. [PMID: 38809491 DOI: 10.1007/s13258-024-01511-z] [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: 06/12/2023] [Accepted: 03/08/2024] [Indexed: 05/30/2024]
Abstract
BACKGROUND The Bradybaenidae snail Karaftohelix adamsi is endemic to Korea, with the species tracked from Island Ulleung in North Gyeongsang Province of South Korea. K. adamsi has been classified under the Endangered Wildlife Class II species of Korea and poses a severe risk of extinction following habitat disturbances. With no available information at the DNA (genome) or mRNA (transcriptome) level for the species, conservation by utilizing informed molecular resources seems difficult. OBJECTIVE In this study, we used the Illumina short-read sequencing and Trinity de novo assembly to draft the reference transcriptome of K. adamsi. RESULTS After assembly, 13,753 unigenes were obtained of which 10,511 were annotated to public databases (a maximum of 10,165 unigenes found homologs in PANM DB). A total of 6,351, 3,535, 358, and 3,407 unigenes were ascribed to the functional categories under KOG, GO, KEGG, and IPS, respectively. The transcripts such as the HSP 70, aquaporin, TLR, and MAPK, among others, were screened as putative functional resources for adaptation. DNA transposons were found to be thickly populated in comparison to retrotransposons in the assembled unigenes. Further, 2,164 SSRs were screened with the promiscuous presence of dinucleotide repeats such as AC/GT and AG/CT. CONCLUSION The transcriptome-guided discovery of molecular resources in K. adamsi will not only serve as a basis for functional genomics studies but also provide sustainable tools to be utilized for the protection of the species in the wild. Moreover, the development of polymorphic SSRs is valuable for the identification of species from newer habitats and cross-species genotyping.
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Affiliation(s)
- Jie Eun Park
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, 31538, South Korea
- Research Support Center for Bio-Bigdata Analysis and Utilization of Biological Resources, Soonchunhyang University, Chungnam, 31, Asan, South Korea
| | - Bharat Bhusan Patnaik
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, 31538, South Korea
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan, 31538, Chungnam, Korea
- PG Department of Biosciences and Biotechnology, Fakir Mohan University, Nuapadhi, Balasore, Odisha, 756089, India
| | - Min Kyu Sang
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, 31538, South Korea
- Research Support Center for Bio-Bigdata Analysis and Utilization of Biological Resources, Soonchunhyang University, Chungnam, 31, Asan, South Korea
| | - Dae Kwon Song
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, 31538, South Korea
- Research Support Center for Bio-Bigdata Analysis and Utilization of Biological Resources, Soonchunhyang University, Chungnam, 31, Asan, South Korea
| | - Jun Yang Jeong
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, 31538, South Korea
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan, 31538, Chungnam, Korea
| | - Chan Eui Hong
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, 31538, South Korea
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan, 31538, Chungnam, Korea
| | - Yong Tae Kim
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, 31538, South Korea
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan, 31538, Chungnam, Korea
| | - Hyeon Jun Shin
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, 31538, South Korea
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan, 31538, Chungnam, Korea
| | - Liu Ziwei
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, 31538, South Korea
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan, 31538, Chungnam, Korea
| | - Hongray Howrelia Patnaik
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, 31538, South Korea
- PG Department of Zoology, BJB Autonomous College, Bhubaneswar, Odisha, 751014, India
| | - Hee Ju Hwang
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan, 31538, Chungnam, Korea
| | - So Young Park
- Biodiversity Research Team, Animal & Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju, Gyeongbuk, South Korea
| | - Se Won Kang
- Biological Resource Center (BRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, Jeonbuk, South Korea
| | - Jung Ho Ko
- Police Science Institute, Korean National Police University, Asan, 31539, Chungnam, Korea
| | - Jun Sang Lee
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, 31538, South Korea
| | - Hong Seog Park
- Research Institute, GnC BIO Co., LTD, 621-6 Banseok-Dong, Yuseong-Gu, Daejeon, 34069, Korea
| | - Yong Hun Jo
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, 31538, South Korea
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan, 31538, Chungnam, Korea
| | - Yeon Soo Han
- College of Agriculture and Life Science, Chonnam National University, 77 Yongbong-Ro, Buk-Gu, Gwangju, 61186, South Korea
| | - Yong Seok Lee
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, 31538, South Korea.
- Research Support Center for Bio-Bigdata Analysis and Utilization of Biological Resources, Soonchunhyang University, Chungnam, 31, Asan, South Korea.
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan, 31538, Chungnam, Korea.
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Lopes D, Aveiro SS, Cruz S, Cartaxana P, Domingues P. Proteomic analysis of the mucus of the photosynthetic sea slug Elysia crispata. J Proteomics 2024; 294:105087. [PMID: 38237665 DOI: 10.1016/j.jprot.2024.105087] [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: 12/05/2023] [Revised: 01/11/2024] [Accepted: 01/15/2024] [Indexed: 01/23/2024]
Abstract
Elysia crispata is a tropical sea slug that can retain intracellular functional chloroplasts from its algae prey, a mechanism termed kleptoplasty. This sea slug, like other gastropods, secretes mucus, a viscous secretion with multiple functions, including lubrication, protection, and locomotion. This study presents the first comprehensive analysis of the mucus proteome of the sea slug E. crispata using gel electrophoresis and HPLC-MS/MS. We identified 306 proteins in the mucus secretions of this animal, despite the limited entries for E. crispata in the Uniprot database. The functional annotation of the mucus proteome using Gene Ontology identified proteins involved in different functions such as hydrolase activity (molecular function), carbohydrate-derived metabolic processes (biological processes) and cytoskeletal organization (cell component). Moreover, a high proportion of proteins with enzymatic activity in the mucus of E. crispata suggests potential biotechnological applications including antimicrobial and antitumor activities. Putative antimicrobial properties are reinforced by the high abundance of hydrolases. This study also identified proteins common in mucus samples from various species, supporting a common mechanism of mucus in protecting cells and tissues while facilitating animal movement. SIGNIFICANCE: Marine species are increasingly drawing the interest of researchers for their role in discovering new bioactive compounds. The study "Proteomic Analysis of the Mucus of the Photosynthetic Sea Slug Elysia crispata" is a pioneering effort that uncovers the complex protein content in this fascinating sea slug's mucus. This detailed proteomic study has revealed proteins with potential use in biotechnology, particularly for antimicrobial and antitumor purposes. This research is a first step in exploring the possibilities within the mucus of Elysia crispata, suggesting the potential for new drug discoveries. These findings could be crucial in developing treatments for severe diseases, especially those caused by multidrug-resistant bacteria, and may lead to significant advances in medical research.
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Affiliation(s)
- Diana Lopes
- ECOMARE - Laboratory for Innovation and Sustainability of Marine Biological Resources, CESAM - Centre for Environmental and Marine Studies, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Susana S Aveiro
- GreenCoLab - Associação Oceano Verde, University of Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
| | - Sónia Cruz
- ECOMARE, CESAM, Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Paulo Cartaxana
- ECOMARE, CESAM, Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Pedro Domingues
- Mass Spectrometry Centre, LAQV-REQUIMTE - Associated Laboratory for Green Chemistry of the Network of Chemistry and Technology, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal.
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3
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Goodheart JA, Rio RA, Taraporevala NF, Fiorenza RA, Barnes SR, Morrill K, Jacob MAC, Whitesel C, Masterson P, Batzel GO, Johnston HT, Ramirez MD, Katz PS, Lyons DC. A chromosome-level genome for the nudibranch gastropod Berghia stephanieae helps parse clade-specific gene expression in novel and conserved phenotypes. BMC Biol 2024; 22:9. [PMID: 38233809 PMCID: PMC10795318 DOI: 10.1186/s12915-024-01814-3] [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: 08/07/2023] [Accepted: 01/03/2024] [Indexed: 01/19/2024] Open
Abstract
BACKGROUND How novel phenotypes originate from conserved genes, processes, and tissues remains a major question in biology. Research that sets out to answer this question often focuses on the conserved genes and processes involved, an approach that explicitly excludes the impact of genetic elements that may be classified as clade-specific, even though many of these genes are known to be important for many novel, or clade-restricted, phenotypes. This is especially true for understudied phyla such as mollusks, where limited genomic and functional biology resources for members of this phylum have long hindered assessments of genetic homology and function. To address this gap, we constructed a chromosome-level genome for the gastropod Berghia stephanieae (Valdés, 2005) to investigate the expression of clade-specific genes across both novel and conserved tissue types in this species. RESULTS The final assembled and filtered Berghia genome is comparable to other high-quality mollusk genomes in terms of size (1.05 Gb) and number of predicted genes (24,960 genes) and is highly contiguous. The proportion of upregulated, clade-specific genes varied across tissues, but with no clear trend between the proportion of clade-specific genes and the novelty of the tissue. However, more complex tissue like the brain had the highest total number of upregulated, clade-specific genes, though the ratio of upregulated clade-specific genes to the total number of upregulated genes was low. CONCLUSIONS Our results, when combined with previous research on the impact of novel genes on phenotypic evolution, highlight the fact that the complexity of the novel tissue or behavior, the type of novelty, and the developmental timing of evolutionary modifications will all influence how novel and conserved genes interact to generate diversity.
