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Iwasa-Arai T, Siqueira SGL, Sobral-Souza T, Leite FPP, Andrade SCS. Continent-island boundary and environment-shaped evolution in the marine amphipod Ampithoe marcuzzii complex (Crustacea: Eumalacostraca: Ampithoidae). Sci Rep 2024; 14:608. [PMID: 38182880 PMCID: PMC10770051 DOI: 10.1038/s41598-023-51049-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 12/29/2023] [Indexed: 01/07/2024] Open
Abstract
Marine amphipods are crustaceans that lack a larval phase and consequently have low dispersion rates. Despite that, these crustaceans present a remarkable ability to be transported by rafting on natural floating substrata, especially macroalgae, where they find shelter, food and a mating ground. The species Ampithoe marcuzzii is widely distributed throughout the western Atlantic Ocean. Here, it was used as a model to study seascape genomics and phylogeography in invertebrates with low dispersion capacities. We anticipated that the lineages would present isolation-by-distance patterns. However, surface currents and other abiotic variables could facilitate connectivity among distant sites. Based on mitochondrial and nuclear genes, SNPs, and environmental associations, we observed the presence of a species complex within A. marcuzzii, separating mainland and insular populations. Each species showed an independent evolutionary history, with a strong latitudinal population structure and evidence of isolation-by-distance and isolation-by-environment, characterizing the 'continent' species. Historical expansion and environmental variables were observed associated with the southeastern population, and ecological niche modeling corroborated the region as a paleorefuge. Conversely, populations from 'islands' presented complicated evolutionary histories, with closer localities genetically isolated and distant localities connected. These findings indicate that insular populations with low dispersion capacity might be more susceptible to spatial connectivity by floating substrata and to changes in surface currents. In contrast, mainland populations might be more vulnerable to local climate changes due to lack of gene flow.
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Affiliation(s)
- Tammy Iwasa-Arai
- Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, Brazil.
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil.
| | - Silvana G L Siqueira
- Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, Brazil
| | - Thadeu Sobral-Souza
- Departamento de Botânica e Ecologia, Universidade Federal do Mato Grosso, Cuiabá, Brazil
| | - Fosca P P Leite
- Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, Brazil
| | - Sónia C S Andrade
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
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Iwasa-Arai T, Andrade SCS, Miguel C, Siqueira SGLB, Werneck MR, Leite FPP, Moraes L, Santos MRD, Medeiros LS, Lopes UH, Serejo C. Coevolutionary Implications of Obligate Commensalism in Sea Turtles: the Case of the Genus Hyachelia Barnard, 1967 (Crustacea, Amphipoda). Zool Stud 2023; 62:e54. [PMID: 38628163 PMCID: PMC11019367 DOI: 10.6620/zs.2023.62-54] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 10/23/2023] [Indexed: 04/26/2024]
Abstract
Obligate commensalism in the marine environment and its evolutionary role are still poorly understood. Although sea turtles may serve as ideal substrates for epibionts, within amphipods, only the genus Hyachelia evolved in obligate commensalism with turtles. Here, we report a new host record for Hyachelia lowryi on the hawksbill turtle and describe a larger distribution of the genus in the Atlantic Ocean on green and loggerhead turtles. Hyachelia spp. were sampled from nesting sites of Caretta caretta and feeding grounds of Eretmochelys imbricata and Chelonia mydas along the Brazilian coast. Insights regarding the coevolution of this remarkable genus with its hosts based on molecular analyses are inferred based on mitochondrial (COI) and nuclear (18SrRNA) genes using new and previously available sequences from the infraorder Talitrida. Divergence times for Hyachelia are around the Cretaceous (~127.66 Mya), corresponding to an ancient origin and in agreement with modern green turtle (Chelonioidea) radiation. Later, diversification of Hyachelia species is dated at about 26 Mya, suggesting a coevolutionary association between amphipods and Carettini/Chelonini sea turtles.
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Affiliation(s)
- Tammy Iwasa-Arai
- Programa de Pós-Graduação em Biologia Animal, Universidade Estadual de Campinas (UNICAMP). Campinas, São Paulo, Brazil. E-mail: (Iwasa-Arai)
- Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas 13083-970, SP, Brazil. E-mail: (Andrade); (Siqueira); (Leite)
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo 05508-090, SP, Brazil. E-mail: (Andrade); (Moraes)
| | - Sónia C S Andrade
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo 05508-090, SP, Brazil. E-mail: (Andrade); (Moraes)
| | - Camila Miguel
- Projeto Chelonia mydas -Instituto Marcos Daniel, R. José Alexandre Buaiz, 190 -Sala 1713 -Enseada do Suá, Vitória, 29050-545, ES, Brazil. E-mail: (Miguel); (Santos)
| | - Silvana G L B Siqueira
- Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas 13083-970, SP, Brazil. E-mail: (Andrade); (Siqueira); (Leite)
| | - Max Rondon Werneck
- Instituto BW para Conservação e Medicina da Fauna Marinha. Araruama, Rio de Janeiro, Brazil. E-mail: (Werneck)
| | - Fosca P P Leite
- Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas 13083-970, SP, Brazil. E-mail: (Andrade); (Siqueira); (Leite)
| | - Lara Moraes
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo 05508-090, SP, Brazil. E-mail: (Andrade); (Moraes)
| | - Marcelo Renan D Santos
- Projeto Chelonia mydas -Instituto Marcos Daniel, R. José Alexandre Buaiz, 190 -Sala 1713 -Enseada do Suá, Vitória, 29050-545, ES, Brazil. E-mail: (Miguel); (Santos)
| | - Luciana S Medeiros
- Programa de Pós-Graduação em Ciência Animal, Universidade Federal de Alagoas (UFAL). Viçosa, 57700-970, AL, Brazil. E-mail: (Medeiros)
- Instituto Biota de Conservação, Maceió, 57038-770, AL, Brazil. E-mail: (Lopes)
| | - Uylia H Lopes
- Instituto Biota de Conservação, Maceió, 57038-770, AL, Brazil. E-mail: (Lopes)
| | - Cristiana Serejo
- Laboratório de Carcinologia, Departamento de Invertebrados, Museu Nacional/UFRJ, Rio de Janeiro, 20940-040, RJ, Brazil. E-mail: (Serejo)
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Sonoda GG, Tobaruela EDC, Norenburg J, Fabi JP, Andrade SCS. Venomous Noodles: The Evolution of Toxins in Nemertea through Positive Selection and Gene Duplication. Toxins (Basel) 2023; 15:650. [PMID: 37999513 PMCID: PMC10674772 DOI: 10.3390/toxins15110650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 10/03/2023] [Accepted: 10/11/2023] [Indexed: 11/25/2023] Open
Abstract
Some, probably most and perhaps all, members of the phylum Nemertea are poisonous, documented so far from marine and benthic specimens. Although the toxicity of these animals has been long known, systematic studies on the characterization of toxins, mechanisms of toxicity, and toxin evolution for this group are scarce. Here, we present the first investigation of the molecular evolution of toxins in Nemertea. Using a proteo-transcriptomic approach, we described toxins in the body and poisonous mucus of the pilidiophoran Lineus sanguineus and the hoplonemertean Nemertopsis pamelaroeae. Using these new and publicly available transcriptomes, we investigated the molecular evolution of six selected toxin gene families. In addition, we also characterized in silico the toxin genes found in the interstitial hoplonemertean, Ototyphlonemertes erneba, a meiofaunal taxa. We successfully identified over 200 toxin transcripts in each of these species. Evidence of positive selection and gene duplication was observed in all investigated toxin genes. We hypothesized that the increased rates of gene duplications observed for Pilidiophora could be involved with the expansion of toxin genes. Studies concerning the natural history of Nemertea are still needed to understand the evolution of their toxins. Nevertheless, our results show evolutionary mechanisms similar to other venomous groups.
