1
|
Villarreal F, Burguener GF, Sosa EJ, Stocchi N, Somoza GM, Turjanski AG, Blanco A, Viñas J, Mechaly AS. Genome sequencing and analysis of black flounder (Paralichthys orbignyanus) reveals new insights into Pleuronectiformes genomic size and structure. BMC Genomics 2024; 25:297. [PMID: 38509481 PMCID: PMC10956332 DOI: 10.1186/s12864-024-10081-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: 07/31/2023] [Accepted: 02/02/2024] [Indexed: 03/22/2024] Open
Abstract
Black flounder (Paralichthys orbignyanus, Pleuronectiformes) is a commercially significant marine fish with promising aquaculture potential in Argentina. Despite extensive studies on Black flounder aquaculture, its limited genetic information available hampers the crucial role genetics plays in the development of this activity. In this study, we first employed Illumina sequencing technology to sequence the entire genome of Black flounder. Utilizing two independent libraries-one from a female and another from a male-with 150 bp paired-end reads, a mean insert length of 350 bp, and over 35 X-fold coverage, we achieved assemblies resulting in a genome size of ~ 538 Mbp. Analysis of the assemblies revealed that more than 98% of the core genes were present, with more than 78% of them having more than 50% coverage. This indicates a somehow complete and accurate genome at the coding sequence level. This genome contains 25,231 protein-coding genes, 445 tRNAs, 3 rRNAs, and more than 1,500 non-coding RNAs of other types. Black flounder, along with pufferfishes, seahorses, pipefishes, and anabantid fish, displays a smaller genome compared to most other teleost groups. In vertebrates, the number of transposable elements (TEs) is often correlated with genome size. However, it remains unclear whether the sizes of introns and exons also play a role in determining genome size. Hence, to elucidate the potential factors contributing to this reduced genome size, we conducted a comparative genomic analysis between Black flounder and other teleost orders to determine if the small genomic size could be explained by repetitive elements or gene features, including the whole genome genes and introns sizes. We show that the smaller genome size of flounders can be attributed to several factors, including changes in the number of repetitive elements, and decreased gene size, particularly due to lower amount of very large and small introns. Thus, these components appear to be involved in the genome reduction in Black flounder. Despite these insights, the full implications and potential benefits of genome reduction in Black flounder for reproduction and aquaculture remain incompletely understood, necessitating further research.
Collapse
Affiliation(s)
- Fernando Villarreal
- Facultad de Ciencias Exactas y Naturales, Instituto de Investigaciones Biológicas (IIB-CONICET-UNMdP), Universidad Nacional de Mar del Plata, Mar del Plata, Argentina
| | - Germán F Burguener
- Plataforma de Bioinformática Argentina, Facultad de Ciencias Exactas y Naturales, Instituto de Cálculo, UBA, Pabellón 2, Ciudad Universitaria, Buenos Aires, Argentina
| | - Ezequiel J Sosa
- Plataforma de Bioinformática Argentina, Facultad de Ciencias Exactas y Naturales, Instituto de Cálculo, UBA, Pabellón 2, Ciudad Universitaria, Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Ciudad Universitaria, Buenos Aires, Argentina
| | - Nicolas Stocchi
- Facultad de Ciencias Exactas y Naturales, Instituto de Investigaciones Biológicas (IIB-CONICET-UNMdP), Universidad Nacional de Mar del Plata, Mar del Plata, Argentina
| | - Gustavo M Somoza
- Instituto Tecnológico de Chascomús (CONICET-UNSAM), Chascomús, Buenos Aires, Argentina
- Escuela de Bio y Nanotecnologías (UNSAM), Buenos Aires, Argentina
| | - Adrián G Turjanski
- Plataforma de Bioinformática Argentina, Facultad de Ciencias Exactas y Naturales, Instituto de Cálculo, UBA, Pabellón 2, Ciudad Universitaria, Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Ciudad Universitaria, Buenos Aires, Argentina
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Andrés Blanco
- Facultade de Veterinaria, Universidade de Santiago de Compostela, Santiago de Compostela, Lugo, Spain
- Departamento de Zoología, Genética y Antropología Física, Facultad de Veterinaria, Campus Terra, Universidade de Santiago de Compostela, Lugo, Spain
| | - Jordi Viñas
- Laboratori d'Ictiologia Genètica, Departament de Biologia, Universitat de Girona, Maria Aurèlia Campmany, 40, Girona, Spain
| | - Alejandro S Mechaly
- Instituto de Investigaciones en Biodiversidad y Biotecnología (INBIOTEC-CONICET), Mar del Plata, Argentina.