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Affiliation(s)
- Jessica A Goodheart
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, USA.
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
| | - Robin A Rio
- Bioengineering Department, Stanford University, Stanford, CA, USA
| | - Neville F Taraporevala
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
- Department of Wildland Resources, Utah State University, Logan, UT, USA
| | - Rose A Fiorenza
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Seth R Barnes
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Kevin Morrill
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Mark Allan C Jacob
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Carl Whitesel
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Park Masterson
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Grant O Batzel
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Hereroa T Johnston
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - M Desmond Ramirez
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, USA
- Institute of Neuroscience, University of Oregon, Eugene, OR, USA
| | - Paul S Katz
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, USA
| | - Deirdre C Lyons
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
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4
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Eastman KE, Pendleton AL, Shaikh MA, Suttiyut T, Ogas R, Tomko P, Gavelis G, Widhalm JR, Wisecaver JH. A reference genome for the long-term kleptoplast-retaining sea slug Elysia crispata morphotype clarki. G3 (BETHESDA, MD.) 2023; 13:jkad234. [PMID: 37816307 PMCID: PMC10700116 DOI: 10.1093/g3journal/jkad234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 09/15/2023] [Accepted: 09/22/2023] [Indexed: 10/12/2023]
Abstract
Several species of sacoglossan sea slugs possess the incredible ability to sequester chloroplasts from the algae they consume. These "photosynthetic animals" incorporate stolen chloroplasts, called kleptoplasts, into the epithelial cells of tubules that extend from their digestive tracts throughout their bodies. The mechanism by which these slugs maintain functioning kleptoplasts in the absence of an algal nuclear genome is unknown. Here, we report a draft genome of the sacoglossan slug Elysia crispata morphotype clarki, a morphotype native to the Florida Keys that can retain photosynthetically active kleptoplasts for several months without feeding. We used a combination of Oxford Nanopore Technologies long reads and Illumina short reads to produce a 786-Mb assembly (N50 = 0.459 Mb) containing 68,514 predicted protein-coding genes. A phylogenetic analysis found no evidence of horizontal acquisition of genes from algae. We performed gene family and gene expression analyses to identify E. crispata genes unique to kleptoplast-containing slugs that were more highly expressed in fed versus unfed developmental life stages. Consistent with analyses in other kleptoplastic slugs, our investigation suggests that genes encoding lectin carbohydrate-binding proteins and those involved in regulation of reactive oxygen species and immunity may play a role in kleptoplast retention. Lastly, we identified four polyketide synthase genes that could potentially encode proteins producing UV- and oxidation-blocking compounds in slug cell membranes. The genome of E. crispata is a quality resource that provides potential targets for functional analyses and enables further investigation into the evolution and mechanisms of kleptoplasty in animals.
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Affiliation(s)
- Katharine E Eastman
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA
| | - Amanda L Pendleton
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA
| | - Mearaj A Shaikh
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA
| | - Thiti Suttiyut
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA
| | - Raeya Ogas
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA
| | - Paxton Tomko
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Gregory Gavelis
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA
| | - Joshua R Widhalm
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA
| | - Jennifer H Wisecaver
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA
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5
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Goodheart JA, Rio RA, Taraporevala NF, Fiorenza RA, Barnes SR, Morrill K, Jacob MAC, Whitesel C, Masterson P, Batzel GO, Johnston HT, Ramirez MD, Katz PS, Lyons DC. A chromosome-level genome for the nudibranch gastropod Berghia stephanieae helps parse clade-specific gene expression in novel and conserved phenotypes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.04.552006. [PMID: 38014205 PMCID: PMC10680569 DOI: 10.1101/2023.08.04.552006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
How novel phenotypes originate from conserved genes, processes, and tissues remains a major question in biology. Research that sets out to answer this question often focuses on the conserved genes and processes involved, an approach that explicitly excludes the impact of genetic elements that may be classified as clade-specific, even though many of these genes are known to be important for many novel, or clade-restricted, phenotypes. This is especially true for understudied phyla such as mollusks, where limited genomic and functional biology resources for members of this phylum has long hindered assessments of genetic homology and function. To address this gap, we constructed a chromosome-level genome for the gastropod Berghia stephanieae (Valdés, 2005) to investigate the expression of clade-specific genes across both novel and conserved tissue types in this species. The final assembled and filtered Berghia genome is comparable to other high quality mollusk genomes in terms of size (1.05 Gb) and number of predicted genes (24,960 genes), and is highly contiguous. The proportion of upregulated, clade-specific genes varied across tissues, but with no clear trend between the proportion of clade-specific genes and the novelty of the tissue. However, more complex tissue like the brain had the highest total number of upregulated, clade-specific genes, though the ratio of upregulated clade-specific genes to the total number of upregulated genes was low. Our results, when combined with previous research on the impact of novel genes on phenotypic evolution, highlight the fact that the complexity of the novel tissue or behavior, the type of novelty, and the developmental timing of evolutionary modifications will all influence how novel and conserved genes interact to generate diversity.
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Affiliation(s)
- Jessica A. Goodheart
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Robin A. Rio
- Bioengineering Department, Stanford University, Stanford, CA, USA
| | - Neville F. Taraporevala
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
- Department of Wildland Resources, Utah State University, Logan, UT, USA
| | - Rose A. Fiorenza
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Seth R. Barnes
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Kevin Morrill
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Mark Allan C. Jacob
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Carl Whitesel
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Park Masterson
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Grant O. Batzel
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Hereroa T. Johnston
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - M. Desmond Ramirez
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, USA
| | - Paul S. Katz
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, USA
| | - Deirdre C. Lyons
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
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6
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Hui M, Zhang Y, Wang A, Sha Z. The First Genome Survey of the Snail Provanna glabra Inhabiting Deep-Sea Hydrothermal Vents. Animals (Basel) 2023; 13:3313. [PMID: 37958068 PMCID: PMC10648102 DOI: 10.3390/ani13213313] [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: 08/31/2023] [Revised: 10/18/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023] Open
Abstract
The snail P. glabra is an endemic species in deep-sea chemosynthetic ecosystems of the Northwest Pacific Ocean. To obtain more genetic information on this species and provide the basis for subsequent whole-genome map construction, a genome survey was performed on this snail from the hydrothermal vent of Okinawa Trough. The genomic size of P. glabra was estimated to be 1.44 Gb, with a heterozygosity of 1.91% and a repeated sequence content of 69.80%. Based on the sequencing data, a draft genome of 1.32 Gb was assembled. Transposal elements (TEs) accounted for 40.17% of the entire genome, with DNA transposons taking the highest proportion. It was found that most TEs were inserted in the genome recently. In the simple sequence repeats, the dinucleotide motif was the most enriched microsatellite type, accounting for 53% of microsatellites. A complete mitochondrial genome of P. glabra with a total length of 16,268 bp was assembled from the sequencing data. After comparison with the published mitochondrial genome of Provanna sp. from a methane seep, 331 potential single nucleotide polymorphism (SNP) sites were identified in protein-coding genes (PCGs). Except for the cox1 gene, nad2, nad4, nad5, and cob genes are expected to be candidate markers for population genetic and phylogenetic studies of P. glabra and other deep-sea snails. Compared with shallow-water species, three mitochondrial genes of deep-sea gastropods exhibited a higher evolutionary rate, indicating strong selection operating on mitochondria of deep-sea species. This study provides insights into the genome characteristics of P. glabra and supplies genomic resources for further studies on the adaptive evolution of the snail in extreme deep-sea chemosynthetic environments.
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Affiliation(s)
- Min Hui
- Department of Marine Organism Taxonomy & Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (M.H.); (A.W.)
- Laoshan Laboratory, Qingdao 266237, China
- Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Yu Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266100, China;
| | - Aiyang Wang
- Department of Marine Organism Taxonomy & Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (M.H.); (A.W.)
- Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Zhongli Sha
- Department of Marine Organism Taxonomy & Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (M.H.); (A.W.)
- Laoshan Laboratory, Qingdao 266237, China
- Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
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7
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Patra AK, Ho PT, Jun S, Lee SJ, Kim Y, Won YJ. Genome assembly of the Korean intertidal mud-creeper Batillaria attramentaria. Sci Data 2023; 10:498. [PMID: 37507420 PMCID: PMC10382545 DOI: 10.1038/s41597-023-02403-9] [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: 03/31/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023] Open
Abstract
Batillaridae is a common gastropod family that occurs abundantly in the shallow coastal zone of the intertidal mudflats of the northwest Pacific Ocean, Australasia, and North America. In this family, Batillaria attramentaria is known for its biological invasion and colonization in estuarine and intertidal zones. It can endure and adapt the harsh intertidal conditions such as frequent temperature alteration, salinity, and air exposure. Therefore, we sequenced and assembled this Korean batillariid genome to get insight into its intertidal adaptive features. Approximately 53 Gb of DNA sequences were generated, and 863 scaffolds were assembled into a draft genome of 0.715 Gb with 97.1% BUSCO completeness value. A total of 40,596 genes were predicted. We estimated that B. attramentaria and Conus consors diverged about 230 million years ago (MYA) based on the phylogenetic analysis of closely related gastropod species. This genome study sets the footstep for genomics studies among native and introduced Batillaria populations and the Batillaridae family members.