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Affiliation(s)
- Gabriel Gonzalez Sonoda
- Departamento de Genética e Biologia Evolutiva, IB-Universidade de São Paulo, São Paulo 05508-090, Brazil;
- Instituto Butantan, São Paulo 05503-900, Brazil
| | - Eric de Castro Tobaruela
- Faculdade de Ciências Farmacêuticas, Food Research Center (FoRC), Universidade de São Paulo, São Paulo 05508-080, Brazil; (E.d.C.T.); (J.P.F.)
| | | | - João Paulo Fabi
- Faculdade de Ciências Farmacêuticas, Food Research Center (FoRC), Universidade de São Paulo, São Paulo 05508-080, Brazil; (E.d.C.T.); (J.P.F.)
| | - Sónia C. S. Andrade
- Departamento de Genética e Biologia Evolutiva, IB-Universidade de São Paulo, São Paulo 05508-090, Brazil;
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Saranholi BH, Rodriguez-Castro KG, Carvalho CS, Chahad-Ehlers S, Gestich CC, Andrade SCS, Freitas PD, Galetti PM. Comparing iDNA from mosquitoes and flies to survey mammals in a semi-controlled Neotropical area. Mol Ecol Resour 2023; 23:1790-1799. [PMID: 37535317 DOI: 10.1111/1755-0998.13851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 06/10/2023] [Accepted: 07/17/2023] [Indexed: 08/04/2023]
Abstract
Ingested-derived DNA (iDNA) from insects represents a powerful tool for assessing vertebrate diversity because insects are easy to sample, have a diverse diet and are widely distributed. Because of these advantages, the use of iDNA for detecting mammals has gained increasing attention. Here we aimed to compare the effectiveness of mosquitoes and flies to detect mammals with a small sampling effort in a semi-controlled area, a zoo that houses native and non-native species. We compared mosquitoes and flies regarding the number of mammal species detected, the amount of mammal sequence reads recovered, and the flight distance range for detecting mammals. We also verified if the combination of two mini-barcodes (12SrRNA and 16SrRNA) would perform better than either mini-barcode alone to inform local mammal biodiversity from iDNA. To capture mosquitoes and flies, we distributed insect traps in eight sampling points during 5 days. We identified 43 Operational Taxonomic Units from 10 orders, from the iDNA of 17 mosquitoes and 46 flies. There was no difference in the number of species recovered per individual insect between mosquitoes and flies, but the number of flies captured was higher, resulting in more mammal species recovered by flies. Eight species were recorded exclusively by mosquitoes and 20 by flies, suggesting that using both samplers would allow a more comprehensive screening of the biodiversity. The maximum distance recorded was 337 m for flies and 289 m for mosquitoes, but the average range distance did not differ between insect groups. Our assay proved to be efficient for mammal detection, considering the high number of species detected with a reduced sampling effort.
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Affiliation(s)
- Bruno H Saranholi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Karen G Rodriguez-Castro
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
- Facultad Ciencias Básicas e Ingeniería, Universidad de los Llanos, Villavicencio, Colombia
| | - Carolina S Carvalho
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
- Instituto Tecnológico Vale, Belém, Brazil
| | - Samira Chahad-Ehlers
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Carla C Gestich
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Sónia C S Andrade
- Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Patrícia D Freitas
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Pedro M Galetti
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
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Zuccarelli R, Rodríguez-Ruiz M, Silva FO, Gomes LDL, Lopes-Oliveira PJ, Zsögön A, Andrade SCS, Demarco D, Corpas FJ, Peres LEP, Rossi M, Freschi L. Loss of S-nitrosoglutathione reductase disturbs phytohormone homeostasis and regulates shoot side branching and fruit growth in tomato. J Exp Bot 2023; 74:6349-6368. [PMID: 37157899 DOI: 10.1093/jxb/erad166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 05/04/2023] [Indexed: 05/10/2023]
Abstract
S-Nitrosoglutathione plays a central role in nitric oxide (NO) homeostasis, and S-nitrosoglutathione reductase (GSNOR) regulates the cellular levels of S-nitrosoglutathione across kingdoms. Here, we investigated the role of endogenous NO in shaping shoot architecture and controlling fruit set and growth in tomato (Solanum lycopersicum). SlGSNOR silencing promoted shoot side branching and led to reduced fruit size, negatively impacting fruit yield. Greatly intensified in slgsnor knockout plants, these phenotypical changes were virtually unaffected by SlGSNOR overexpression. Silencing or knocking out of SlGSNOR intensified protein tyrosine nitration and S-nitrosation and led to aberrant auxin production and signaling in leaf primordia and fruit-setting ovaries, besides restricting the shoot basipetal polar auxin transport stream. SlGSNOR deficiency triggered extensive transcriptional reprogramming at early fruit development, reducing pericarp cell proliferation due to restrictions on auxin, gibberellin, and cytokinin production and signaling. Abnormal chloroplast development and carbon metabolism were also detected in early-developing NO-overaccumulating fruits, possibly limiting energy supply and building blocks for fruit growth. These findings provide new insights into the mechanisms by which endogenous NO fine-tunes the delicate hormonal network controlling shoot architecture, fruit set, and post-anthesis fruit development, emphasizing the relevance of NO-auxin interaction for plant development and productivity.
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Affiliation(s)
- Rafael Zuccarelli
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, 05508-900, São Paulo, SP, Brazil
| | - Marta Rodríguez-Ruiz
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, 05508-900, São Paulo, SP, Brazil
| | - Fernanda O Silva
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, 05508-900, São Paulo, SP, Brazil
| | - Letícia D L Gomes
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, 05508-900, São Paulo, SP, Brazil
| | - Patrícia J Lopes-Oliveira
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, 05508-900, São Paulo, SP, Brazil
| | - Agustin Zsögön
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, MG, Brazil
| | - Sónia C S Andrade
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, 05508-900, São Paulo, SP, Brazil
| | - Diego Demarco
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, 05508-900, São Paulo, SP, Brazil
| | - Francisco J Corpas
- Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín, Spanish National Research Council (CSIC), Granada, Spain
| | - Lázaro E P Peres
- Departamento de Ciências Biológicas, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, 13418-900, Piracicaba, SP, Brazil
| | - Magdalena Rossi
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, 05508-900, São Paulo, SP, Brazil
| | - Luciano Freschi
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, 05508-900, São Paulo, SP, Brazil
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Chernyshev AV, Alfaya JEF, Anadón N, Andrade SCS, Bartolomaeus T, Döhren JVON, Fernández-Álvarez FÁ, Giribet G, Junoy J, Kajihara H, Kem WR, Kuris A, Kvist S, Machordom A, McEvoy EG, Norenburg JL, Okazaki RK, Rogers AD, Strand M, Sun SC, Sundberg P, Thiel M. Raymond Gibson (1938-2023): in memoriam. Zootaxa 2023; 5311:596-599. [PMID: 37518627 DOI: 10.11646/zootaxa.5311.4.7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Indexed: 08/01/2023]
Affiliation(s)
- Alexei V Chernyshev
- A.V. Zhirmunsky National Scientific Center of Marine Biology; Far Eastern Branch; Russian Academy of Sciences; Palchevskogo Street 17; Vladivostok 690041; Russia.
| | - José E Fernández Alfaya
- Instituto de Biología de Organismos Marinos; LARBIM-IBIOMAR (CONICET); Bvd. Brown 2915 (U9120ACD); Puerto Madryn; Chubut; Argentina.
| | - Nuria Anadón
- Departamento de Biología de Organismos y Sistemas; Universidad de Oviedo; Catedrático Rodrigo Uría s/n; Oviedo 33071; Spain.
| | - Sónia C S Andrade
- Departamento de Genética e Biologia Evolutiva; IB; Universidade de São Paulo; 05508090 São Paulo; SP; Brazil.
| | - Thomas Bartolomaeus
- Institute of Evolutionary Biology and Ecology; University of Bonn; An der Immenburg 1; D-53121 Bonn; Germany.
| | - Jörn VON Döhren
- Institute of Evolutionary Biology and Ecology; University of Bonn; An der Immenburg 1; D-53121 Bonn; Germany.
| | | | - Gonzalo Giribet
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology; Harvard University; 26 Oxford Street; Cambridge; MA 02138; USA.
| | - Juan Junoy
- Departamento de Ciencias de la Vida; AP 20 Campus Universitario; Universidad de Alcalá; Alcalá de Henares; 28805; Spain.
| | - Hiroshi Kajihara
- Faculty of Science; Hokkaido University; N10W8; Sapporo 060-0810; Japan.
| | - William R Kem
- Department of Pharmacology; University of Florida; Gainesville; Florida 32603; USA.
| | - Armand Kuris
- Department of Ecology Evolution and Marine Biology; College of Creative Studies; University of California; Santa Barbara; California 93106; USA.