- Fundación Para Investigaciones Biológicas Aplicadas (FIBA), Mar del Plata, Argentina.
| |
Collapse
|
2
|
Girardini KN, Olthof AM, Kanadia RN. Introns: the "dark matter" of the eukaryotic genome. Front Genet 2023; 14:1150212. [PMID: 37260773 PMCID: PMC10228655 DOI: 10.3389/fgene.2023.1150212] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 04/28/2023] [Indexed: 06/02/2023] Open
Abstract
The emergence of introns was a significant evolutionary leap that is a major distinguishing feature between prokaryotic and eukaryotic genomes. While historically introns were regarded merely as the sequences that are removed to produce spliced transcripts encoding functional products, increasingly data suggests that introns play important roles in the regulation of gene expression. Here, we use an intron-centric lens to review the role of introns in eukaryotic gene expression. First, we focus on intron architecture and how it may influence mechanisms of splicing. Second, we focus on the implications of spliceosomal snRNAs and their variants on intron splicing. Finally, we discuss how the presence of introns and the need to splice them influences transcription regulation. Despite the abundance of introns in the eukaryotic genome and their emerging role regulating gene expression, a lot remains unexplored. Therefore, here we refer to introns as the "dark matter" of the eukaryotic genome and discuss some of the outstanding questions in the field.
Collapse
Affiliation(s)
- Kaitlin N. Girardini
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT, United States
| | - Anouk M. Olthof
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT, United States
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Rahul N. Kanadia
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT, United States
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, United States
| |
Collapse
|
3
|
Fanelli E, Troccoli A, Tarasco E, De Luca F. Molecular Characterization and Functional Analysis of the Hb-hsp90-1 Gene in Relation to Temperature Changes in Heterorhabditis bacteriophora. Front Physiol 2021; 12:615653. [PMID: 33732162 PMCID: PMC7959791 DOI: 10.3389/fphys.2021.615653] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 01/26/2021] [Indexed: 12/17/2022] Open
Abstract
Understanding how entomopathogenic nematodes respond to temperature changes and have adapted to the local environment is crucial to improve their potential as biocontrol agents. In order to improve understanding of Heterorhabditis bacteriophora's potential adaptability to future climate changes, full-length cDNA and the corresponding gene of heat shock protein 90 (Hsp90) were isolated and fully characterized. The reproductive potential of the Apulian strain of H. bacteriophora increased when the temperature rose from 23 to 30°C, but no reproduction was found at 12°C. Expression analyses revealed that Hb-hsp90-1 was differentially expressed in Infective Juveniles (IJs) and adults (hermaphrodites, females and males). Up-regulation of Hb-hsp90-1 was higher during the recovery process in Galleria mellonella larvae than adults, thus confirming the protective role of Hb-hsp90-1 in coping with the host environment. Silencing of Hb-hsp90-1 resulted in a significant reduction (76%) in the expression level. Silenced IJs took longer than untreated nematodes to infect G. mellonella, showing that Hb-hsp90-1 could be also involved in chemosensation. Furthermore, the number of adults and IJs recovered from G. mellonella infected with silenced nematodes and incubated at 30°C was higher than that obtained from G. mellonella infected with untreated nematodes. These data confirm the crucial role of Hb-hsp90-1 allowing acclimation to increased temperatures and modulation of the recovery process.
Collapse
Affiliation(s)
- Elena Fanelli
- Institute for Sustainable Plant Protection-CNR, Bari, Italy
| | | | - Eustachio Tarasco
- Institute for Sustainable Plant Protection-CNR, Bari, Italy
- Section of Entomology and Zoology, Department of Soil, Plant and Food Sciences, University of Bari “A. Moro”, Bari, Italy
| | | |
Collapse
|
4
|
Zhang W, Yu H, Lv Y, Bushley KE, Wickham JD, Gao S, Hu S, Zhao L, Sun J. Gene family expansion of pinewood nematode to detoxify its host defence chemicals. Mol Ecol 2020; 29:940-955. [DOI: 10.1111/mec.15378] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 02/02/2020] [Accepted: 02/02/2020] [Indexed: 02/07/2023]
Affiliation(s)
- Wei Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents Institute of Zoology Chinese Academy of Sciences Beijing China
- Laboratory of Forest Pathogen Integrated Biology Research Institute of Forestry New Technology Chinese Academy of Forestry Beijing China
| | - Haiying Yu
- State Key Laboratory of Microbial Resources Institute of Microbiology Chinese Academy of Sciences Beijing China
| | - Yunxue Lv
- State Key Laboratory of Integrated Management of Pest Insects and Rodents Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Kathryn E. Bushley
- Department of Plant and Microbial Biology University of Minnesota Twin Cities Saint Paul MN USA
| | - Jacob D. Wickham
- State Key Laboratory of Integrated Management of Pest Insects and Rodents Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Shenghan Gao
- State Key Laboratory of Microbial Resources Institute of Microbiology Chinese Academy of Sciences Beijing China
| | - Songnian Hu
- State Key Laboratory of Microbial Resources Institute of Microbiology Chinese Academy of Sciences Beijing China
| | - Lilin Zhao