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Affiliation(s)
- Ajit Kumar Patra
- Department of Life Science, Division of EcoScience, Ewha Womans University, Seoul, South Korea
| | - Phuong-Thao Ho
- Department of Life Science, Division of EcoScience, Ewha Womans University, Seoul, South Korea
- Laboratory of Ecology and Environmental Management, Science and Technology Advanced Institute, Van Lang University, Ho Chi Minh City, Vietnam
- Department of International Program, US Vietnam Talent International School, Ho Chi Minh city, Viet Nam
| | - Siyeong Jun
- Department of Life Science, Division of EcoScience, Ewha Womans University, Seoul, South Korea
| | | | - Yuseob Kim
- Department of Life Science, Division of EcoScience, Ewha Womans University, Seoul, South Korea.
| | - Yong-Jin Won
- Department of Life Science, Division of EcoScience, Ewha Womans University, Seoul, South Korea.
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8
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Zhang P, Zhu Y, Guo Q, Li J, Zhan X, Yu H, Xie N, Tan H, Lundholm N, Garcia-Cuetos L, Martin MD, Subirats MA, Su YH, Ruiz-Trillo I, Martindale MQ, Yu JK, Gilbert MTP, Zhang G, Li Q. On the origin and evolution of RNA editing in metazoans. Cell Rep 2023; 42:112112. [PMID: 36795564 PMCID: PMC9989829 DOI: 10.1016/j.celrep.2023.112112] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 11/28/2022] [Accepted: 01/30/2023] [Indexed: 02/16/2023] Open
Abstract
Extensive adenosine-to-inosine (A-to-I) editing of nuclear-transcribed mRNAs is the hallmark of metazoan transcriptional regulation. Here, by profiling the RNA editomes of 22 species that cover major groups of Holozoa, we provide substantial evidence supporting A-to-I mRNA editing as a regulatory innovation originating in the last common ancestor of extant metazoans. This ancient biochemistry process is preserved in most extant metazoan phyla and primarily targets endogenous double-stranded RNA (dsRNA) formed by evolutionarily young repeats. We also find intermolecular pairing of sense-antisense transcripts as an important mechanism for forming dsRNA substrates for A-to-I editing in some but not all lineages. Likewise, recoding editing is rarely shared across lineages but preferentially targets genes involved in neural and cytoskeleton systems in bilaterians. We conclude that metazoan A-to-I editing might first emerge as a safeguard mechanism against repeat-derived dsRNA and was later co-opted into diverse biological processes due to its mutagenic nature.
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Affiliation(s)
- Pei Zhang
- BGI-Shenzhen, Shenzhen 518083, China; Section for Ecology and Evolution, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | | | - Qunfei Guo
- BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ji Li
- BGI Research-Wuhan, BGI, Wuhan 430074, China
| | | | - Hao Yu
- BGI-Shenzhen, Shenzhen 518083, China
| | - Nianxia Xie
- BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | | | - Nina Lundholm
- Natural History Museum of Denmark, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Lydia Garcia-Cuetos
- Natural History Museum of Denmark, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Michael D Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway; Center for Theoretical Evolutionary Genomics, Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | | | - Yi-Hsien Su
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Iñaki Ruiz-Trillo
- Institute of Evolutionary Biology, UPF-CSIC Barcelona, 08003 Barcelona, Spain; ICREA, Passeig Lluís Companys 23, 08010 Barcelona, Catalonia, Spain; Departament de Genètica, Microbiologia i Estadística, Facultat de Bilogia, Universitat de Barcelona (UB), 08028 Barcelona, Spain
| | - Mark Q Martindale
- The Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080, USA
| | - Jr-Kai Yu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan; Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan 26242, Taiwan
| | - M Thomas P Gilbert
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway; Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Guojie Zhang
- Center of Evolutionary and Organismal Biology, & Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China; Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou 311121, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark.
| | - Qiye Li
- BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
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9
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Jiang D, Liu Q, Sun J, Liu S, Fan G, Wang L, Zhang Y, Seim I, An S, Liu X, Li Q, Zheng X. The gold-ringed octopus (Amphioctopus fangsiao) genome and cerebral single-nucleus transcriptomes provide insights into the evolution of karyotype and neural novelties. BMC Biol 2022; 20:289. [PMID: 36575497 PMCID: PMC9795677 DOI: 10.1186/s12915-022-01500-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 12/08/2022] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Coleoid cephalopods have distinctive neural and morphological characteristics compared to other invertebrates. Early studies reported massive genomic rearrangements occurred before the split of octopus and squid lineages (Proc Natl Acad Sci U S A 116:3030-5, 2019), which might be related to the neural innovations of their brain, yet the details remain elusive. Here we combine genomic and single-nucleus transcriptome analyses to investigate the octopod chromosome evolution and cerebral characteristics. RESULTS We present a chromosome-level genome assembly of a gold-ringed octopus, Amphioctopus fangsiao, and a single-nucleus transcriptome of its supra-esophageal brain. Chromosome-level synteny analyses estimate that the chromosomes of the ancestral octopods experienced multiple chromosome fission/fusion and loss/gain events by comparing with the nautilus genome as outgroup, and that a conserved genome organization was detected during the evolutionary process from the last common octopod ancestor to their descendants. Besides, protocadherin, GPCR, and C2H2 ZNF genes are thought to be highly related to the neural innovations in cephalopods (Nature 524:220-4, 2015), and the chromosome analyses pinpointed several collinear modes of these genes on the octopod chromosomes, such as the collinearity between PCDH and C2H2 ZNF, as well as between GPCR and C2H2 ZNF. Phylogenetic analyses show that the expansion of the octopod protocadherin genes is driven by a tandem-duplication mechanism on one single chromosome, including two separate expansions at 65 million years ago (Ma) and 8-14 Ma, respectively. Furthermore, we identify eight cell types (i.e., cholinergic and glutamatergic neurons) in the supra-esophageal brain of A. fangsiao, and the single-cell expression analyses reveal the co-expression of protocadherin and GPCR in specific neural cells, which may contribute to the neural development and signal transductions in the octopod brain. CONCLUSIONS The octopod genome analyses reveal the dynamic evolutionary history of octopod chromosomes and neural-related gene families. The single-nucleus transcriptomes of the supra-esophageal brain indicate their cellular heterogeneities and functional interactions with other tissues (i.e., gill), which provides a foundation for further octopod cerebral studies.
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Affiliation(s)
- Dianhang Jiang
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Ocean University of China, Qingdao, 266003, China
- Institute of Evolution & Marine Biodiversity (IEMB), Qingdao, 266003, China
| | - Qun Liu
- BGI-QingDao, BGI-Shenzhen, Qingdao, 266555, China
| | - Jin Sun
- Institute of Evolution & Marine Biodiversity (IEMB), Qingdao, 266003, China
| | - Shikai Liu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Ocean University of China, Qingdao, 266003, China
| | - Guangyi Fan
- BGI-QingDao, BGI-Shenzhen, Qingdao, 266555, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Lihua Wang
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Ocean University of China, Qingdao, 266003, China
- Institute of Evolution & Marine Biodiversity (IEMB), Qingdao, 266003, China
| | - Yaolei Zhang
- BGI-QingDao, BGI-Shenzhen, Qingdao, 266555, China
| | - Inge Seim
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing, 210046, China
- School of Biology and Environmental Science, Queensland University of Technology, Brisbane, 4000, Australia
| | - Shucai An
- The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Xin Liu
- BGI-QingDao, BGI-Shenzhen, Qingdao, 266555, China
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Ocean University of China, Qingdao, 266003, China
| | - Xiaodong Zheng
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Ocean University of China, Qingdao, 266003, China.
- Institute of Evolution & Marine Biodiversity (IEMB), Qingdao, 266003, China.
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10
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The Natural Product Domain Seeker version 2 (NaPDoS2) webtool relates ketosynthase phylogeny to biosynthetic function. J Biol Chem 2022; 298:102480. [PMID: 36108739 PMCID: PMC9582728 DOI: 10.1016/j.jbc.2022.102480] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 09/06/2022] [Accepted: 09/07/2022] [Indexed: 12/01/2022] Open
Abstract
The Natural Product Domain Seeker (NaPDoS) webtool detects and classifies ketosynthase (KS) and condensation domains from genomic, metagenomic, and amplicon sequence data. Unlike other tools, a phylogeny-based classification scheme is used to make broader predictions about the polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) genes in which these domains are found. NaPDoS is particularly useful for the analysis of incomplete biosynthetic genes or gene clusters, as are often observed in poorly assembled genomes and metagenomes, or when loci are not clustered, as in eukaryotic genomes. To help support the growing interest in sequence-based analyses of natural product biosynthetic diversity, here we introduce version 2 of the webtool, NaPDoS2, available at http://napdos.ucsd.edu/napdos2. This update includes the addition of 1417 KS sequences, representing a major expansion of the taxonomic and functional diversity represented in the webtool database. The phylogeny-based KS classification scheme now recognizes 41 class and subclass assignments, including new type II PKS subclasses. Workflow modifications accelerate run times, allowing larger datasets to be analyzed. In addition, default parameters were established using statistical validation tests to maximize KS detection and classification accuracy while minimizing false positives. We further demonstrate the applications of NaPDoS2 to assess PKS biosynthetic potential using genomic, metagenomic, and PCR amplicon datasets. These examples illustrate how NaPDoS2 can be used to predict biosynthetic potential and detect genes involved in the biosynthesis of specific structure classes or new biosynthetic mechanisms.