| | - Sebastian Kvist
- Department of Natural History; Royal Ontario Museum; 100 Queen's Park; Toronto; ON; M5S 2C6; Canada Department of Ecology and Evolutionary Biology; University of Toronto; 25 Willcocks Street; Toronto; ON; M5S 2B4; Canada.
| | - Annie Machordom
- Dpto Biodiversidad y Biología Evolutiva; Museo Nacional de Ciencias Naturales (CSIC); C/ José Gutiérrez Abascal 2; 28006 Madrid; Spain.
| | - Eric G McEvoy
- School of Natural Sciences and Psychology; Liverpool John Moores University; Liverpool L32AJ; UK.
| | - Jon L Norenburg
- Department of Invertebrate Zoology; Smithsonians National Museum of Natural History; Washington; DC 20560-0163; USA.
| | - Robert K Okazaki
- Department of Zoology; Weber State University; 1415 Edvalson Street; Dept. 2505 Ogden; Utah 84408-2505; USA.
| | - Alex D Rogers
- REV Ocean; Oksenøyveien 10; Lysaker; Norway Somerville College; University of Oxford; Woodstock Road; Oxford; OC2 6HK; England; UK.
| | - Malin Strand
- Swedish Species Information Centre; Swedish University of Agricultural Sciences; Box 7007; SE-750 07 Uppsala; Sweden.
| | - Shi-Chun Sun
- Institute of Evolution & Marine Biodiversity; Ocean University of China; 5 Yushan Road; Qingdao 266003; China.
| | - Per Sundberg
- Department of Marine Sciences; P.O.Box 461; SE-405 30; Gothenburg; Sweden.
| | - Martin Thiel
- Facultad Ciencias del Mar; Universidad Catolica del Norte; Larrondo 1281; Coquimbo; Chile.
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Cortez T, Montenegro H, Coutinho LL, Regitano LCA, Andrade SCS. Molecular evolution and signatures of selective pressures on Bos, focusing on the Nelore breed (Bos indicus). PLoS One 2022; 17:e0279091. [PMID: 36548260 PMCID: PMC9778527 DOI: 10.1371/journal.pone.0279091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 11/30/2022] [Indexed: 12/24/2022] Open
Abstract
Evolutionary history leads to genome changes over time, especially for species that have experienced intense selective pressures over a short period. Here, we investigated the genomic evolution of Bos species by searching for potential selection signatures, focusing on Nelore, an economically relevant cattle breed in Brazil. We assessed the genomic processes determining the molecular evolution across Nelore and thirteen other related taxa by evaluating (i) amino acid sequence conservation, (ii) the dN/dS ratio, and (iii) gene families' turnover rate (λ). Low conserved regions potentially associated with fatty acid metabolism seem to reflect differences in meat fat content in taxa with different evolutionary histories. All Bos species presented genes under positive selection, especially B. indicus and Nelore, which include transport protein cobalamin, glycolipid metabolism, and hormone signaling. These findings could be explained by constant selective pressures to obtain higher immune resistance and efficient metabolism. The gene contraction rate across the Nelore + B. indicus branch was almost nine times higher than that in other lineages (λ = 0.01043 vs. 0.00121), indicating gene losses during the domestication process. Amino acid biosynthesis, reproductive and innate immune system-related pathways were associated with genes recognized within the most frequent rapidly evolving gene families and in genes under positive selection, supporting the substantial relevance of such traits from a domestication perspective. Our data provide new insights into how the genome may respond to intense artificial selection in distinct taxa, and reinforces the presence of selective pressures on traits potentially relevant for future animal breeding investments.
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Affiliation(s)
- Thainá Cortez
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo (USP), São Paulo, SP, Brazil
- * E-mail: (SCSA); (TC)
| | - Horácio Montenegro
- Departamento de Zootecnia, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo (ESALQ), Piracicaba, SP, Brazil
| | - Luiz L. Coutinho
- Departamento de Zootecnia, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo (ESALQ), Piracicaba, SP, Brazil
| | - Luciana C. A. Regitano
- Empresa Brasileira de Pesquisa Agropecuária, Embrapa Pecuária Sudeste, São Carlos, SP, Brazil
| | - Sónia C. S. Andrade
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo (USP), São Paulo, SP, Brazil
- * E-mail: (SCSA); (TC)
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8
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Santander MD, Maronna MM, Ryan JF, Andrade SCS. The state of Medusozoa genomics: current evidence and future challenges. Gigascience 2022; 11:6586816. [PMID: 35579552 PMCID: PMC9112765 DOI: 10.1093/gigascience/giac036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 02/18/2022] [Accepted: 03/15/2022] [Indexed: 12/13/2022] Open
Abstract
Medusozoa is a widely distributed ancient lineage that harbors one-third of Cnidaria diversity divided into 4 classes. This clade is characterized by the succession of stages and modes of reproduction during metagenic lifecycles, and includes some of the most plastic body plans and life cycles among animals. The characterization of traditional genomic features, such as chromosome numbers and genome sizes, was rather overlooked in Medusozoa and many evolutionary questions still remain unanswered. Modern genomic DNA sequencing in this group started in 2010 with the publication of the Hydra vulgaris genome and has experienced an exponential increase in the past 3 years. Therefore, an update of the state of Medusozoa genomics is warranted. We reviewed different sources of evidence, including cytogenetic records and high-throughput sequencing projects. We focused on 4 main topics that would be relevant for the broad Cnidaria research community: (i) taxonomic coverage of genomic information; (ii) continuity, quality, and completeness of high-throughput sequencing datasets; (iii) overview of the Medusozoa specific research questions approached with genomics; and (iv) the accessibility of data and metadata. We highlight a lack of standardization in genomic projects and their reports, and reinforce a series of recommendations to enhance future collaborative research.
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Affiliation(s)
- Mylena D Santander
- Correspondence address. Mylena D. Santander, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade São Paulo, 277 Rua do Matão, Cidade Universitária, São Paulo 05508-090, Brazil. E-mail:
| | - Maximiliano M Maronna
- Correspondence address. Maximiliano M. Maronna, Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, 101 Rua do Matão Cidade Universitária, São Paulo 05508-090, Brazil. E-mail:
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Blvd, St. Augustine, FL 32080, USA,Department of Biology, University of Florida, 220 Bartram Hall, Gainesville, FL 32611, USA
| | - Sónia C S Andrade
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade São Paulo, 277 Rua do Matão, Cidade Universitária, São Paulo 05508-090, Brazil
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Soares CG, do Prado SBR, Andrade SCS, Fabi JP. Systems Biology Applied to the Study of Papaya Fruit Ripening: The Influence of Ethylene on Pulp Softening. Cells 2021; 10:2339. [PMID: 34571988 PMCID: PMC8467500 DOI: 10.3390/cells10092339] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 09/02/2021] [Accepted: 09/03/2021] [Indexed: 11/16/2022] Open
Abstract
Papaya is a fleshy fruit that undergoes fast ethylene-induced modifications. The fruit becomes edible, but the fast pulp softening is the main factor that limits the post-harvest period. Papaya fast pulp softening occurs due to cell wall disassembling coordinated by ethylene triggering that massively expresses pectinases. In this work, RNA-seq analysis of ethylene-treated and non-treated papayas enabled a wide transcriptome overview that indicated the role of ethylene during ripening at the gene expression level. Several families of transcription factors (AP2/ERF, NAC, and MADS-box) were differentially expressed. ACO, ACS, and SAM-Mtase genes were upregulated, indicating a high rate of ethylene biosynthesis after ethylene treatment. The correlation among gene expression and physiological data demonstrated ethylene treatment can indeed simulate ripening, and regulation of changes in fruit color, aroma, and flavor could be attributed to the coordinated expression of several related genes. Especially about pulp firmness, the identification of 157 expressed genes related to cell wall metabolism demonstrated that pulp softening is accomplished by a coordinated action of several different cell wall-related enzymes. The mechanism is different from other commercially important fruits, such as strawberry, tomato, kiwifruit, and apple. The observed behavior of this new transcriptomic data confirms ethylene triggering is the main event that elicits fast pulp softening in papayas.
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Affiliation(s)
- Caroline Giacomelli Soares
- Department of Food Science and Experimental Nutrition, School of Pharmaceutical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (C.G.S.); (S.B.R.d.P.)
