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Grover A, Sharma P, Sharma R, Sinha R. Ultrastructural and molecular approach as a tool for taxonomic identification of aquatic macroinvertebrates: A review. Heliyon 2022; 8:e12236. [DOI: 10.1016/j.heliyon.2022.e12236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 10/16/2022] [Accepted: 12/01/2022] [Indexed: 12/14/2022] Open
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Curzon AY, Shirak A, Benet-Perlberg A, Naor A, Low-Tanne SI, Sharkawi H, Ron M, Seroussi E. Absence of Figla-like Gene Is Concordant with Femaleness in Cichlids Harboring the LG1 Sex-Determination System. Int J Mol Sci 2022; 23:ijms23147636. [PMID: 35886982 PMCID: PMC9316214 DOI: 10.3390/ijms23147636] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/05/2022] [Accepted: 07/08/2022] [Indexed: 02/04/2023] Open
Abstract
Oreochromis niloticus has been used as a reference genome for studies of tilapia sex determination (SD) revealing segregating genetic loci on linkage groups (LGs) 1, 3, and 23. The master key regulator genes (MKR) underlying the SD regions on LGs 3 and 23 have been already found. To identify the MKR in fish that segregate for the LG1 XX/XY SD-system, we applied short variant discovery within the sequence reads of the genomic libraries of the Amherst hybrid stock, Coptodon zillii and Sarotherodon galilaeus, which were aligned to a 3-Mbp-region of the O. aureus genome. We obtained 66,372 variants of which six were concordant with the XX/XY model of SD and were conserved across these species, disclosing the male specific figla-like gene. We further validated this observation in O. mossambicus and in the Chitralada hybrid stock. Genome alignment of the 1252-bp transcript showed that the figla-like gene’s size was 2664 bp, and that its three exons were capable of encoding 99 amino acids including a 45-amino-acid basic helix–loop–helix domain that is typical of the ovary development regulator—factor-in-the-germline-alpha (FIGLA). In Amherst gonads, the figla-like gene was exclusively expressed in testes. Thus, the figla-like genomic presence determines male fate by interrupting the female developmental program. This indicates that the figla-like gene is the long-sought SD MKR on LG1.
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Affiliation(s)
- Arie Yehuda Curzon
- Institute of Animal Science, Agricultural Research Organization, Rishon LeTsiyon 75288, Israel; (A.Y.C.); (A.S.); (M.R.)
- Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Andrey Shirak
- Institute of Animal Science, Agricultural Research Organization, Rishon LeTsiyon 75288, Israel; (A.Y.C.); (A.S.); (M.R.)
| | - Ayana Benet-Perlberg
- Dor Research Station, Division of Fishery and Aquaculture, Hof HaCarmel 30820, Israel; (A.B.-P.); (A.N.); (S.I.L.-T.); (H.S.)
| | - Alon Naor
- Dor Research Station, Division of Fishery and Aquaculture, Hof HaCarmel 30820, Israel; (A.B.-P.); (A.N.); (S.I.L.-T.); (H.S.)
| | - Shay Israel Low-Tanne
- Dor Research Station, Division of Fishery and Aquaculture, Hof HaCarmel 30820, Israel; (A.B.-P.); (A.N.); (S.I.L.-T.); (H.S.)
| | - Haled Sharkawi
- Dor Research Station, Division of Fishery and Aquaculture, Hof HaCarmel 30820, Israel; (A.B.-P.); (A.N.); (S.I.L.-T.); (H.S.)
| | - Micha Ron
- Institute of Animal Science, Agricultural Research Organization, Rishon LeTsiyon 75288, Israel; (A.Y.C.); (A.S.); (M.R.)
| | - Eyal Seroussi
- Institute of Animal Science, Agricultural Research Organization, Rishon LeTsiyon 75288, Israel; (A.Y.C.); (A.S.); (M.R.)