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11
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Havurinne V, Aitokari R, Mattila H, Käpylä V, Tyystjärvi E. Ultraviolet screening by slug tissue and tight packing of plastids protect photosynthetic sea slugs from photoinhibition. PHOTOSYNTHESIS RESEARCH 2022; 152:373-387. [PMID: 34826025 PMCID: PMC9458594 DOI: 10.1007/s11120-021-00883-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 10/22/2021] [Indexed: 05/16/2023]
Abstract
One of the main mysteries regarding photosynthetic sea slugs is how the slug plastids handle photoinhibition, the constant light-induced damage to Photosystem II of photosynthesis. Recovery from photoinhibition involves proteins encoded by both the nuclear and plastid genomes, and slugs with plastids isolated from the algal nucleus are therefore expected to be incapable of constantly repairing the damage as the plastids inside the slugs grow old. We studied photoinhibition-related properties of the sea slug Elysia timida that ingests its plastids from the green alga Acetabularia acetabulum. Spectral analysis of both the slugs and the algae revealed that there are two ways the slugs use to avoid major photoinhibition of their plastids. Firstly, highly photoinhibitory UV radiation is screened by the slug tissue or mucus before it reaches the plastids. Secondly, the slugs pack the plastids tightly in their thick bodies, and therefore plastids in the outer layers protect the inner ones from photoinhibition. Both properties are expected to greatly improve the longevity of the plastids inside the slugs, as the plastids do not need to repair excessive amounts of damage.
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Affiliation(s)
- Vesa Havurinne
- Department of Life Technologies/Molecular Plant Biology, University of Turku, Turku, Finland
| | - Riina Aitokari
- Department of Life Technologies/Molecular Plant Biology, University of Turku, Turku, Finland
| | - Heta Mattila
- Department of Life Technologies/Molecular Plant Biology, University of Turku, Turku, Finland
| | - Ville Käpylä
- Department of Life Technologies/Molecular Plant Biology, University of Turku, Turku, Finland
| | - Esa Tyystjärvi
- Department of Life Technologies/Molecular Plant Biology, University of Turku, Turku, Finland.
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12
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Morino Y. Dynamic evolutionary history of spiralian-specific TALE homeobox genes in mollusks. Dev Growth Differ 2022; 64:198-209. [PMID: 35441397 DOI: 10.1111/dgd.12779] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/17/2022] [Accepted: 03/22/2022] [Indexed: 12/18/2022]
Abstract
Homeobox genes play essential roles in the early development of many animals. Although the repertoire of most homeobox genes, including three amino acid loop extension (TALE)-type homeobox genes, is conserved in animals, spiralian-TALE (SPILE) genes are a notable exception. In this study, SPILE genes were extracted from the genomic data of 22 mollusk species and classified into four clades (-A/C, -B, -D, and -E) to determine which SPILE genes exhibit dynamic repertoire changes. While SPILE-D and -E duplications were rarely observed, SPILE-B duplication was observed in the bivalve lineage and SPILE-A/C duplication was observed in multiple clades. Conversely, most or all SPILE genes were lost in cephalopods and in some gastropod lineages. SPILE gene expression patterns were also analyzed in multiple mollusk species using publicly available RNA-seq data. The majority of SPILE genes examined, particularly those in the A/C- and B-clades, were specifically expressed during early development, suggesting that most SPILE genes exert specific roles in early development. This comprehensive cataloging and characterization revealed a dynamic evolutionary history, including SPILE-A/C and -B gene duplications and the loss of SPILE genes in several lineages. Furthermore, this study provides a useful resource for studying the molecular mechanism of spiralian early development and the evolution of young and lineage-specific transcription factors.
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Affiliation(s)
- Yoshiaki Morino
- Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
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13
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Chen Z, Schrödl M. How many single-copy orthologous genes from whole genomes reveal deep gastropod relationships? PeerJ 2022; 10:e13285. [PMID: 35497189 PMCID: PMC9048639 DOI: 10.7717/peerj.13285] [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: 01/19/2022] [Accepted: 03/28/2022] [Indexed: 01/13/2023] Open
Abstract
The Gastropoda contains 80% of existing mollusks and is the most diverse animal class second only to the Insecta. However, the deep phylogeny of gastropods has been controversial for a long time. Especially the position of Patellogastropoda is a major uncertainty. Morphology and some mitochondria studies concluded that Patellogastropoda is likely to be sister to all other gastropods (Orthogastropoda hypothesis), while transcriptomic and other mitogenomic studies indicated that Patellogastropoda and Vetigastropoda are sister taxa (Psilogastropoda). With the release of high-quality genomes, orthologous genes can be better identified and serve as powerful candidates for phylogenetic analysis. The question is, given the current limitations on the taxon sampling side, how many markers are needed to provide robust results. Here, we identified single-copy orthologous genes (SOGs) from 14 gastropods species with whole genomes available which cover five main gastropod subclasses. We generated different datasets from 395 to 1610 SOGs by allowing species missing in different levels. We constructed gene trees of each SOG, and inferred species trees from different collections of gene trees. We found as the number of SOGs increased, the inferred topology changed from Patellogastropoda being sister to all other gastropods to Patellogastropoda being sister to Vetigastropoda + Neomphalina (Psilogastropoda s.l.), with considerable support. Our study thus rejects the Orthogastropoda concept showing that the selection of the representative species and use of sufficient informative sites greatly influence the analysis of deep gastropod phylogeny.
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Affiliation(s)
- Zeyuan Chen
- Mollusca, SNSB-Bavarian State Collection of Zoology, Munich, Bavaria, Germany,Department Biology II, Ludwig-Maximilians-Universität München, Munich, Bavaria, Germany
| | - Michael Schrödl
- Mollusca, SNSB-Bavarian State Collection of Zoology, Munich, Bavaria, Germany,Department Biology II, Ludwig-Maximilians-Universität München, Munich, Bavaria, Germany,GeoBio-Center LMU, Munich, Bavaria, Germany
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14
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Maroni PJ, Baker BJ, Moran AL, Woods HA, Avila C, Johnstone GJ, Stark JS, Kocot KM, Lockhart S, Saucède T, Rouse GW, Wilson NG. One Antarctic slug to confuse them all: the underestimated diversity of Doris kerguelenensis. INVERTEBR SYST 2022. [DOI: 10.1071/is21073] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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15
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Chueca LJ, Schell T, Pfenninger M. De novo genome assembly of the land snail Candidula unifasciata (Mollusca: Gastropoda). G3 (BETHESDA, MD.) 2021; 11:6287656. [PMID: 34849805 PMCID: PMC8496239 DOI: 10.1093/g3journal/jkab180] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 05/18/2021] [Indexed: 11/14/2022]
Abstract
Among all molluscs, land snails are a scientifically and economically interesting group comprising edible species, alien species and agricultural pests. Yet, despite their high diversity, the number of genome drafts publicly available is still scarce. Here, we present the draft genome assembly of the land snail Candidula unifasciata, a widely distributed species along central Europe, belonging to the Geomitridae family, a highly diversified taxon in the Western-Palearctic region. We performed whole genome sequencing, assembly and annotation of an adult specimen based on PacBio and Oxford Nanopore long read sequences as well as Illumina data. A genome draft of about 1.29 Gb was generated with a N50 length of 246 kb. More than 60% of the assembled genome was identified as repetitive elements. In total, 22,464 protein-coding genes were identified in the genome, of which 62.27% were functionally annotated. This is the first assembled and annotated genome for a geometrid snail and will serve as reference for further evolutionary, genomic and population genetic studies of this important and interesting group.
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Affiliation(s)
- Luis J Chueca
- LOEWE-Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Nature Research Society, Frankfurt am Main 60325, Germany.,Department of Zoology and Animal Cell Biology, University of the Basque Country (UPV-EHU), Vitoria-Gasteiz 01006, Spain
| | - Tilman Schell
- LOEWE-Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Nature Research Society, Frankfurt am Main 60325, Germany
| | - Markus Pfenninger
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main 60325, Germany.,Faculty of Biology, Institute of Organismic and Molecular Evolution (iOME), Johannes Gutenberg University, Mainz 55128, Germany
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16
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Seasonality and Longevity of the Functional Chloroplasts Retained by the Sacoglossan Sea Slug Plakobranchus ocellatus van Hasselt, 1824 Inhabiting A Subtropical Back Reef Off Okinawa-jima Island, Japan. Zool Stud 2021; 59:e65. [PMID: 34140982 DOI: 10.6620/zs.2020.59-65] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 10/12/2020] [Indexed: 01/19/2023]
Abstract
Plakobranchus ocellatus is a sacoglossan sea slug that feeds on multiple algal species and retains chloroplasts as kleptoplasts for several months. The seasonal differences in the photosynthetic properties of kleptoplasts were examined in sacoglossans collected from a subtropical back reef off of Okinawa-jima (26°21'55"N 127°44'10"E) in 2017-2018. The effective quantum yield of photosystem II in kleptoplasts indicated that stronger ambient light causes more stress in kleptoplasts. The maximum quantum yields (QY) at 20°C, 30°C, and 40°C indicated that kleptoplasts were more functional in photosynthesis in winter than in spring or summer, whereas kleptoplasts may have the highest tolerance to high temperatures in summer. In the long-starvation experiment (LSE), the relative ratio of body weight (relW) linearly decreased and the sacoglossans died within 2 months in the total dark condition, whereas in the LSE with illumination, the animals survived up to 5 months. The time course for the decrease in the relative ratio of the QY (relQY) in the LSE indicated that the photosynthetic function was almost normal for 2 months, regardless of the presence or absence of illumination, after which time relQY gradually decreased to zero. In the field, P. ocellatus continuously took up new kleptoplasts that have suitable properties of photosynthetic ability for each season. In a subtropical environment, in which water temperatures vary from below 20°C to above 30°C, seasonal changes could cause a temporary shortage of algal food and affect the photosynthetic activity of P. ocellatus kleptoplast. Our results, however, indicated the kleptoplasts of P. ocellatus functioned normally for several months and maintained the presence of this sacoglossan in a subtropical environment throughout the year.