- Food Research Center (FoRC), CEPID-FAPESP (Research, Innovation and Dissemination Centers, São Paulo Research Foundation), São Paulo 05508-080, Brazil
| | - Samira Bernardino Ramos do Prado
- Department of Food Science and Experimental Nutrition, School of Pharmaceutical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (C.G.S.); (S.B.R.d.P.)
- Food Research Center (FoRC), CEPID-FAPESP (Research, Innovation and Dissemination Centers, São Paulo Research Foundation), São Paulo 05508-080, Brazil
| | - Sónia C. S. Andrade
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade São Paulo, São Paulo 05508-060, Brazil;
| | - João Paulo Fabi
- Department of Food Science and Experimental Nutrition, School of Pharmaceutical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (C.G.S.); (S.B.R.d.P.)
- Food Research Center (FoRC), CEPID-FAPESP (Research, Innovation and Dissemination Centers, São Paulo Research Foundation), São Paulo 05508-080, Brazil
- Food and Nutrition Research Center (NAPAN), University of São Paulo, São Paulo 05508-060, Brazil
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10
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Cortez T, Amaral RV, Sobral-Souza T, Andrade SCS. Genome-wide assessment elucidates connectivity and the evolutionary history of the highly dispersive marine invertebrate Littoraria flava (Littorinidae: Gastropoda). Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blab055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
An important goal of marine population genetics is to understand how spatial connectivity patterns are influenced by historical and evolutionary factors. In this study, we evaluate the demographic history and population structure of Littoraria flava, a highly dispersive marine gastropod in the Brazilian intertidal zone. To test the hypotheses that the species has (1) historically high levels of gene flow on a macrogeographical spatial scale and (2) a distribution in rocky shores that consists of subpopulations, we collected specimens along the Brazilian coastline and combined different sets of genetic markers (mitochondrial DNA, ITS-2 and single nucleotide polymorphisms) with niche-based modelling to predict its palaeodistribution. Low genetic structure was observed, as well as high gene flow over long distances. The demographic analyses suggest that L. flava has had periods of population bottlenecks followed by expansion. According to both palaeodistribution and coalescent simulations, these expansion events occurred during the Pleistocene interglacial cycles (21 kya) and the associated climatic changes were the probable drivers of the distribution of the species. This is the first phylogeographical study of a marine gastropod on the South American coast based on genomic markers associated with niche modelling.
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Affiliation(s)
- Thainá Cortez
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, SPBrazil
| | - Rafael V Amaral
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, SPBrazil
| | - Thadeu Sobral-Souza
- Departamento de Botânica e Ecologia, Universidade Federal do Mato Grosso, Cuiabá, MTBrazil
| | - Sónia C S Andrade
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, SPBrazil
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11
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Santos CA, Sonoda GG, Cortez T, Coutinho LL, Andrade SCS. Transcriptome Expression of Biomineralization Genes in Littoraria flava Gastropod in Brazilian Rocky Shore Reveals Evidence of Local Adaptation. Genome Biol Evol 2021; 13:6171147. [PMID: 33720344 PMCID: PMC8070887 DOI: 10.1093/gbe/evab050] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 02/09/2021] [Accepted: 03/11/2021] [Indexed: 12/11/2022] Open
Abstract
Understanding how selection shapes population differentiation and local adaptation in marine species remains one of the greatest challenges in the field of evolutionary biology. The selection of genes in response to environment-specific factors and microenvironmental variation often results in chaotic genetic patchiness, which is commonly observed in rocky shore organisms. To identify these genes, the expression profile of the marine gastropod Littoraria flava collected from four Southeast Brazilian locations in ten rocky shore sites was analyzed. In this first L. flava transcriptome, 250,641 unigenes were generated, and 24% returned hits after functional annotation. Independent paired comparisons between 1) transects, 2) sites within transects, and 3) sites from different transects were performed for differential expression, detecting 8,622 unique differentially expressed genes. Araçá (AR) and São João (SJ) transect comparisons showed the most divergent gene products. For local adaptation, fitness-related differentially expressed genes were chosen for selection tests. Nine and 24 genes under adaptative and purifying selection, respectively, were most related to biomineralization in AR and chaperones in SJ. The biomineralization-genes perlucin and gigasin-6 were positively selected exclusively in the site toward the open ocean in AR, with sequence variants leading to pronounced protein structure changes. Despite an intense gene flow among L. flava populations due to its planktonic larva, gene expression patterns within transects may be the result of selective pressures. Our findings represent the first step in understanding how microenvironmental genetic variation is maintained in rocky shore populations and the mechanisms underlying local adaptation in marine species.
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Affiliation(s)
- Camilla A Santos
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Gabriel G Sonoda
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Thainá Cortez
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Luiz L Coutinho
- Departamento de Ciência Animal, Escola Superior de Agricultura Luiz de Queiroz (ESALQ), Universidade de São Paulo, Piracicaba, São Paulo, SP, Brazil
| | - Sónia C S Andrade
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
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12
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Zuccarelli R, Rodríguez-Ruiz M, Lopes-Oliveira PJ, Pascoal GB, Andrade SCS, Furlan CM, Purgatto E, Palma JM, Corpas FJ, Rossi M, Freschi L. Multifaceted roles of nitric oxide in tomato fruit ripening: NO-induced metabolic rewiring and consequences for fruit quality traits. J Exp Bot 2021; 72:941-958. [PMID: 33165620 DOI: 10.1093/jxb/eraa526] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 10/30/2020] [Indexed: 06/11/2023]
Abstract
Nitric oxide (NO) has been implicated as part of the ripening regulatory network in fleshy fruits. However, very little is known about the simultaneous action of NO on the network of regulatory events and metabolic reactions behind ripening-related changes in fruit color, taste, aroma and nutritional value. Here, we performed an in-depth characterization of the concomitant changes in tomato (Solanum lycopersicum) fruit transcriptome and metabolome associated with the delayed-ripening phenotype caused by NO supplementation at the pre-climacteric stage. Approximately one-third of the fruit transcriptome was altered in response to NO, including a multilevel down-regulation of ripening regulatory genes, which in turn restricted the production and tissue sensitivity to ethylene. NO also repressed hydrogen peroxide-scavenging enzymes, intensifying nitro-oxidative stress and S-nitrosation and nitration events throughout ripening. Carotenoid, tocopherol, flavonoid and ascorbate biosynthesis were differentially affected by NO, resulting in overaccumulation of ascorbate (25%) and flavonoids (60%), and impaired lycopene production. In contrast, the biosynthesis of compounds related to tomato taste (sugars, organic acids, amino acids) and aroma (volatiles) was slightly affected by NO. Our findings indicate that NO triggers extensive transcriptional and metabolic rewiring at the early ripening stage, modifying tomato antioxidant composition with minimal impact on fruit taste and aroma.
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Affiliation(s)
- Rafael Zuccarelli
- Departamento de Botânica, Universidade de São Paulo, USP, São Paulo, Brazil
| | | | | | - Grazieli B Pascoal
- Departamento de Alimentos e Nutrição Experimental, Universidade de São Paulo, USP, São Paulo, Brazil
- Curso de Graduação em Nutrição, Universidade Federal de Uberlândia, Minas Gerais, Brazil
| | - Sónia C S Andrade
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, USP, São Paulo, Brazil
| | - Cláudia M Furlan
- Departamento de Botânica, Universidade de São Paulo, USP, São Paulo, Brazil
| | - Eduardo Purgatto
- Departamento de Alimentos e Nutrição Experimental, Universidade de São Paulo, USP, São Paulo, Brazil
| | - José M Palma
- Group of Antioxidants, Free Radicals, and Nitric Oxide in Biotechnology, Food and Agriculture, Estación Experimental del Zaidín, CSIC, Granada, Spain
| | - Francisco J Corpas
- Group of Antioxidants, Free Radicals, and Nitric Oxide in Biotechnology, Food and Agriculture, Estación Experimental del Zaidín, CSIC, Granada, Spain
| | - Magdalena Rossi
- Departamento de Botânica, Universidade de São Paulo, USP, São Paulo, Brazil
| | - Luciano Freschi
- Departamento de Botânica, Universidade de São Paulo, USP, São Paulo, Brazil
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13
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Mendes CB, Norenburg JL, Andrade SCS. Species delimitation integrative approach reveals three new species in the Nemertopsis bivittata complex. INVERTEBR SYST 2021. [DOI: 10.1071/is20048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The presence of cryptic species is fairly frequent in many invertebrate groups and even more so among invertebrates with simple morphology, such as nemerteans. Consequently, the use of molecular methods for species delimitation has become a needed tool to complement morphological analyses to better recognise such species. Nemertopsis bivittata is one example of species with subtle morphological variation, but ample geographic distribution, being a good candidate for a species complex study. Here we applied two mitochondrial genes, and 2903 single nucleotide polymorphism (SNP) variants in addition to morphological characters to investigate the presence of cryptic species among specimens previously identified as N. bivittata along the Brazilian Coast. To do so, specimens were collected at 15 different sites in the north-east, south-east and southern regions. Three new species of Nemertopsis are described based on morphological and molecular analyses: Nemertopsis caete sp. nov., Nemertopsis pamelaroeae sp. nov. and Nemertopsis berthalutzae sp. nov. The species N. pamelaroeae and N. berthalutzae present broad distributions from north-east to south-east; N. caete, however, is restricted to the north-east coast. This is the first study to use this combined approach in nemerteans and shows the advantages of integrating genomic markers with classical taxonomy, and applying objective approaches to delimiting species as independently evolving entities.
