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Made available in DSpace on 2020-12-12T02:21:52Z (GMT). No. of bitstreams: 0 Previous issue date: 2020-11-01 European Regional Development Fund Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) The shortfin mako, Isurus oxyrinchus is an oceanic pelagic shark found worldwide in tropical and subtropical waters. However, the understanding of its biology at molecular level is still incipient. We sequenced the messenger RNA isolated from eye and liver tissues. De novo transcriptome yielded a total of 705,940 transcripts. A total of 3774 genes were differentially expressed (DEGs), with 1612 in the eye and 2162 in the liver. Most DEGs in the eye were related to structural and signaling functions, including nonocular and ocular opsin genes, whereas nine out of ten most overexpressed genes in the liver were related to tumor suppression, wound healing, and human diseases. Furthermore, DEGs findings provide insights on the monochromatic shark vision and a repertory of cancer-related genes, which may be insightful to elucidate shark resistance to cancer. Therefore, our results provide valuable sequence resources for future functional and population studies. Departamento de Ciências do Mar Instituto do Mar Universidade Federal de São Paulo – UNIFESP, Rua Carvalho de Mendonça, 144 Centro de Aquicultura da UNESP Universidade Estadual Paulista – UNESP, Via de Acesso Prof. Paulo Donato Castellane, s/n Instituto Português do Mar e da Atmosfera (IPMA I.P.), Av. 5 Outubro Centro de Ciências do Mar (CCMAR) Universidade do Algarve, Campus de Gambelas Laboratório de Biologia e Genética de Peixes Instituto de Biociências de Botucatu Universidade Estadual Paulista – UNESP CIIMAR/CIMAR Centro Interdisciplinar de Investigação Marinha e Ambiental Universidade do Porto, Av. General Norton de Matos, s/n Departmento de Biologia Faculdade de Ciências Universidade do Porto, Rua do Campo Alegre, s/n Centro de Aquicultura da UNESP Universidade Estadual Paulista – UNESP, Via de Acesso Prof. Paulo Donato Castellane, s/n Laboratório de Biologia e Genética de Peixes Instituto de Biociências de Botucatu Universidade Estadual Paulista – UNESP FAPESP: 2014/19740-7 FAPESP: 2017/02420-8 FAPESP: 2018/21319-9

Made available in DSpace on 2022-04-29T08:34:55Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-12-01 Comisión Nacional de Investigación Científica y Tecnológica Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Scarce genomic resources have limited the development of breeding programs for serrasalmid fish Colossoma macropomum (tambaqui) and Piaractus mesopotamicus (pacu), the key native freshwater fish species produced in South America. The main objectives of this study were to design a dense SNP array for this fish group and to validate its performance on farmed populations from several locations in South America. Using multiple approaches based on different populations of tambaqui and pacu, a final list of 29,575 and 29,612 putative SNPs was selected, respectively, to print an Axiom AFFYMETRIX (THERMOFISHER) SerraSNP array. After validation, 74.17% (n = 21,963) and 71.25% (n = 21,072) of SNPs were classified as polymorphic variants in pacu and tambaqui, respectively. Most of the SNPs segregated within each population ranging from 14,199 to 19,856 in pacu; and from 15,075 to 20,380 in tambaqui. Our results indicate high levels of genetic diversity and clustered samples according to their hatchery origin. The developed SerraSNP array represents a valuable genomic tool approaching in-depth genetic studies for these species. São Paulo State University (Unesp) Aquaculture Center of Unesp Facultad de Ciencias Veterinarias y Pecuarias Universidad de Chile Facultad de Zootecnia Universidad Nacional Agraria de la Selva Facultad de Ciencias Agrarias Universidad de Antioquia São Paulo State University (Unesp) Aquaculture Center of Unesp CNPq: 140740/2016–3 FAPESP: 2016/18294–9 FAPESP: 2016/21011–9 FAPESP: 2017/19717-3 CNPq: 311559/2018–2