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17
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Maeda T, Takahashi S, Yoshida T, Shimamura S, Takaki Y, Nagai Y, Toyoda A, Suzuki Y, Arimoto A, Ishii H, Satoh N, Nishiyama T, Hasebe M, Maruyama T, Minagawa J, Obokata J, Shigenobu S. Chloroplast acquisition without the gene transfer in kleptoplastic sea slugs, Plakobranchus ocellatus. eLife 2021; 10:60176. [PMID: 33902812 PMCID: PMC8079154 DOI: 10.7554/elife.60176] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 04/01/2021] [Indexed: 12/14/2022] Open
Abstract
Some sea slugs sequester chloroplasts from algal food in their intestinal cells and photosynthesize for months. This phenomenon, kleptoplasty, poses a question of how the chloroplast retains its activity without the algal nucleus. There have been debates on the horizontal transfer of algal genes to the animal nucleus. To settle the arguments, this study reported the genome of a kleptoplastic sea slug, Plakobranchus ocellatus, and found no evidence of photosynthetic genes encoded on the nucleus. Nevertheless, it was confirmed that light illumination prolongs the life of mollusk under starvation. These data presented a paradigm that a complex adaptive trait, as typified by photosynthesis, can be transferred between eukaryotic kingdoms by a unique organelle transmission without nuclear gene transfer. Our phylogenomic analysis showed that genes for proteolysis and immunity undergo gene expansion and are up-regulated in chloroplast-enriched tissue, suggesting that these molluskan genes are involved in the phenotype acquisition without horizontal gene transfer.
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Affiliation(s)
- Taro Maeda
- National Institute for Basic Biology, Okazaki, Japan
| | - Shunichi Takahashi
- Sesoko Station, Tropical Biosphere Research Center, University of the Ryukyu, Okinawa, Japan
| | - Takao Yoshida
- Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Shigeru Shimamura
- Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Yoshihiro Takaki
- Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Yukiko Nagai
- Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | | | | | - Asuka Arimoto
- Marine Biological Laboratory, Hiroshima University, Hiroshima, Japan
| | | | - Nori Satoh
- Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Tomoaki Nishiyama
- Research Center for Experimental Modeling of Human Disease, Kanazawa University, Kanazawa, Japan
| | - Mitsuyasu Hasebe
- National Institute for Basic Biology, Okazaki, Japan.,SOKENDAI, the Graduate University for Advanced Studies, Okazaki, Japan
| | | | - Jun Minagawa
- National Institute for Basic Biology, Okazaki, Japan.,SOKENDAI, the Graduate University for Advanced Studies, Okazaki, Japan
| | - Junichi Obokata
- Kyoto Prefectural University, Kyoto, Japan.,Setsunan Universiy, Hirakata, Japan
| | - Shuji Shigenobu
- National Institute for Basic Biology, Okazaki, Japan.,SOKENDAI, the Graduate University for Advanced Studies, Okazaki, Japan
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18
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Identification and classification of innexin gene transcripts in the central nervous system of the terrestrial slug Limax valentianus. PLoS One 2021; 16:e0244902. [PMID: 33857131 PMCID: PMC8049302 DOI: 10.1371/journal.pone.0244902] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 03/09/2021] [Indexed: 12/20/2022] Open
Abstract
Intercellular gap junction channels and single-membrane channels have been reported to regulate electrical synapse and the brain function. Innexin is known as a gap junction-related protein in invertebrates and is involved in the formation of intercellular gap junction channels and single-cell membrane channels. Multiple isoforms of innexin protein in each species enable the precise regulation of channel function. In molluscan species, sequence information of innexins is still limited and the sequences of multiple innexin isoforms have not been classified. This study examined the innexin transcripts expressed in the central nervous system of the terrestrial slug Limax valentianus and identified 16 transcripts of 12 innexin isoforms, including the splicing variants. We performed phylogenetic analysis and classified the isoforms with other molluscan innexin sequences. Next, the phosphorylation, N-glycosylation, and S-nitrosylation sites were predicted to characterize the innexin isoforms. Further, we identified 16 circular RNA sequences of nine innexin isoforms in the central nervous system of Limax. The identification and classification of molluscan innexin isoforms provided novel insights for understanding the regulatory mechanism of innexin in this phylum.
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19
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Sigwart JD, Lindberg DR, Chen C, Sun J. Molluscan phylogenomics requires strategically selected genomes. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200161. [PMID: 33813889 DOI: 10.1098/rstb.2020.0161] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The extraordinary diversity in molluscan body plans, and the genomic mechanisms that enable it, remains one of the great questions of evolution. The eight distinct living taxonomic classes of molluscs are each unambiguously monophyletic; however, significant controversy remains about the phylogenetic relationships among those eight branches. Molluscs are the second-largest animal phylum, with over 100 000 living species with broad biological, economic and medical interest. To date, only around 53 genome assemblies have been accessioned to NCBI GenBank covering only four of the eight living molluscan classes. Furthermore, the molluscan taxa where partial or whole-genome assemblies are available are often aberrantly fast evolving or recently derived lineages. Characteristic adaptations provide interesting targets for whole-genome projects, in animals like the scaly-foot snail or octopus, but without basal-branching lineages for comparison, the context of recently derived features cannot be assessed. The currently available genomes also create a non-optimal set of taxa for resolving deeper phylogenetic branches: they are a small sample representing a large group, and those that are available come primarily from a rarefied pool. Thoughtful selection of taxa for future projects should focus on the blank areas of the molluscan tree, which are ripe with opportunities to delve into peculiarities of genome evolution, and reveal the biology and evolutionary history of molluscs. This article is part of the Theo Murphy meeting issue 'Molluscan genomics: broad insights and future directions for a neglected phylum'.
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Affiliation(s)
- Julia D Sigwart
- Senckenberg Research Institute, 60325 Frankfurt am Main, Germany.,Queen's University Belfast Marine Laboratory, Portaferry, Newtownards BT22 1PF, UK.,Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Hong Kong
| | - David R Lindberg
- Department of Integrative Biology, University of California, Berkeley, USA
| | - Chong Chen
- X-STAR, Japan Agency for Marine Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Jin Sun
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, People's Republic of China
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20
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Liu F, Li Y, Yu H, Zhang L, Hu J, Bao Z, Wang S. MolluscDB: an integrated functional and evolutionary genomics database for the hyper-diverse animal phylum Mollusca. Nucleic Acids Res 2021; 49:D988-D997. [PMID: 33219670 PMCID: PMC7779068 DOI: 10.1093/nar/gkaa918] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/16/2020] [Accepted: 10/03/2020] [Indexed: 12/11/2022] Open
Abstract
Mollusca represents the second largest animal phylum but remains poorly explored from a genomic perspective. While the recent increase in genomic resources holds great promise for a deep understanding of molluscan biology and evolution, access and utilization of these resources still pose a challenge. Here, we present the first comprehensive molluscan genomics database, MolluscDB (http://mgbase.qnlm.ac), which compiles and integrates current molluscan genomic/transcriptomic resources and provides convenient tools for multi-level integrative and comparative genomic analyses. MolluscDB enables a systematic view of genomic information from various aspects, such as genome assembly statistics, genome phylogenies, fossil records, gene information, expression profiles, gene families, transcription factors, transposable elements and mitogenome organization information. Moreover, MolluscDB offers valuable customized datasets or resources, such as gene coexpression networks across various developmental stages and adult tissues/organs, core gene repertoires inferred for major molluscan lineages, and macrosynteny analysis for chromosomal evolution. MolluscDB presents an integrative and comprehensive genomics platform that will allow the molluscan community to cope with ever-growing genomic resources and will expedite new scientific discoveries for understanding molluscan biology and evolution.