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14
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Nunes JRS, Pértille F, Andrade SCS, Perazza CA, Villela PMS, Almeida-Val VMF, Gao ZX, Coutinho LL, Hilsdorf AWS. Genome-wide association study reveals genes associated with the absence of intermuscular bones in tambaqui (Colossoma macropomum). Anim Genet 2020; 51:899-909. [PMID: 33006182 DOI: 10.1111/age.13001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2020] [Indexed: 01/21/2023]
Abstract
The presence of intermuscular bones in fisheries products limits the consumption and commercialization potential of many fish species, including tambaqui (Colossoma macropomum). These bones have caused medical emergencies and are an undesirable characteristic for fish farming because their removal is labor-intensive during fish processing. Despite the difficulty in identifying genes related to the lack of intermuscular bone in diverse species of fish, the discovery of individuals lacking intermuscular bones in a Neotropical freshwater characiform fish has provided a unique opportunity to delve into the genetic mechanisms underlying the pathways of intermuscular bone formation. In this study, we carried out a GWAS among boneless and wt tambaqui populations to identify markers associated with a lack of intermuscular bone. After analyzing 11 416 SNPs in 360 individuals (12 boneless and 348 bony), we report 675 significant (Padj < 0.003) associations for this trait. Of those, 13 associations were located near candidate genes related to the reduction of bone mass, promotion of bone formation, inhibition of bone resorption, central control of bone remodeling, bone mineralization and other related functions. To the best of our knowledge, for the first time, we have successfully identified genes related to a lack of intermuscular bones using GWAS in a non-model species.
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Affiliation(s)
- J R S Nunes
- Nature and Culture Institute, Federal University of Amazon (UFAM), Benjamin Constant, Amazonas, 69630-000, Brazil.,Animal Science Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, 13418-900, Brazil
| | - F Pértille
- Animal Science Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, 13418-900, Brazil.,Avian Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, Linköping, 58 183, Sweden
| | - S C S Andrade
- Genetics and Evolutionary Biology Department, University of São Paulo (USP)/Bioscience Institute (IB), São Paulo, São Paulo, 05508-090, Brazil
| | - C A Perazza
- Unit of Biotechnology, University of Mogi das Cruzes, Mogi das Cruzes, São Paulo, 08780-911, Brazil
| | - P M S Villela
- Animal Science Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, 13418-900, Brazil
| | - V M F Almeida-Val
- Brazilian National Institute for Research of the Amazon, Laboratory of Ecophysiology and Molecular Evolution, Manaus, Amazonas, 69067-375, Brazil
| | - Z-X Gao
- College of Fisheries, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Hongshan District, Wuhan, 430070, China
| | - L L Coutinho
- Animal Science Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, 13418-900, Brazil
| | - A W S Hilsdorf
- Unit of Biotechnology, University of Mogi das Cruzes, Mogi das Cruzes, São Paulo, 08780-911, Brazil
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15
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Santos CA, Andrade SCS, Fernandes JMO, Freitas PD. Shedding the Light on Litopenaeus vannamei Differential Muscle and Hepatopancreas Immune Responses in White Spot Syndrome Virus (WSSV) Exposure. Genes (Basel) 2020; 11:E805. [PMID: 32708590 PMCID: PMC7397224 DOI: 10.3390/genes11070805] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/05/2020] [Accepted: 07/13/2020] [Indexed: 11/17/2022] Open
Abstract
White Spot Syndrome Virus (WSSV) is one of the main threats to farming Litopenaeus vannamei, the most important crustacean commercialized in aquaculture worldwide. Here, we performed RNA-seq analyses in hepatopancreas and muscle from WSSV-negative (healthy) and WSSV-positive (unhealthy) L. vannamei, previously exposed to the virus, to obtain new insights about the molecular basis of resistance to WSSV. We detected 71% of our reads mapped against the recently described L. vannamei genome. This is the first report mapping RNA-seq transcripts from shrimps exposed to WSSV against the species reference genome. Differentially expressed gene (DEG) analyses were performed for four independent comparisons, and 13,338 DEGs were identified. When the redundancies and isoforms were disregarded, we observed 8351 and 6514 DEGs, respectively. Interestingly, after crossing the data, we detected a common set of DEGs for hepatopancreas and healthy shrimps, as well as another one for muscle and unhealthy shrimps. Our findings indicate that genes related to apoptosis, melanization, and the Imd pathway are likely to be involved in response to WSSV, offering knowledge about WSSV defense in shrimps exposed to the virus but not infected. These data present potential to be applied in further genetic studies in penaeids and other farmed shrimp species.
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Affiliation(s)
- Camilla A. Santos
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos 676, Brazil
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo 05508-090, Brazil;
| | - Sónia C. S. Andrade
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo 05508-090, Brazil;
| | | | - Patrícia D. Freitas
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos 676, Brazil
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16
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Claudiano GS, Andrade SCS, Souza EC, Yunis-Aguinaga J, Coutinho LL, Moreira DKT, Gonçalves FC, Mundim AV, Marzocchi-Machado CM, de Moraes FR, Moraes JRE. Role of neuroendocrine modulation and biochemistry in the sepsis in Piaractus mesopotamicus. Gen Comp Endocrinol 2020; 288:113338. [PMID: 31812532 DOI: 10.1016/j.ygcen.2019.113338] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 11/17/2019] [Indexed: 12/26/2022]
Abstract
Sepsis is a systemic process with multifactorial pathophysiology that affects most animal species. It is responsible for high rates of morbidity and mortality. This work aimed to study the biochemical and neuroendocrine changes of the sepsis process in Piaractus mesopotamicus after Aeromonas hydrophila inoculation analyzing changes in blood leukocyte and differences in neuroendocrine-biochemical modulation using RNA-seq. Fish showed hypercortisolemia, inhibition of glucose absorption, followed by hypocortisolemia and then hyperglycemia. Thyroid hormones (T3 and T4) showed immediate decrease in serum and T4 increased 6 h post-inoculation (HPI). Sepsis-induced hormonal alterations triggered changes in the metabolic pathways increasing protein and lipid catabolism, use of transient anaerobic glycolysis and liver injury. A reference transcriptome was constructed based on blood leukocytes from P. mesopotamicus. The assembly resulted in total 266,272 contigs with a N50 of 2786 bp. There was a reorganization of plasma membrane of leukocytes at the beginning of the septic process with increased expression of neuroendocrine receptors and with continuous flow of neurotransmitters, hormones and solutes with compensatory regulation at 6 HPI. Three and nine HPI seemed to be critical, the expression of a number of transcription factors was increased, including the modulatory DEGs related to glucocorticoid and thyroid hormones induced and suppressed (FDR < 0.05). Neuroendocrine modulation can regulate leukocytes and biochemical parameters of peripheral blood, being important sources for the study of the pathophysiology of sepsis. These finding highlights the importance of further studies focusing on biochemical-neuroendocrine changes in blood leukocytes and systemic sepsis.