- Correspondence:
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Windsor AM, Moore MK, Warner KA, Stadig SR, Deeds JR. Evaluation of variation within the barcode region of Cytochrome c Oxidase I (COI) for the detection of commercial Callinectes sapidus Rathbun, 1896 (blue crab) products of non-US origin. PeerJ 2019; 7:e7827. [PMID: 31720100 DOI: 10.7717/peerj.7827] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 09/03/2019] [Indexed: 11/20/2022] Open
Abstract
Callinectes sapidus Rathbun, 1896 is a western Atlantic species with a disjointed natural geographic range from Massachusetts, USA to Venezuela (distribution area 1) and from Alagoas, Brazil to northern Argentina (distribution area 2). It is the only species of portunid crab commercially harvested in the continental United States but is also imported into the US from several Latin American countries, Venezuela and Mexico in particular. In the United States, crab products labeled as "blue crab" and "Product of the USA" may not legally contain other species of crab or C. sapidus not harvested in the United States. The present study documents nucleotide variation within the barcode region of cytochrome c oxidase I (COI) in 417 reference specimens of C. sapidus collected from throughout its natural range. The goal of this study is to determine if this variation can be utilized to detect mislabeled C. sapidus products sold in interstate commerce by comparing genetic signatures in reference specimens to those observed in commercial crabmeat labeled as "Product of the USA" and "Product of Venezuela." In reference specimens, we observed high levels of genetic variation in the barcode region. However, three lineages were consistently observed with significant pairwise F st values between the lineages. Lineage 1 was observed throughout the natural geographic range but predominated in the continental US and was the only lineage observed in the major crabmeat-producing states (MD, LA, VA, NC). Lineage 2 primarily occurred in the Caribbean region of distribution area 1 but was also infrequently encountered in the South Atlantic Bight region of the US coast. Finally, Lineage 3 was only observed in Brazilian waters and had the lowest haplotype and nucleotide diversity values. Lineages 1 and 2 were separated by a mean pairwise distance (p-distance) of 3.15%, whereas Lineage 3 had a mean p-distance of 2.55% and 1.35% to Lineages 1 and 2, respectively. Within lineage mean p-distances were 0.45%, 0.19%, and 0.07% for Lineages 1, 2, and 3, respectively. Among all vouchered reference specimens collected from the continental United States, Mexico, Puerto Rico, and Venezuela, we identified 22 phylogenetically informative sites that drive observed lineage divergences. Haplotypes identified from barcode COI sequences from commercial C. sapidus products labeled as originating from the US all aligned with haplotypes from Lineage 1 reference specimens and haplotypes from commercial products labeled as originating from Venezuela all aligned with Lineage 2, suggesting that these lineages may be useful for indicating whether products originate from the continental US or are imported when package labeling is in question.
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Affiliation(s)
- Amanda M Windsor
- Office of Regulatory Science, United States Food and Drug Administration, College Park, MD, USA
| | - M Katherine Moore
- Conservation Biology Division, Forensic Laboratory, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Charleston, SC, USA
| | | | - Sarah R Stadig
- Office of Regulatory Science, United States Food and Drug Administration, College Park, MD, USA
| | - Jonathan R Deeds
- Office of Regulatory Science, United States Food and Drug Administration, College Park, MD, USA
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Sanna D, Lai T, Cossu P, Scarpa F, Dedola GL, Cristo B, Francalacci P, Curini-Galletti M, Mura L, Fois N, Maltagliati F, Casu M. Cytochrome c oxidase subunit I variability in Ruditapes decussatus (Veneridae) from the western Mediterranean. EUROPEAN ZOOLOGICAL JOURNAL 2017. [DOI: 10.1080/24750263.2017.1395914] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- D. Sanna
- Dipartimento di Scienze della Natura e del Territorio – Sezione di Zoologia, Archeozoologia e Genetica, Università di Sassari , Sassari (SS), Italy
| | - T. Lai
- Dipartimento di Scienze della Natura e del Territorio – Sezione di Zoologia, Archeozoologia e Genetica, Università di Sassari , Sassari (SS), Italy
| | - P. Cossu
- Dipartimento di Scienze della Natura e del Territorio – Sezione di Zoologia, Archeozoologia e Genetica, Università di Sassari , Sassari (SS), Italy
| | - F. Scarpa
- Dipartimento di Scienze della Natura e del Territorio – Sezione di Zoologia, Archeozoologia e Genetica, Università di Sassari , Sassari (SS), Italy
| | - G. L. Dedola
- Dipartimento di Scienze della Natura e del Territorio – Sezione di Zoologia, Archeozoologia e Genetica, Università di Sassari , Sassari (SS), Italy
| | - B. Cristo
- Dipartimento di Scienze della Natura e del Territorio – Sezione di Zoologia, Archeozoologia e Genetica, Università di Sassari , Sassari (SS), Italy