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Affiliation(s)
- Fuyun Liu
- MOE Key Laboratory of Marine Genetics and Breeding and Sars-Fang Centre, Ocean University of China, Qingdao 266003, China
| | - Yuli Li
- MOE Key Laboratory of Marine Genetics and Breeding and Sars-Fang Centre, Ocean University of China, Qingdao 266003, China.,Laboratory for Marine Biology and Biotechnology, Pilot Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Hongwei Yu
- MOE Key Laboratory of Marine Genetics and Breeding and Sars-Fang Centre, Ocean University of China, Qingdao 266003, China
| | - Lingling Zhang
- MOE Key Laboratory of Marine Genetics and Breeding and Sars-Fang Centre, Ocean University of China, Qingdao 266003, China.,Laboratory for Marine Biology and Biotechnology, Pilot Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Jingjie Hu
- MOE Key Laboratory of Marine Genetics and Breeding and Sars-Fang Centre, Ocean University of China, Qingdao 266003, China.,Laboratory of Tropical Marine Germplasm Resources and Breeding Engineering, Sanya Oceanographic Institution, Ocean University of China, Sanya 572000, China
| | - Zhenmin Bao
- MOE Key Laboratory of Marine Genetics and Breeding and Sars-Fang Centre, Ocean University of China, Qingdao 266003, China.,Laboratory of Tropical Marine Germplasm Resources and Breeding Engineering, Sanya Oceanographic Institution, Ocean University of China, Sanya 572000, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Pilot Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Shi Wang
- MOE Key Laboratory of Marine Genetics and Breeding and Sars-Fang Centre, Ocean University of China, Qingdao 266003, China.,Laboratory for Marine Biology and Biotechnology, Pilot Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.,Laboratory of Tropical Marine Germplasm Resources and Breeding Engineering, Sanya Oceanographic Institution, Ocean University of China, Sanya 572000, China
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21
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Varney RM, Speiser DI, McDougall C, Degnan BM, Kocot KM. The Iron-Responsive Genome of the Chiton Acanthopleura granulata. Genome Biol Evol 2021; 13:evaa263. [PMID: 33320175 PMCID: PMC7850002 DOI: 10.1093/gbe/evaa263] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/11/2020] [Indexed: 12/27/2022] Open
Abstract
Molluscs biomineralize structures that vary in composition, form, and function, prompting questions about the genetic mechanisms responsible for their production and the evolution of these mechanisms. Chitons (Mollusca, Polyplacophora) are a promising system for studies of biomineralization because they build a range of calcified structures including shell plates and spine- or scale-like sclerites. Chitons also harden the calcified teeth of their rasp-like radula with a coat of iron (as magnetite). Here we present the genome of the West Indian fuzzy chiton Acanthopleura granulata, the first from any aculiferan mollusc. The A. granulata genome contains homologs of many genes associated with biomineralization in conchiferan molluscs. We expected chitons to lack genes previously identified from pathways conchiferans use to make biominerals like calcite and nacre because chitons do not use these materials in their shells. Surprisingly, the A. granulata genome has homologs of many of these genes, suggesting that the ancestral mollusc may have had a more diverse biomineralization toolkit than expected. The A. granulata genome has features that may be specialized for iron biomineralization, including a higher proportion of genes regulated directly by iron than other molluscs. A. granulata also produces two isoforms of soma-like ferritin: one is regulated by iron and similar in sequence to the soma-like ferritins of other molluscs, and the other is constitutively translated and is not found in other molluscs. The A. granulata genome is a resource for future studies of molluscan evolution and biomineralization.
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Affiliation(s)
- Rebecca M Varney
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama
| | - Daniel I Speiser
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina
| | - Carmel McDougall
- Australian Rivers Institute, Griffith University, Nathan, Queensland, Australia
| | - Bernard M Degnan
- School of Biological Sciences, University of Queensland, Brisbane, Queensland, Australia
| | - Kevin M Kocot
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama
- Alabama Museum of Natural History, Tuscaloosa, Alabama
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22
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Whitelaw BL, Cooke IR, Finn J, da Fonseca RR, Ritschard EA, Gilbert MTP, Simakov O, Strugnell JM. Adaptive venom evolution and toxicity in octopods is driven by extensive novel gene formation, expansion, and loss. Gigascience 2020; 9:giaa120. [PMID: 33175168 PMCID: PMC7656900 DOI: 10.1093/gigascience/giaa120] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 08/10/2020] [Accepted: 10/06/2020] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Cephalopods represent a rich system for investigating the genetic basis underlying organismal novelties. This diverse group of specialized predators has evolved many adaptations including proteinaceous venom. Of particular interest is the blue-ringed octopus genus (Hapalochlaena), which are the only octopods known to store large quantities of the potent neurotoxin, tetrodotoxin, within their tissues and venom gland. FINDINGS To reveal genomic correlates of organismal novelties, we conducted a comparative study of 3 octopod genomes, including the Southern blue-ringed octopus (Hapalochlaena maculosa). We present the genome of this species and reveal highly dynamic evolutionary patterns at both non-coding and coding organizational levels. Gene family expansions previously reported in Octopus bimaculoides (e.g., zinc finger and cadherins, both associated with neural functions), as well as formation of novel gene families, dominate the genomic landscape in all octopods. Examination of tissue-specific genes in the posterior salivary gland revealed that expression was dominated by serine proteases in non-tetrodotoxin-bearing octopods, while this family was a minor component in H. maculosa. Moreover, voltage-gated sodium channels in H. maculosa contain a resistance mutation found in pufferfish and garter snakes, which is exclusive to the genus. Analysis of the posterior salivary gland microbiome revealed a diverse array of bacterial species, including genera that can produce tetrodotoxin, suggestive of a possible production source. CONCLUSIONS We present the first tetrodotoxin-bearing octopod genome H. maculosa, which displays lineage-specific adaptations to tetrodotoxin acquisition. This genome, along with other recently published cephalopod genomes, represents a valuable resource from which future work could advance our understanding of the evolution of genomic novelty in this family.
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Affiliation(s)
- Brooke L Whitelaw
- Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, 1 James Cook Dr, Douglas QLD 4811 , Australia
- Sciences, Museum Victoria, 11 Nicholson St, Carlton, Victoria 3053, Australia
| | - Ira R Cooke
- College of Public Health, Medical and Vet Sciences, James Cook University,1 James Cook Dr, Douglas QLD 4811 , Australia
- La Trobe Institute of Molecular Science, La Trobe University, Plenty Rd &, Kingsbury Dr, Bundoora, Melbourne, Victoria 3086, Australia
| | - Julian Finn
- Sciences, Museum Victoria, 11 Nicholson St, Carlton, Victoria 3053, Australia
| | - Rute R da Fonseca
- Center for Macroecology, Evolution and Climate (CMEC), GLOBE Institute, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Elena A Ritschard
- Department of Neurosciences and Developmental Biology, University of Vienna,Universitätsring 1, 1010 Wien, Vienna, Austria
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - M T P Gilbert
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Øster Voldgade 5–7, 1350 Copenhagen, Denmark
| | - Oleg Simakov
- Department of Neurosciences and Developmental Biology, University of Vienna,Universitätsring 1, 1010 Wien, Vienna, Austria
| | - Jan M Strugnell
- Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, 1 James Cook Dr, Douglas QLD 4811 , Australia
- Department of Ecology, Environment and Evolution, La Trobe University, Plenty Rd &, Kingsbury Dr, Bundoora, Melbourne, Victoria 3086, Australia
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23
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Li Y, Nong W, Baril T, Yip HY, Swale T, Hayward A, Ferrier DEK, Hui JHL. Reconstruction of ancient homeobox gene linkages inferred from a new high-quality assembly of the Hong Kong oyster (Magallana hongkongensis) genome. BMC Genomics 2020; 21:713. [PMID: 33059600 PMCID: PMC7566022 DOI: 10.1186/s12864-020-07027-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 08/25/2020] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Homeobox-containing genes encode crucial transcription factors involved in animal, plant and fungal development, and changes to homeobox genes have been linked to the evolution of novel body plans and morphologies. In animals, some homeobox genes are clustered together in the genome, either as remnants from ancestral genomic arrangements, or due to coordinated gene regulation. Consequently, analyses of homeobox gene organization across animal phylogeny provide important insights into the evolution of genome organization and developmental gene control, and their interaction. However, homeobox gene organization remains to be fully elucidated in several key animal ancestors, including those of molluscs, lophotrochozoans and bilaterians. RESULTS Here, we present a high-quality chromosome-level genome assembly of the Hong Kong oyster, Magallana hongkongensis (2n = 20), for which 93.2% of the genomic sequences are contained on 10 pseudomolecules (~ 758 Mb, scaffold N50 = 72.3 Mb). Our genome assembly was scaffolded using Hi-C reads, facilitating a larger scaffold size compared to the recently published M. hongkongensis genome of Peng et al. (Mol Ecol Resources, 2020), which was scaffolded using the Crassostrea gigas assembly. A total of 46,963 predicted gene models (45,308 protein coding genes) were incorporated in our genome, and genome completeness estimated by BUSCO was 94.6%. Homeobox gene linkages were analysed in detail relative to available data for other mollusc lineages. CONCLUSIONS The analyses performed in this study and the accompanying genome sequence provide important genetic resources for this economically and culturally valuable oyster species, and offer a platform to improve understanding of animal biology and evolution more generally. Transposable element content is comparable to that found in other mollusc species, contrary to the conclusion of another recent analysis. Also, our chromosome-level assembly allows the inference of ancient gene linkages (synteny) for the homeobox-containing genes, even though a number of the homeobox gene clusters, like the Hox/ParaHox clusters, are undergoing dispersal in molluscs such as this oyster.