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Affiliation(s)
- Gustavo S Claudiano
- Department of Veterinarian Pathology, Faculty of Agrarian and Veterinarian Sciences, São Paulo State University, Unesp, Jaboticabal, Brazil; Institute of Biodiversity and Forests, Federal University of Western Pará, UFOPA, Santarém, PA, Brazil.
| | - Sónia C S Andrade
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, São Paulo University, USP, Brazil
| | - Elaine C Souza
- Educational Foundation of Penápolis, FUNEPE, Penápolis, São Paulo, Brazil
| | - Jefferson Yunis-Aguinaga
- Aquaculture Center of UNESP, Jaboticabal, São Paulo, Brazil; Instituto del Mar del Perú, IMARPE, Lima, Perú
| | - Luiz L Coutinho
- Department of Animal Science, São Paulo University, USP, ESALQ, Brazil
| | - Débora K T Moreira
- Institute of Biodiversity and Forests, Federal University of Western Pará, UFOPA, Santarém, PA, Brazil
| | - Felipe C Gonçalves
- Clinical Analysis Laboratory, Veterinary Hospital, Federal University of Uberlândia, UFU, Uberlândia, MG, Brazil
| | - Antonio V Mundim
- Clinical Analysis Laboratory, Veterinary Hospital, Federal University of Uberlândia, UFU, Uberlândia, MG, Brazil
| | - Cleni M Marzocchi-Machado
- Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, USP, Brazil
| | - Flávio R de Moraes
- Department of Veterinarian Pathology, Faculty of Agrarian and Veterinarian Sciences, São Paulo State University, Unesp, Jaboticabal, Brazil; Aquaculture Center of UNESP, Jaboticabal, São Paulo, Brazil
| | - Julieta R E Moraes
- Department of Veterinarian Pathology, Faculty of Agrarian and Veterinarian Sciences, São Paulo State University, Unesp, Jaboticabal, Brazil; Aquaculture Center of UNESP, Jaboticabal, São Paulo, Brazil.
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17
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Ferrari RC, Bittencourt PP, Rodrigues MA, Moreno-Villena JJ, Alves FRR, Gastaldi VD, Boxall SF, Dever LV, Demarco D, Andrade SCS, Edwards EJ, Hartwell J, Freschi L. C 4 and crassulacean acid metabolism within a single leaf: deciphering key components behind a rare photosynthetic adaptation. New Phytol 2020; 225:1699-1714. [PMID: 31610019 DOI: 10.1111/nph.16265] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 10/07/2019] [Indexed: 06/10/2023]
Abstract
Although biochemically related, C4 and crassulacean acid metabolism (CAM) systems are expected to be incompatible. However, Portulaca species, including P. oleracea, operate C4 and CAM within a single leaf, and the mechanisms behind this unique photosynthetic arrangement remain largely unknown. Here, we employed RNA-seq to identify candidate genes involved exclusively or shared by C4 or CAM, and provided an in-depth characterization of their transcript abundance patterns during the drought-induced photosynthetic transitions in P. oleracea. Data revealed fewer candidate CAM-specific genes than those recruited to function in C4 . The putative CAM-specific genes were predominantly involved in night-time primary carboxylation reactions and malate movement across the tonoplast. Analysis of gene transcript-abundance regulation and photosynthetic physiology indicated that C4 and CAM coexist within a single P. oleracea leaf under mild drought conditions. Developmental and environmental cues were shown to regulate CAM expression in stems, whereas the shift from C4 to C4 -CAM hybrid photosynthesis in leaves was strictly under environmental control. Moreover, efficient starch turnover was identified as part of the metabolic adjustments required for CAM operation in both organs. These findings provide insights into C4 /CAM connectivity and compatibility, contributing to a deeper understanding of alternative ways to engineer CAM into C4 crop species.
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Affiliation(s)
- Renata C Ferrari
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, 05508-090, Brasil
| | - Priscila P Bittencourt
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, 05508-090, Brasil
| | - Maria A Rodrigues
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, 05508-090, Brasil
| | - Jose J Moreno-Villena
- Department of Ecology and Evolutionary Biology, Yale University, PO Box 208105, New Haven, CT, 06520, USA
| | - Frederico R R Alves
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, 05508-090, Brasil
| | - Vinícius D Gastaldi
- Departamento e Instituto de Psiquiatria, Hospital das Clínicas (HCFMUSP), Faculdade de Medicina, Universidade de São Paulo, São Paulo, 05403-903, Brasil
| | - Susanna F Boxall
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Louisa V Dever
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Diego Demarco
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, 05508-090, Brasil
| | - Sónia C S Andrade
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, 05508-090, Brasil
| | - Erika J Edwards
- Department of Ecology and Evolutionary Biology, Yale University, PO Box 208105, New Haven, CT, 06520, USA
| | - James Hartwell
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Luciano Freschi
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, 05508-090, Brasil
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18
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Laumer CE, Fernández R, Lemer S, Combosch D, Kocot KM, Riesgo A, Andrade SCS, Sterrer W, Sørensen MV, Giribet G. Revisiting metazoan phylogeny with genomic sampling of all phyla. Proc Biol Sci 2019; 286:20190831. [PMID: 31288696 PMCID: PMC6650721 DOI: 10.1098/rspb.2019.0831] [Citation(s) in RCA: 123] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 06/17/2019] [Indexed: 11/21/2022] Open
Abstract
Proper biological interpretation of a phylogeny can sometimes hinge on the placement of key taxa-or fail when such key taxa are not sampled. In this light, we here present the first attempt to investigate (though not conclusively resolve) animal relationships using genome-scale data from all phyla. Results from the site-heterogeneous CAT + GTR model recapitulate many established major clades, and strongly confirm some recent discoveries, such as a monophyletic Lophophorata, and a sister group relationship between Gnathifera and Chaetognatha, raising continued questions on the nature of the spiralian ancestor. We also explore matrix construction with an eye towards testing specific relationships; this approach uniquely recovers support for Panarthropoda, and shows that Lophotrochozoa (a subclade of Spiralia) can be constructed in strongly conflicting ways using different taxon- and/or orthologue sets. Dayhoff-6 recoding sacrifices information, but can also reveal surprising outcomes, e.g. full support for a clade of Lophophorata and Entoprocta + Cycliophora, a clade of Placozoa + Cnidaria, and raising support for Ctenophora as sister group to the remaining Metazoa, in a manner dependent on the gene and/or taxon sampling of the matrix in question. Future work should test the hypothesis that the few remaining uncertainties in animal phylogeny might reflect violations of the various stationarity assumptions used in contemporary inference methods.