| | - P. Francalacci
- Dipartimento di Scienze della Natura e del Territorio – Sezione di Zoologia, Archeozoologia e Genetica, Università di Sassari , Sassari (SS), Italy
| | - M. Curini-Galletti
- Dipartimento di Scienze della Natura e del Territorio – Sezione di Zoologia, Archeozoologia e Genetica, Università di Sassari , Sassari (SS), Italy
| | - L. Mura
- Dipartimento per la Ricerca nelle Produzioni Animali, Agris Sardegna, Agenzia per la Ricerca in Agricoltura , Olmedo (SS), Italy
| | - N. Fois
- Dipartimento per la Ricerca nelle Produzioni Animali, Agris Sardegna, Agenzia per la Ricerca in Agricoltura , Olmedo (SS), Italy
| | - F. Maltagliati
- Dipartimento di Biologia, Università di Pisa , Pisa (PI), Italy
| | - M. Casu
- Dipartimento di Scienze della Natura e del Territorio – Sezione di Zoologia, Archeozoologia e Genetica, Università di Sassari , Sassari (SS), Italy
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De Luca D, Catanese G, Procaccini G, Fiorito G. Octopus vulgaris (Cuvier, 1797) in the Mediterranean Sea: Genetic Diversity and Population Structure. PLoS One 2016; 11:e0149496. [PMID: 26881847 PMCID: PMC4755602 DOI: 10.1371/journal.pone.0149496] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2015] [Accepted: 02/02/2016] [Indexed: 11/22/2022] Open
Abstract
The common octopus, Octopus vulgaris Cuvier 1797, is a largely exploited cephalopod species in the Mediterranean Sea and the Atlantic Ocean, as well as along the coasts of Africa, Brazil and Japan, where its taxonomic identity is still debated. The assessment of its genetic structure is a pressing need to correctly manage the resource and to avoid overfishing and collapsing of local stocks. Here we analysed genetic variation and population structure of O. vulgaris using thirteen microsatellite loci in seven sampling localities from the Mediterranean Sea and one from the Atlantic Ocean. We also used a DNA barcoding approach by COI gene fragment to understand the phylogenetic relationships among the specimens here investigated and the ones whose sequences are available in literature. Our results reveal high levels of allelic richness and moderate heterozygosity in all samples investigated, and a pronounced differentiation of the Atlantic and Sicilian specimens. This latter aspect seems to support the isolation of the biota within the Strait of Messina. A certain degree of differentiation was detected among the other geographic samples within the Mediterranean Sea, which is more compatible with an island model than isolation by distance. The occurrence of null alleles affected more genetic diversity indices than population structure estimations. This study provides new insights about the genetic diversity and structure of O. vulgaris in the area of interest, which can be used as guidelines for a fisheries management perspective.
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Affiliation(s)
- Daniele De Luca
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy
- * E-mail:
| | - Gaetano Catanese
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy
| | | | - Graziano Fiorito
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy
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Carvalho-Batista A, Negri M, Pileggi LG, Castilho AL, Costa RC, Mantelatto FL. Inferring population connectivity across the range of distribution of the stiletto shrimp Artemesialonginaris Spence Bate, 1888 (Decapoda, Penaeidae) from DNA barcoding: implications for fishery management. Zookeys 2014:271-88. [PMID: 25561842 PMCID: PMC4283376 DOI: 10.3897/zookeys.457.6569] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Accepted: 03/21/2014] [Indexed: 11/12/2022] Open
Abstract
Artemesialonginaris is a marine shrimp endemic to the southwestern Atlantic and distributed from Atafona, Rio de Janeiro (Brazil) to Rawson, Chubut (Argentina). In recent years, this species has become an important target of the commercial fishery as a consequence of the decline in the fishery of more traditional and profitable marine shrimps. In addition, phenotypic variations have been documented in populations along its distribution. Therefore, investigations on the genetics of the fishing stocks are necessary for the development of sustainable management strategies and for understanding the possible sources of these variations. The mitochondrial gene Cytochrome Oxidase I (COI) was used to search for evidence of genetic structure among the populations of Artemesialonginaris and to analyze the phylogenetic relationships among them. A total of 60 specimens were collected from seven different localities, covering its geographical range. The final alignment showed 53 haplotypes (48 individuals and 5 shared), with no biogeographical pattern. The low genetic divergence found, with a non-significant FST value, also suggests the absence of population structure for this gene. These findings indicate a continuous gene flow among the populations analyzed, suggesting that the phenotypic variation is a consequence of different environmental conditions among the localities.