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Affiliation(s)
- Yiqian Li
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Wenyan Nong
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Tobias Baril
- Department of Conservation and Ecology, Penryn Campus, University of Exeter, Exeter, UK
| | - Ho Yin Yip
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | | | - Alexander Hayward
- Department of Conservation and Ecology, Penryn Campus, University of Exeter, Exeter, UK.
| | - David E K Ferrier
- The Scottish Oceans Institute, Gatty Martine Laboratory, University of St. Andrews, St Andrews, UK.
| | - Jerome H L Hui
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong.
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24
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Liang P, Saqib HSA, Ni X, Shen Y. Long-read sequencing and de novo genome assembly of marine medaka (Oryzias melastigma). BMC Genomics 2020; 21:640. [PMID: 32938378 PMCID: PMC7493909 DOI: 10.1186/s12864-020-07042-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 08/31/2020] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Marine medaka (Oryzias melastigma) is considered as an important ecotoxicological indicator to study the biochemical, physiological and molecular responses of marine organisms towards increasing amount of pollutants in marine and estuarine waters. RESULTS In this study, we reported a high-quality and accurate de novo genome assembly of marine medaka through the integration of single-molecule sequencing, Illumina paired-end sequencing, and 10X Genomics linked-reads. The 844.17 Mb assembly is estimated to cover more than 98% of the genome and is more continuous with fewer gaps and errors than the previous genome assembly. Comparison of O. melastigma with closely related species showed significant expansion of gene families associated with DNA repair and ATP-binding cassette (ABC) transporter pathways. We identified 274 genes that appear to be under significant positive selection and are involved in DNA repair, cellular transportation processes, conservation and stability of the genome. The positive selection of genes and the considerable expansion in gene numbers, especially related to stimulus responses provide strong supports for adaptations of O. melastigma under varying environmental stresses. CONCLUSIONS The highly contiguous marine medaka genome and comparative genomic analyses will increase our understanding of the underlying mechanisms related to its extraordinary adaptation capability, leading towards acceleration in the ongoing and future investigations in marine ecotoxicology.
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Affiliation(s)
- Pingping Liang
- College of the Environment and Ecology, Xiamen University, Xiamen, 361102, China
| | - Hafiz Sohaib Ahmed Saqib
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiaomin Ni
- College of the Environment and Ecology, Xiamen University, Xiamen, 361102, China
- Fudan University, Shanghai, 200240, China
| | - Yingjia Shen
- College of the Environment and Ecology, Xiamen University, Xiamen, 361102, China.
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25
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Li Q, Guo Q, Zhou Y, Tan H, Bertozzi T, Zhu Y, Li J, Donnellan S, Zhang G. A draft genome assembly of the eastern banjo frog Limnodynastes dumerilii dumerilii (Anura: Limnodynastidae). GIGABYTE 2020; 2020:gigabyte2. [PMID: 36824594 PMCID: PMC9632003 DOI: 10.46471/gigabyte.2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 05/15/2020] [Indexed: 01/09/2023] Open
Abstract
Amphibian genomes are usually challenging to assemble due to their large genome size and high repeat content. The Limnodynastidae is a family of frogs native to Australia, Tasmania and New Guinea. As an anuran lineage that successfully diversified on the Australian continent, it represents an important lineage in the amphibian tree of life but lacks reference genomes. Here we sequenced and annotated the genome of the eastern banjo frog Limnodynastes dumerilii dumerilii to fill this gap. The total length of the genome assembly is 2.38 Gb with a scaffold N50 of 285.9 kb. We identified 1.21 Gb of non-redundant sequences as repetitive elements and annotated 24,548 protein-coding genes in the assembly. BUSCO assessment indicated that more than 94% of the expected vertebrate genes were present in the genome assembly and the gene set. We anticipate that this annotated genome assembly will advance the future study of anuran phylogeny and amphibian genome evolution.
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Affiliation(s)
- Qiye Li
- BGI-Shenzhen, Shenzhen 518083, China
| | - Qunfei Guo
- BGI-Shenzhen, Shenzhen 518083, China,College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Yang Zhou
- BGI-Shenzhen, Shenzhen 518083, China
| | - Huishuang Tan
- BGI-Shenzhen, Shenzhen 518083, China,Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Terry Bertozzi
- South Australian Museum, North Terrace, Adelaide 5000, Australia,School of Biological Sciences, University of Adelaide, North Terrace, Adelaide 5005, Australia
| | - Yuanzhen Zhu
- BGI-Shenzhen, Shenzhen 518083, China,School of Basic Medicine, Qingdao University, Qingdao 266071, China
| | - Ji Li
- BGI-Shenzhen, Shenzhen 518083, China,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | | | - Guojie Zhang
- BGI-Shenzhen, Shenzhen 518083, China,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 650223 Kunming, China,Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark, Corresponding author. E-mail:
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26
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Torres JP, Lin Z, Winter JM, Krug PJ, Schmidt EW. Animal biosynthesis of complex polyketides in a photosynthetic partnership. Nat Commun 2020; 11:2882. [PMID: 32513940 PMCID: PMC7280274 DOI: 10.1038/s41467-020-16376-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Accepted: 04/29/2020] [Indexed: 11/09/2022] Open
Abstract
Complex polyketides are typically associated with microbial metabolism. Here, we report that animals also make complex, microbe-like polyketides. We show there is a widespread branch of fatty acid synthase- (FAS)-like polyketide synthase (PKS) proteins, which sacoglossan animals use to synthesize complex products. The purified sacogolassan protein EcPKS1 uses only methylmalonyl-CoA as a substrate, otherwise unknown in animal lipid metabolism. Sacoglossans are sea slugs, some of which eat algae, digesting the cells but maintaining functional chloroplasts. Here, we provide evidence that polyketides support this unusual photosynthetic partnership. The FAS-like PKS family represents an uncharacterized branch of polyketide and fatty acid metabolism, encoding a large diversity of biomedically relevant animal enzymes and chemicals awaiting discovery. The biochemical characterization of an intact animal polyketide biosynthetic enzyme opens the door to understanding the immense untapped metabolic potential of metazoans. Complex polyketides are usually produced by microbes, whereas the origin of polyketides found in animals remained unknown. This study shows that sacoglossan animals, such as sea slugs, employ fatty acid synthase-like proteins to produce microbe-like polyketides.
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Affiliation(s)
- Joshua P Torres
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT, 84112, USA
| | - Zhenjian Lin
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT, 84112, USA
| | - Jaclyn M Winter
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT, 84112, USA
| | - Patrick J Krug
- Department of Biological Sciences, California State University, Los Angeles, CA, 90032, USA
| | - Eric W Schmidt
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT, 84112, USA.
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27
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Liu R, Wang K, Liu J, Xu W, Zhou Y, Zhu C, Wu B, Li Y, Wang W, He S, Feng C, Zhang H. De Novo Genome Assembly of Limpet Bathyacmaea lactea (Gastropoda: Pectinodontidae): The First Reference Genome of a Deep-Sea Gastropod Endemic to Cold Seeps. Genome Biol Evol 2020; 12:905-910. [PMID: 32467969 PMCID: PMC7313663 DOI: 10.1093/gbe/evaa100] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/03/2017] [Indexed: 12/12/2022] Open
Abstract
Cold seeps, characterized by the methane, hydrogen sulfide, and other hydrocarbon chemicals, foster one of the most widespread chemosynthetic ecosystems in deep sea that are densely populated by specialized benthos. However, scarce genomic resources severely limit our knowledge about the origin and adaptation of life in this unique ecosystem. Here, we present a genome of a deep-sea limpet Bathyacmaea lactea, a common species associated with the dominant mussel beds in cold seeps. We yielded 54.6 gigabases (Gb) of Nanopore reads and 77.9-Gb BGI-seq raw reads, respectively. Assembly harvested a 754.3-Mb genome for B. lactea, with 3,720 contigs and a contig N50 of 1.57 Mb, covering 94.3% of metazoan Benchmarking Universal Single-Copy Orthologs. In total, 23,574 protein-coding genes and 463.4 Mb of repetitive elements were identified. We analyzed the phylogenetic position, substitution rate, demographic history, and TE activity of B. lactea. We also identified 80 expanded gene families and 87 rapidly evolving Gene Ontology categories in the B. lactea genome. Many of these genes were associated with heterocyclic compound metabolism, membrane-bounded organelle, metal ion binding, and nitrogen and phosphorus metabolism. The high-quality assembly and in-depth characterization suggest the B. lactea genome will serve as an essential resource for understanding the origin and adaptation of life in the cold seeps.