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Affiliation(s)
- Christopher E. Laumer
- Museum of Comparative Zoology (MCZ) and Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
- EMBL-European Bioinformatics Institute (EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Rosa Fernández
- Museum of Comparative Zoology (MCZ) and Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
- Bioinformatics & Genomics Unit, Center for Genomic Regulation, Carrer del Dr. Aiguader 88, 08003 Barcelona (Spain)
| | - Sarah Lemer
- Museum of Comparative Zoology (MCZ) and Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
- Marine Laboratory, University of Guam, UOG Station, Mangilao, Guam 96923, USA
| | - David Combosch
- Museum of Comparative Zoology (MCZ) and Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
- Marine Laboratory, University of Guam, UOG Station, Mangilao, Guam 96923, USA
| | - Kevin M. Kocot
- Department of Biological Sciences and Alabama Museum of Natural History, The University of Alabama, Campus Box 870344, Tuscaoosa, AL 35487, USA
| | - Ana Riesgo
- Department of Life Sciences, Natural History Museum of London, Cromwell Road, London SW7 5BD, UK
| | - Sónia C. S. Andrade
- Departamento de Genética e Biologia Evolutiva, IB, Universidade de São Paulo, 05508090 São Paulo, SP, Brazil
| | - Wolfgang Sterrer
- Bermuda Natural History Museum, PO Box FL 145, Flatts, FLBX, Bermuda
| | - Martin V. Sørensen
- Natural History Museum of Denmark, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Gonzalo Giribet
- Museum of Comparative Zoology (MCZ) and Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
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19
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Jaffé R, Veiga JC, Pope NS, Lanes ÉCM, Carvalho CS, Alves R, Andrade SCS, Arias MC, Bonatti V, Carvalho AT, de Castro MS, Contrera FAL, Francoy TM, Freitas BM, Giannini TC, Hrncir M, Martins CF, Oliveira G, Saraiva AM, Souza BA, Imperatriz‐Fonseca VL. Landscape genomics to the rescue of a tropical bee threatened by habitat loss and climate change. Evol Appl 2019; 12:1164-1177. [PMID: 31293629 PMCID: PMC6597871 DOI: 10.1111/eva.12794] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 03/14/2019] [Accepted: 03/19/2019] [Indexed: 12/25/2022] Open
Abstract
Habitat degradation and climate change are currently threatening wild pollinators, compromising their ability to provide pollination services to wild and cultivated plants. Landscape genomics offers powerful tools to assess the influence of landscape modifications on genetic diversity and functional connectivity, and to identify adaptations to local environmental conditions that could facilitate future bee survival. Here, we assessed range-wide patterns of genetic structure, genetic diversity, gene flow, and local adaptation in the stingless bee Melipona subnitida, a tropical pollinator of key biological and economic importance inhabiting one of the driest and hottest regions of South America. Our results reveal four genetic clusters across the species' full distribution range. All populations were found to be under a mutation-drift equilibrium, and genetic diversity was not influenced by the amount of reminiscent natural habitats. However, genetic relatedness was spatially autocorrelated and isolation by landscape resistance explained range-wide relatedness patterns better than isolation by geographic distance, contradicting earlier findings for stingless bees. Specifically, gene flow was enhanced by increased thermal stability, higher forest cover, lower elevations, and less corrugated terrains. Finally, we detected genomic signatures of adaptation to temperature, precipitation, and forest cover, spatially distributed in latitudinal and altitudinal patterns. Taken together, our findings shed important light on the life history of M. subnitida and highlight the role of regions with large thermal fluctuations, deforested areas, and mountain ranges as dispersal barriers. Conservation actions such as restricting long-distance colony transportation, preserving local adaptations, and improving the connectivity between highlands and lowlands are likely to assure future pollination services.
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Affiliation(s)
- Rodolfo Jaffé
- Instituto Tecnológico ValeBelémBrazil
- Departamento de EcologiaUniversidade de São PauloSão PauloBrazil
- Departamento de BiociênciasUniversidade Federal Rural do Semi‐ÁridoMossoróBrazil
| | - Jamille C. Veiga
- Instituto de Ciências BiológicasUniversidade Federal do ParáBelémBrazil
| | | | | | | | | | - Sónia C. S. Andrade
- Departamento de Genética e Biologia EvolutivaUniversidade de São PauloSão PauloBrazil
| | - Maria C. Arias
- Departamento de Genética e Biologia EvolutivaUniversidade de São PauloSão PauloBrazil
| | - Vanessa Bonatti
- Departamento de Genética, Faculdade de Medicina de Ribeirão PretoUniversidade de São PauloRibeirão PretoBrazil
| | - Airton T. Carvalho
- Unidade Acadêmica de Serra TalhadaUniversidade Federal Rural de PernambucoSerra TalhadaBrazil
| | - Marina S. de Castro
- Centro de Agroecologia Rio SecoUniversidade Estadual de Feira de SantanaAmélia RodriguesBrazil
| | | | - Tiago M. Francoy
- Departamento de Genética, Faculdade de Medicina de Ribeirão PretoUniversidade de São PauloRibeirão PretoBrazil
| | - Breno M. Freitas
- Departamento de ZootecniaUniversidade Federal do CearáFortalezaBrazil
| | | | - Michael Hrncir
- Departamento de BiociênciasUniversidade Federal Rural do Semi‐ÁridoMossoróBrazil
| | - Celso F. Martins
- Departamento de Sistemática e EcologiaUniversidade Federal da ParaíbaJoão PessoaBrazil
| | | | - Antonio M. Saraiva
- Escola Politécnica da Universidade de São PauloUniversidade de São PauloSão PauloBrazil
| | | | - Vera L. Imperatriz‐Fonseca
- Instituto Tecnológico ValeBelémBrazil
- Departamento de EcologiaUniversidade de São PauloSão PauloBrazil
- Departamento de BiociênciasUniversidade Federal Rural do Semi‐ÁridoMossoróBrazil
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20
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Affiliation(s)
- Pedro A Peres
- Department of Animal Biology, Institute of Biology, University of Campinas (UNICAMP), Brazil
| | - Marianne Azevedo-Silva
- Department of Animal Biology, Institute of Biology, University of Campinas (UNICAMP), Brazil
| | - Sónia C S Andrade
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo (USP), Brazil
| | - Fosca P P Leite
- Department of Animal Biology, Institute of Biology, University of Campinas (UNICAMP), Brazil
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21
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Faria LCD, Di Domenico M, Andrade SCS, Santos MCD, Fonseca G, Zanol J, Amaral ACZ. The use of metabarcoding for meiofauna ecological patterns assessment. Mar Environ Res 2018; 140:160-168. [PMID: 29933903 DOI: 10.1016/j.marenvres.2018.06.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 06/03/2018] [Accepted: 06/13/2018] [Indexed: 06/08/2023]
Abstract
Marine meiofauna comprises up to 22 phyla. Its morphological identification requires time and taxonomists' expertise, and molecular tools can make this task faster. We aim to disentangle meiofaunal diversity patterns at Araçá Bay by applying a model selection approach and estimating the effectiveness of metabarcoding (18S rDNA) and morphological methods for estimating the response of meiofauna diversity in small-scale interactions with environmental variables. A rarefaction curve indicated that ten samples were sufficient for estimating the total number of meiofauna OTUs in a tidal flat. In both approaches, richness was predicted by mean sand percentage, sediment sorting, and bacteria concentration. Nematode genera composition differed significantly between approaches, the result of taxonomic mismatch in the genetic database. The similarity between the model selected for diversity descriptors, the richness of nematode genera and meiofauna composition emphasized the utility of predictive models for metabarcoding estimates to detect small-scale interactions of these organisms.
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Affiliation(s)
- Laiza Cabral de Faria
- Centro de Estudos do Mar, Universidade Federal do Paraná, Av. Beira-Mar, s/n, Pontal do Sul, PO Box 61, Pontal do Paraná, PR, Zip Code 83255-976, Brazil
| | - Maikon Di Domenico
- Centro de Estudos do Mar, Universidade Federal do Paraná, Av. Beira-Mar, s/n, Pontal do Sul, PO Box 61, Pontal do Paraná, PR, Zip Code 83255-976, Brazil.
| | - Sónia C S Andrade
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, Cidade Universitária, Rua do Matão 277, Zip Code 05508-090, São Paulo, SP, Brazil
| | - Monique Cristina Dos Santos
- Departamento de Zoologia, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373 CCS, Bloco A, Sala A0-108, Cidade Universitária, Rio de Janeiro, RJ, 21941-599, Brazil
| | - Gustavo Fonseca
- Instituto do Mar. Universidade Federal de São Paulo, Rua Carvalho de Mendonça 144, Santos, SP, 11070-100, Brazil
| | - Joana Zanol
- Departamento de Zoologia, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373 CCS, Bloco A, Sala A0-108, Cidade Universitária, Rio de Janeiro, RJ, 21941-599, Brazil; Campus Duque de Caxias, Universidade Federal do Rio de Janeiro, Estr. de Xerém, 27, Duque de Caxias, RJ, Brazil
| | - A Cecilia Z Amaral
- Departamento de Biologia Animal, Universidade Estadual de Campinas Cidade Universitária, Rua Monteiro Lobato, 255, Campinas, SP, 13083-862, Brazil
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22
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Santos CA, Andrade SCS, Freitas PD. Identification of SNPs potentially related to immune responses and growth performance in Litopenaeus vannamei by RNA-seq analyses. PeerJ 2018; 6:e5154. [PMID: 30013834 PMCID: PMC6035726 DOI: 10.7717/peerj.5154] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 06/11/2018] [Indexed: 11/20/2022] Open
Abstract
Litopenaeus vannamei is one of the most important shrimp species for worldwide aquaculture. Despite this, little genomic information is available for this penaeid and other closely related taxonomic crustaceans. Consequently, genes, proteins and their respective polymorphisms are poorly known for these species. In this work, we used the RNA sequencing technology (RNA-seq) in L. vannamei shrimp evaluated for growth performance, and exposed to the White Spot Syndrome Virus (WSSV), in order to investigate the presence of Single Nucleotide Polymorphisms (SNPs) within genes related to innate immunity and growth, both features of great interest for aquaculture activity. We analyzed individuals with higher and lower growth rates; and infected (unhealthy) and non-infected (healthy), after exposure to WSSV. Approximately 7,000 SNPs were detected in the samples evaluated for growth, being 3,186 and 3,978 exclusive for individuals with higher and lower growth rates, respectively. In the animals exposed to WSSV we found about 16,300 unique SNPs, in which 9,338 were specific to non-infected shrimp, and 7,008 were exclusive to individuals infected with WSSV and symptomatic. In total, we describe 4,312 unigenes containing SNPs. About 60% of these unigenes returned GO blastX hits for Biological Process, Molecular Function and Cellular Component ontologies. We identified 512 KEGG unique KOs distributed among 275 pathways, elucidating the majority of metabolism roles related to high protein metabolism, growth and immunity. These polymorphisms are all located in coding regions, and certainly can be applied in further studies involving phenotype expression of complex traits, such as growth and immunity. Overall, the set of variants raised herein enriches the genomic databases available for shrimp, given that SNPs originated from nextgen are still rare for this relevant crustacean group, despite their huge potential of use in genomic selection approaches.