Fish species exhibit substantial variation in the degree of genetic differentiation between sex chromosome pairs, and therefore offer the opportunity to study the full range of sex chromosome evolution. We used restriction-site associated DNA sequencing (RAD-seq) to study the sex chromosomes of Characidium gomesi, a species with conspicuous heteromorphic ZW/ZZ sex chromosomes. We screened 9863 single-nucleotide polymorphisms (SNPs), corresponding to ~1 marker/100 kb distributed across the genome for sex-linked variation. With this data set, we identified 26 female-specific RAD loci, putatively located on the W chromosome, as well as 148 sex-associated SNPs showing significant differentiation (average FST=0.144) between males and females, and therefore in regions of more recent divergence between the Z and W chromosomes. In addition, we detected 25 RAD loci showing extreme heterozygote deficiency in females but which were in Hardy–Weinberg equilibrium in males, consistent with degeneration of the W chromosome and therefore female hemizygosity. We validated seven female-specific and two sex-associated markers in a larger sample of C. gomesi, of which three localised to the W chromosome, thereby providing useful markers for sexing wild samples. Validated markers were evaluated in other populations and species of the genus Characidium, this exploration suggesting a rapid turnover of W-specific repetitive elements. Together, our analyses point to a complex origin for the sex chromosome of C. gomesi and highlight the utility of RAD-seq for studying the composition and evolution of sex chromosomes systems in wild populations.

Summary Salminus brasiliensis, a characin regionally named ‘dourado’ (meaning goldfish), is the biggest characid fish, this species is cited in a list of fishes that are vulnerable. The goal of the present work was to try to identify, through AFLP technique to convert them into single locus markers (SCARs), in order to improve the sex identification in S. brasiliensis. Between possible sex-specific AFLP markers in this study, one male-specific were isolated (Les1) and converted into a SCAR marker. Les1 marker was confirmed sex-specific in all samples tested. A sex-specific DNA marker applicable to fish would be very useful for elucidating sex determination mechanism in fish.

Made available in DSpace on 2018-11-26T17:48:18Z (GMT). No. of bitstreams: 0 Previous issue date: 2018-02-22 Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) PROPE/UNESP The pirapitinga, Piaractus brachypomus (Characiformes, Serrasalmidae), is a fish from the Amazon basin and is considered to be one of the main native species used in aquaculture production in South America. The objectives of this study were: (1) to perform liver transcriptome sequencing of pirapitinga through NGS and then validate a set of microsatellite markers for this species; and (2) to use polymorphic microsatellites for analysis of genetic variability in farmed stocks. The transcriptome sequencing was carried out through the Roche/454 technology, which resulted in 3,696 non-redundant contigs. Of this total, 2,568 contigs had similarity in the non-redundant (nr) protein database (Genbank) and 2,075 sequences were characterized in the categories of Gene Ontology (GO). After the validation process of 30 microsatellite loci, eight markers showed polymorphism. The analysis of these polymorphic markers in farmed stocks revealed that fish farms from North Brazil had a higher genetic diversity than fish farms from Southeast Brazil. AMOVA demonstrated that the highest proportion of variation was presented within the populations. However, when comparing different groups (1: Wild; 2: North fish farms; 3: Southeast fish farms), a considerable variation between the groups was observed. The F-ST values showed the occurrence of genetic structure among the broodstocks from different regions of Brazil. The transcriptome sequencing in pirapitinga provided important genetic resources for biological studies in this non-model species, and microsatellite data can be used as the framework for the genetic management of breeding stocks in Brazil, which might provide a basis for a genetic pre-breeding programme. Sao Paulo State Univ, Univ Estadual Paulista Julio Mesquita Filho, Aquaculture Ctr, Jaboticabal, Brazil Univ Santiago Compostela, Vet Fac, Lugo, Spain Sao Paulo State Univ, Sch Sci, Bauru, Brazil Sao Paulo State Univ, Univ Estadual Paulista Julio Mesquita Filho, Aquaculture Ctr, Jaboticabal, Brazil Sao Paulo State Univ, Sch Sci, Bauru, Brazil FAPESP: 2014/03772-7 FAPESP: 2014/05732-2 CNPq: 446779/2014-8 CNPq: 305916/2015-7

Among the pelagic shark species most impacted by fisheries, the oceanic whitetip shark (Carcharhinus longimanus) has shown signs of population declines. In this study, we developed 12 microsatellite markers using next generation sequencing (454 pyrosequencing) in C. longimanus for further use in population screening. The genetic diversity of these loci was assessed in 28 individuals and a total of 35 alleles were identified, ranging from four to eight alleles per locus (5.9 alleles on average). Cross-species amplification of these markers was successful in five loci for C. acronotus, C. perezi and Galeocerdo cuvier. The developed microsatellite markers will be useful in analyzing the population genetics structure of the oceanic whitetip shark and other Carcharhinidae species.