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Affiliation(s)
- Ruoyu Liu
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Kun Wang
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi’an, China
| | - Jun Liu
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Wenjie Xu
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi’an, China
| | - Yang Zhou
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chenglong Zhu
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi’an, China
| | - Baosheng Wu
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yongxin Li
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi’an, China
| | - Wen Wang
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi’an, China
| | - Shunping He
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Chenguang Feng
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi’an, China
| | - Haibin Zhang
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
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28
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Miller PW, Dunkel J. Gait-optimized locomotion of wave-driven soft sheets. SOFT MATTER 2020; 16:3991-3999. [PMID: 32255142 DOI: 10.1039/c9sm02103e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Inspired by the robust locomotion of limbless animals in a range of environments, the development of soft robots capable of moving by localized swelling, bending, and other forms of differential growth has become a target for soft matter research over the last decade. Engineered soft robots exhibit a wide range of morphologies, but theoretical investigations of soft robot locomotion have largely been limited to slender bodied or one-dimensional examples. Here, we demonstrate design principles regarding the locomotion of two-dimensional soft materials driven by morphoelastic waves along a dry substrate. Focusing on the essential common aspects of many natural and man-made soft actuators, a continuum model is developed which links the deformation of a thin elastic sheet to surface-bound excitation waves. Through a combination of analytic and numerical methods, we investigate the relationship between induced active stress and self-propulsion performance of self-propelling sheets driven by FitzHugh-Nagumo type chemical waves. Examining the role of both sheet geometry and terrain geography on locomotion, our results can provide guidance for the design of more efficient soft crawling devices.
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Affiliation(s)
- Pearson W Miller
- Department of Mathematics, 77 Massachusetts Avenue, Cambridge, MA, USA.
| | - Jörn Dunkel
- Department of Mathematics, 77 Massachusetts Avenue, Cambridge, MA, USA.
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29
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Yang Z, Zhang L, Hu J, Wang J, Bao Z, Wang S. The evo-devo of molluscs: Insights from a genomic perspective. Evol Dev 2020; 22:409-424. [PMID: 32291964 DOI: 10.1111/ede.12336] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Molluscs represent one of ancient and evolutionarily most successful groups of marine invertebrates, with a tremendous diversity of morphology, behavior, and lifestyle. Molluscs are excellent subjects for evo-devo studies; however, understanding of the evo-devo of molluscs has been largely hampered by incomplete fossil records and limited molecular data. Recent advancement of genomics and other technologies has greatly fueled the molluscan "evo-devo" field, and decoding of several molluscan genomes provides unprecedented insights into molluscan biology and evolution. Here, we review the recent progress of molluscan genome sequencing as well as novel insights gained from their genomes, by emphasizing how molluscan genomics enhances our understanding of the evo-devo of molluscs.
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Affiliation(s)
- Zhihui Yang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Lingling Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jingjie Hu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Jing Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Zhenmin Bao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Pilot Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Shi Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,The Sars-Fang Centre, Ocean University of China, Qingdao, China
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Mikalsen SO, Tausen M, Í Kongsstovu S. Phylogeny of teleost connexins reveals highly inconsistent intra- and interspecies use of nomenclature and misassemblies in recent teleost chromosome assemblies. BMC Genomics 2020; 21:223. [PMID: 32160866 PMCID: PMC7066803 DOI: 10.1186/s12864-020-6620-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 02/25/2020] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Based on an initial collecting of database sequences from the gap junction protein gene family (also called connexin genes) in a few teleosts, the naming of these sequences appeared variable. The reasons could be (i) that the structure in this family is variable across teleosts, or (ii) unfortunate naming. Rather clear rules for the naming of genes in fish and mammals have been outlined by nomenclature committees, including the naming of orthologous and ohnologous genes. We therefore analyzed the connexin gene family in teleosts in more detail. We covered the range of divergence times in teleosts (eel, Atlantic herring, zebrafish, Atlantic cod, three-spined stickleback, Japanese pufferfish and spotted pufferfish; listed from early divergence to late divergence). RESULTS The gene family pattern of connexin genes is similar across the analyzed teleosts. However, (i) several nomenclature systems are used, (ii) specific orthologous groups contain genes that are named differently in different species, (iii) several distinct genes have the same name in a species, and (iv) some genes have incorrect names. The latter includes a human connexin pseudogene, claimed as GJA4P, but which in reality is Cx39.2P (a delta subfamily gene often called GJD2like). We point out the ohnologous pairs of genes in teleosts, and we suggest a more consistent nomenclature following the outlined rules from the nomenclature committees. We further show that connexin sequences can indicate some errors in two high-quality chromosome assemblies that became available very recently. CONCLUSIONS Minimal consistency exists in the present practice of naming teleost connexin genes. A consistent and unified nomenclature would be an advantage for future automatic annotations and would make various types of subsequent genetic analyses easier. Additionally, roughly 5% of the connexin sequences point out misassemblies in the new high-quality chromosome assemblies from herring and cod.
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Affiliation(s)
- Svein-Ole Mikalsen
- Faculty of Science and Technology, University of the Faroe Islands, Vestara Bryggja 15, FO-100, Tórshavn, Faroe Islands.
| | - Marni Tausen
- Faculty of Science and Technology, University of the Faroe Islands, Vestara Bryggja 15, FO-100, Tórshavn, Faroe Islands
- Present affiliation: Bioinformatics Research Centre, Aarhus University, C. F. Møllers Allé 8, 8000, Aarhus C, Denmark
| | - Sunnvør Í Kongsstovu
- Faculty of Science and Technology, University of the Faroe Islands, Vestara Bryggja 15, FO-100, Tórshavn, Faroe Islands
- Amplexa Genetics A/S, Hoyvíksvegur 51, FO-100, Tórshavn, Faroe Islands
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Ganley JG, Derbyshire ER. Linking Genes to Molecules in Eukaryotic Sources: An Endeavor to Expand Our Biosynthetic Repertoire. Molecules 2020; 25:E625. [PMID: 32023950 PMCID: PMC7036892 DOI: 10.3390/molecules25030625] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 01/23/2020] [Accepted: 01/30/2020] [Indexed: 02/06/2023] Open
Abstract
The discovery of natural products continues to interest chemists and biologists for their utility in medicine as well as facilitating our understanding of signaling, pathogenesis, and evolution. Despite an attenuation in the discovery rate of new molecules, the current genomics and transcriptomics revolution has illuminated the untapped biosynthetic potential of many diverse organisms. Today, natural product discovery can be driven by biosynthetic gene cluster (BGC) analysis, which is capable of predicting enzymes that catalyze novel reactions and organisms that synthesize new chemical structures. This approach has been particularly effective in mining bacterial and fungal genomes where it has facilitated the discovery of new molecules, increased the understanding of metabolite assembly, and in some instances uncovered enzymes with intriguing synthetic utility. While relatively less is known about the biosynthetic potential of non-fungal eukaryotes, there is compelling evidence to suggest many encode biosynthetic enzymes that produce molecules with unique bioactivities. In this review, we highlight how the advances in genomics and transcriptomics have aided natural product discovery in sources from eukaryotic lineages. We summarize work that has successfully connected genes to previously identified molecules and how advancing these techniques can lead to genetics-guided discovery of novel chemical structures and reactions distributed throughout the tree of life. Ultimately, we discuss the advantage of increasing the known biosynthetic space to ease access to complex natural and non-natural small molecules.
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Affiliation(s)
- Jack G Ganley
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC 27708-0346, USA
| | - Emily R Derbyshire
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC 27708-0346, USA
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, 213 Research Drive, Durham, NC 27710, USA
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Wang X, Xu W, Wei L, Zhu C, He C, Song H, Cai Z, Yu W, Jiang Q, Li L, Wang K, Feng C. Nanopore Sequencing and De Novo Assembly of a Black-Shelled Pacific Oyster ( Crassostrea gigas) Genome. Front Genet 2019; 10:1211. [PMID: 31824581 PMCID: PMC6884003 DOI: 10.3389/fgene.2019.01211] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Accepted: 11/04/2019] [Indexed: 12/21/2022] Open
Abstract
The Pacific oyster, Crassostrea gigas, belongs to one of the most species-rich phyla and provides important ecological and economical services. Here we present a genome assembly for a variety of this species, black-shelled Pacific oyster, using a combination of 61.8 Gb Nanopore long reads and 105.6 Gb raw BGI-seq short reads. The genome assembly comprised 3,676 contigs, with a total length of 587 Mb and a contig N50 of 581 kb. Annotation of the genome assembly identified 283 Mb (48.32%) of repetitive sequences and a total of 26,811 protein-coding genes. A long-term transposable element active, accompanied by recent expansion (1 million years ago), was detected in this genome. The divergence between black-shelled and the previous published Pacific oysters was estimated at about 2.2 million years ago, which implies that species C. gigas had great intraspecific genetic variations. Moreover, we identified 148/188 specifically expanded/contracted gene families in this genome. We believe this genome assembly will be a valuable resource for understanding the genetic breeding, conservation, and evolution of oysters and bivalves.
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Affiliation(s)
- Xiaotong Wang
- School of Agriculture, Ludong University, Yantai, China
| | - Wenjie Xu
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi’an, China
| | - Lei Wei
- School of Agriculture, Ludong University, Yantai, China
| | - Chenglong Zhu
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi’an, China
| | - Cheng He
- School of Agriculture, Ludong University, Yantai, China
| | - Hongce Song
- School of Agriculture, Ludong University, Yantai, China
| | - Zhongqiang Cai
- Changdao Enhancement and Experiment Station, Chinese Academy of Fishery Sciences, Changdao, China
| | - Wenchao Yu
- School of Agriculture, Ludong University, Yantai, China
| | - Qiuyun Jiang
- School of Agriculture, Ludong University, Yantai, China
| | - Lingling Li
- School of Agriculture, Ludong University, Yantai, China
| | - Kun Wang
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi’an, China
| | - Chenguang Feng
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi’an, China
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