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Affiliation(s)
- Abner Carvalho-Batista
- Laboratory of Biology of Marine and Fresh Water Shrimps, Faculty of Science, Department of Biological Sciences, São Paulo State University (UNESP), Bauru, São Paulo, Brazil
| | - Mariana Negri
- Laboratory of Bioecology and Crustacean Systematics, Faculty of Philosophy, Sciences and Letters at Ribeirão Preto (FFCLRP), University of São Paulo (USP), Postgraduate Program in Comparative Biology, Ribeirão Preto, São Paulo, Brazil
| | - Leonardo G Pileggi
- Laboratory of Bioecology and Crustacean Systematics, Faculty of Philosophy, Sciences and Letters at Ribeirão Preto (FFCLRP), University of São Paulo (USP), Postgraduate Program in Comparative Biology, Ribeirão Preto, São Paulo, Brazil
| | - Antonio L Castilho
- São Paulo State University (UNESP), Biosciences Institute of Botucatu, Zoology Department, Botucatu, Brazil
| | - Rogério C Costa
- Laboratory of Biology of Marine and Fresh Water Shrimps, Faculty of Science, Department of Biological Sciences, São Paulo State University (UNESP), Bauru, São Paulo, Brazil
| | - Fernando L Mantelatto
- Laboratory of Bioecology and Crustacean Systematics, Faculty of Philosophy, Sciences and Letters at Ribeirão Preto (FFCLRP), University of São Paulo (USP), Postgraduate Program in Comparative Biology, Ribeirão Preto, São Paulo, Brazil
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Niu D, Wang L, Sun F, Liu Z, Li J. Development of molecular resources for an intertidal clam, Sinonovacula constricta, using 454 transcriptome sequencing. PLoS One 2013; 8:e67456. [PMID: 23935831 PMCID: PMC3723811 DOI: 10.1371/journal.pone.0067456] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Accepted: 05/17/2013] [Indexed: 12/02/2022] Open
Abstract
Background The razor clam Sinonovacula constricta is a benthic intertidal bivalve species with important commercial value. Despite its economic importance, knowledge of its transcriptome is scarce. Next generation sequencing technologies offer rapid and efficient tools for generating large numbers of sequences, which can be used to characterize the transcriptome, to develop effective molecular markers and to identify genes associated with growth, a key breeding trait. Results Total RNA was isolated from the mantle, gill, liver, siphon, gonad and muscular foot tissues. High-throughput deep sequencing of S. constricta using 454 pyrosequencing technology yielded 859,313 high-quality reads with an average read length of 489 bp. Clustering and assembly of these reads produced 16,323 contigs and 131,346 singletons with average lengths of 1,376 bp and 458 bp, respectively. Based on transcriptome sequencing, 14,615 sequences had significant matches with known genes encoding 147,669 predicted proteins. Subsequently, previously unknown growth-related genes were identified. A total of 13,563 microsatellites (SSRs) and 13,634 high-confidence single nucleotide polymorphism loci (SNPs) were discovered, of which almost half were validated. Conclusion De novo sequencing of the razor clam S. constricta transcriptome on the 454 GS FLX platform generated a large number of ESTs. Candidate growth factors and a large number of SSRs and SNPs were identified. These results will impact genetic studies of S. constricta.
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Affiliation(s)
- Donghong Niu
- Key Laboratory of Freshwater Aquatic Genetic Resources Certificated by Ministry of Agriculture, Shanghai Ocean University, Shanghai, China
- Shanghai Engineering Research Center of Aquaculture, Shanghai, China
| | - Lie Wang
- Key Laboratory of Freshwater Aquatic Genetic Resources Certificated by Ministry of Agriculture, Shanghai Ocean University, Shanghai, China
- Shanghai Engineering Research Center of Aquaculture, Shanghai, China
| | - Fanyue Sun
- Department of Fisheries and Allied Aquacultures, Auburn University, Auburn, Alabama, United States of America
| | - Zhanjiang Liu
- Department of Fisheries and Allied Aquacultures, Auburn University, Auburn, Alabama, United States of America
| | - Jiale Li
- Key Laboratory of Freshwater Aquatic Genetic Resources Certificated by Ministry of Agriculture, Shanghai Ocean University, Shanghai, China
- Shanghai Engineering Research Center of Aquaculture, Shanghai, China
- * E-mail:
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