Made available in DSpace on 2018-11-26T17:06:08Z (GMT). No. of bitstreams: 0 Previous issue date: 2016-08-30 Investigador-FCT contract from the Portuguese Foundation for Science and Technology (FCT, Fundacao para a Ciencia e Tecnologia) - EU European Social Fund Programa Operacional Potencial Humano Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) The tiger shark (Galeocerdo cuvier) has a global distribution in tropical and warm temperate seas, and it is caught in numerous fisheries worldwide, mainly as bycatch. It is currently assessed as near threatened by the International Union for Conservation of Nature (IUCN) Red List. In this study, we identified nine microsatellite loci through next generation sequencing (454 pyrosequencing) using 29 samples from the western Atlantic. The genetic diversity of these loci were assessed and revealed a total of 48 alleles ranging from 3 to 7 alleles per locus (average of 5.3 alleles). Cross-species amplification was successful at most loci for other species such as Carcharhinus longimanus, C. acronotus and Alopias superciliosus. Given the potential applicability of genetic markers for biological conservation, these data may contribute to the population assessment of this and other species of sharks worldwide. Univ Estadual Paulista, Lab Biol & Genet Peixes, Botucatu, SP, Brazil Univ Fed Sao Paulo, Inst Marine Sci, Lab Genet Pesqueira & Conservacao, Santos, SP, Brazil Valencia Coll, Lake Nona Campus, Orlando, FL USA Univ Florida, Florida Museum Nat Hist, Florida Program Shark Res, Gainesville, FL 32611 USA Portuguese Inst Ocean & Atmosphere, IPMA, Algarve, Portugal Univ Estadual Paulista, Lab Biol & Genet Peixes, Botucatu, SP, Brazil Programa Operacional Potencial Humano: IF/00253/2014 FAPESP: 2013/14555-4 FAPESP: BIOTA 2011/23787-0

The tiger shark (Galeocerdo cuvier) has a global distribution in tropical and warm temperate seas, and is caught in numerous fisheries worldwide, mainly as bycatch. It is currently assessed as near threatened by the International Union for Conservation of Nature (IUCN) Red List. In this study we identified 9 microsatellite loci through next generation sequencing (454 pyrosequencing) using 29 samples from the western Atlantic. The genetic diversity of these loci was assessed and revealed a total of 48 alleles ranging from 3 to 7 alleles per locus (average of 5.3 alleles). Cross-species amplification was assessed in three other species: Carcharhinus longimanus, C. acronotus and Alopias superciliosus. Given the potential applicability of genetic markers for biological conservation, these data may contribute to the population assessment of this and other species of sharks worldwide.

Made available in DSpace on 2018-12-11T17:03:01Z (GMT). No. of bitstreams: 0 Previous issue date: 2016-05-01 Information regarding population structure and genetic connectivity is an important contribution when establishing conservation strategies to manage threatened species. The oceanic whitetip shark, Carcharhinus longimanus, is a highly migratory, large-bodied, pelagic shark listed by the IUCN (International Union for Conservation of Nature) Red List as vulnerable throughout its range and critically endangered in the western north Atlantic. In 2014, the species was protected globally under Appendix II of CITES (Convention on International Trade in Endangered Species), limiting and regulating trade. This study used partial sequences of mitochondrial DNA (mtDNA) control region to determine the population genetic structure of oceanic whitetip sharks across the Atlantic and Indian Oceans. 724 base pairs were obtained from 215 individuals that identifed nine polymorphic sites and defined 12 distinct haplotypes. Total nucleotide diversity (τ) was 0.0013 and haplotype diversity (h) was 0.5953. The Analysis of Molecular Variance (AMOVA) evidenced moderate levels of population structure (ØST = 0.1039) with restricted gene flow between the western and eastern Atlantic Ocean, and a strong relationship between the latter region and the Indian Ocean. Even though the oceanic whitetip is a highly migratory animal the results presented here show that their genetic variability is slightly below average of other pelagic sharks. Additionally, this study recommends that at least two populations in the Atlantic Ocean should be considered distinct (eastern and western Atlantic) and conservation efforts should be focused in areas with the greatest genetic diversity by environmental managers. Laboratório de Biologia e Genética de Peixes Instituto de Biociências de Botucatu Universidade Estadual Paulista (UNESP) Instituto Português Do Mar e DaAtmosfera (IPMA) Centro de Ciências Do Mar (CCMAR) Universidade Algarve School of Marine and Atmospheric Science Stony Brook University Microwave Telemetry Inc. Shark Research and Conservation Program Cape Eleuthera Institute Manta Trust Catemwood House Department of Biology and Environmental Science Linnaeus University Blue Resources Departamento de Pesca e Aquicultura Universidade Federal Rural de Pernambuco Laboratório de Genética Pesqueira e Conservação Instituto Do Mar Universidade Federal de São Paulo (UNIFESP) Laboratório de Biologia e Genética de Peixes Instituto de Biociências de Botucatu Universidade Estadual Paulista (UNESP)