- State Key Laboratory of Integrated Management of Pest Insects and Rodents Institute of Zoology Chinese Academy of Sciences Beijing China
- CAS Center for Excellence in Biotic Interactions University of Chinese Academy of Sciences Beijing China
| | - Jianghua Sun
- State Key Laboratory of Integrated Management of Pest Insects and Rodents Institute of Zoology Chinese Academy of Sciences Beijing China
- CAS Center for Excellence in Biotic Interactions University of Chinese Academy of Sciences Beijing China
| |
Collapse
|
5
|
Fan H, Wang L, Wen H, Wang K, Qi X, Li J, He F, Li Y. Genome-wide identification and characterization of toll-like receptor genes in spotted sea bass (Lateolabrax maculatus) and their involvement in the host immune response to Vibrio harveyi infection. FISH & SHELLFISH IMMUNOLOGY 2019; 92:782-791. [PMID: 31288100 DOI: 10.1016/j.fsi.2019.07.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 07/04/2019] [Accepted: 07/05/2019] [Indexed: 06/09/2023]
Abstract
Toll-like receptor (TLR) genes are the earliest reported pathogen recognition receptors (PRRs) and have been extensively studied. These genes play pivotal roles in the innate immune defense against pathogen invasion. In this study, a total of 16 tlr genes were identified and characterized in spotted sea bass (Lateolabrax maculatus). The tlr genes of spotted sea bass were classified into five subfamilies (tlr1-subfamily, tlr3-subfamily, tlr5-subfamily, tlr7-subfamily, and tlr11-subfamily) according to the phylogenetic analysis, and their annotations were confirmed by a syntenic analysis. The protein domain analysis indicated that most tlr genes had the following three major TLR protein domains: a leucine-rich repeat (LRR) domain, a transmembrane region (TM) and a Toll/interleukin-1 receptor (TIR) domain. The tlr genes in spotted sea bass were distributed in 11 of 24 chromosomes. The mRNA expression levels of 16 tlr genes in response to Vibrio harveyi infection were quantified in the head kidney. Most genes were downregulated following V. harveyi infection, while only 5 tlr genes, including tlr1-1, tlr1-2, tlr2-2, tlr5, and tlr7, were significantly upregulated. Collectively, these results help elucidate the crucial roles of tlr genes in the immune response of spotted sea bass and may supply valuable genomic resources for future studies investigating fish disease management.
Collapse
Affiliation(s)
- Hongying Fan
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, 266003, China
| | - Lingyu Wang
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, 266003, China
| | - Haishen Wen
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, 266003, China
| | - Kuiqin Wang
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, 266003, China
| | - Xin Qi
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, 266003, China
| | - Jifang Li
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, 266003, China
| | - Feng He
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, 266003, China
| | - Yun Li
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, 266003, China.
| |
Collapse
|
6
|
Vasconcelos ACN, Streit DP, Octavera A, Miwa M, Kabeya N, Yoshizaki G. The germ cell marker dead end reveals alternatively spliced transcripts with dissimilar expression. Sci Rep 2019; 9:2407. [PMID: 30787383 PMCID: PMC6382762 DOI: 10.1038/s41598-019-39101-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 01/17/2019] [Indexed: 01/15/2023] Open
Abstract
Since the late 19th century, the Amazon species Colossoma macropomum (tambaqui) has been exploited commercially and the climate change has contributed to decline in tambaqui numbers. Although germ cell cryopreservation and transplantation can help preserve the species’ genetic resources semipermanently, its germ cell behavior has not been analyzed to date. In this study, we isolated the tambaqui’s dead end gene (dnd) homolog (tdnd) and used it as a molecular marker for germ cells to obtain basic information essential for transplantation. The amino acid sequence showed 98% similarity and 53% identity with the zebrafish dnd. Phylogenetic analysis and the presence of consensus motifs known for dnd revealed that tdnd encodes the dnd ortholog and its transcript is detectable only in the testes and ovaries, showing a strong positive signal in oocytes and spermatogonia. The tambaqui possesses, at least, three different transcripts of tdnd which show dissimilar expression profile in undifferentiated and sexually mature animals, suggesting that they play distinct roles in germline development and they may influence the choice of donors for the cell transplantation study.
Collapse
Affiliation(s)
- Ana Carina Nogueira Vasconcelos
- Tokyo University of Marine Science and Technology, Department of Marine Biosciences, Tokyo, 108-8477, Japan. .,Johns Hopkins University, Institute for Nanobiotechnology, Whiting School of Engineering, Baltimore, Maryland, 21218, USA.
| | - Danilo Pedro Streit
- Federal University of Rio Grande do Sul, Department of Animal Science, Porto Alegre, 91540-000, Brazil
| | - Anna Octavera
- Tokyo University of Marine Science and Technology, Department of Marine Biosciences, Tokyo, 108-8477, Japan
| | - Misako Miwa
- Tokyo University of Marine Science and Technology, Department of Marine Biosciences, Tokyo, 108-8477, Japan
| | - Naoki Kabeya
- The University of Tokyo, Department of Aquatic Bioscience, Tokyo, 113-8654, Japan
| | - Goro Yoshizaki
- Tokyo University of Marine Science and Technology, Department of Marine Biosciences, Tokyo, 108-8477, Japan
| |
Collapse
|