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Affiliation(s)
- Camilla A Santos
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - Sónia C S Andrade
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Patrícia D Freitas
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
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23
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Mendes CB, Norenburg JL, Solferini VN, Andrade SCS. Hidden diversity: Phylogeography of genus Ototyphlonemertes Diesing, 1863 (Ototyphlonemertidae: Hoplonemertea) reveals cryptic species and high diversity in Chilean populations. PLoS One 2018; 13:e0195833. [PMID: 29698411 PMCID: PMC5919620 DOI: 10.1371/journal.pone.0195833] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 04/01/2018] [Indexed: 11/18/2022] Open
Abstract
Ototyphlonemertes is a cosmopolitan genus of meiofaunal nemerteans. Their morphological characters are insufficient to reliably identify and delimit species. Consequently, some of the species are considered cosmopolitan despite anticipated low dispersion capability of the adults and a short planktonic larval phase. Indeed, recent studies show that some species actually comprise cryptic species, and populations are connected by stochastic events of long-distance dispersion. Based solely on morphological traits, a Lactea and a Pallida morph of Ototyphlonemertes are recognized here from collections at eight and five locations respectively along the Chilean coast. To assess the phylogeographic patterns of their populations, two mitochondrial markers (COI and COX3) of 162 specimens of Lactea and 25 of Pallida were sequenced. Final sequences are 605bp and 362bp for COI and COX3, respectively. Results from phylogenetic and haplotype network analyses suggest that the Lactea morph comprises up to three independent evolutionary units (one with only COX3 sequences). A COI gene tree including other previously published Ototyphlonemertes sequences groups the Chilean Lactea with other Lactea, while the Chilean Pallida is grouped with other Pallida. Different structuring and gene flow patterns found for the four groups support the hypothesis that these are four independent evolutionary entities with different ecological, dispersal and demographical characteristics.
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Affiliation(s)
- Cecili B. Mendes
- Laboratório de Diversidade Genômica, Departamento de Genética e Biologia Evolutiva, IB (USP), São Paulo, SP, Brazil
| | - Jon L. Norenburg
- National Museum of Natural History, Smithsonian Institution, Washington, DC, United States of America
| | - Vera N. Solferini
- Laboratório de Diversidade Genética, Departamento de Genética, Evolução Microbiologia e Imunologia, IB (UNICAMP), Campinas, SP, Brazil
| | - Sónia C. S. Andrade
- Laboratório de Diversidade Genômica, Departamento de Genética e Biologia Evolutiva, IB (USP), São Paulo, SP, Brazil
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24
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Santos CA, Andrade SCS, Teixeira AK, Farias F, Kurkjian K, Guerrelhas AC, Rocha JL, Galetti PM, Freitas PD. Litopenaeus vannamei Transcriptome Profile of Populations Evaluated for Growth Performance and Exposed to White Spot Syndrome Virus (WSSV). Front Genet 2018; 9:120. [PMID: 29692800 PMCID: PMC5902700 DOI: 10.3389/fgene.2018.00120] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 03/26/2018] [Indexed: 11/22/2022] Open
Affiliation(s)
- Camilla A Santos
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Sónia C S Andrade
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | | | | | - Karin Kurkjian
- Aquatec Larvicultura de Camarão Marinho, Canguaretama, Brazil
| | | | | | - Pedro M Galetti
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Patrícia D Freitas
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
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25
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Cesar ASM, Regitano LCA, Poleti MD, Andrade SCS, Tizioto PC, Oliveira PSN, Felício AM, do Nascimento ML, Chaves AS, Lanna DPD, Tullio RR, Nassu RT, Koltes JE, Fritz-Waters E, Mourão GB, Zerlotini-Neto A, Reecy JM, Coutinho LL. Differences in the skeletal muscle transcriptome profile associated with extreme values of fatty acids content. BMC Genomics 2016; 17:961. [PMID: 27875996 PMCID: PMC5120530 DOI: 10.1186/s12864-016-3306-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 11/17/2016] [Indexed: 12/19/2022] Open
Abstract
Background Lipids are a class of molecules that play an important role in cellular structure and metabolism in all cell types. In the last few decades, it has been reported that long-chain fatty acids (FAs) are involved in several biological functions from transcriptional regulation to physiological processes. Several fatty acids have been both positively and negatively implicated in different biological processes in skeletal muscle and other tissues. To gain insight into biological processes associated with fatty acid content in skeletal muscle, the aim of the present study was to identify differentially expressed genes (DEGs) and functional pathways related to gene expression regulation associated with FA content in cattle. Results Skeletal muscle transcriptome analysis of 164 Nellore steers revealed no differentially expressed genes (DEGs, FDR 10%) for samples with extreme values for linoleic acid (LA) or stearic acid (SA), and only a few DEGs for eicosapentaenoic acid (EPA, 5 DEGs), docosahexaenoic acid (DHA, 4 DEGs) and palmitic acid (PA, 123 DEGs), while large numbers of DEGs were associated with oleic acid (OA, 1134 DEGs) and conjugated linoleic acid cis9 trans11 (CLA-c9t11, 872 DEGs). Functional annotation and functional enrichment from OA DEGs identified important genes, canonical pathways and upstream regulators such as SCD, PLIN5, UCP3, CPT1, CPT1B, oxidative phosphorylation mitochondrial dysfunction, PPARGC1A, and FOXO1. Two important genes associated with lipid metabolism, gene expression and cancer were identified as DEGs between animals with high and low CLA-c9t11, specifically, epidermal growth factor receptor (EGFR) and RNPS. Conclusion Only two out of seven classes of molecules of FA studied were associated with large changes in the expression profile of skeletal muscle. OA and CLA-c9t11 content had significant effects on the expression level of genes related to important biological processes associated with oxidative phosphorylation, and cell growth, survival, and migration. These results contribute to our understanding of how some FAs modulate metabolism and may have protective health function. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3306-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Aline S M Cesar
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418-900, Brazil.,Department of Animal Science, Iowa State University, Ames, IA, 50011, USA
| | | | - Mirele D Poleti
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | - Sónia C S Andrade
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418-900, Brazil.,Departament of Genetics and Evolutionary Biology-IB, USP, São Paulo, SP, 05508-090, Brazil
| | | | | | - Andrezza M Felício
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | | | - Amália S Chaves
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | - Dante P D Lanna
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | - Rymer R Tullio
- Embrapa Pecuária Sudeste, São Carlos, SP, 13560-970, Brazil
| | - Renata T Nassu
- Embrapa Pecuária Sudeste, São Carlos, SP, 13560-970, Brazil
| | - James E Koltes
- Department of Animal Science, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Eric Fritz-Waters
- Department of Animal Science, Iowa State University, Ames, IA, 50011, USA
| | - Gerson B Mourão
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | | | - James M Reecy
- Department of Animal Science, Iowa State University, Ames, IA, 50011, USA
| | - Luiz L Coutinho
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418-900, Brazil.
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26
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Sundberg P, Andrade SCS, Bartolomaeus T, Beckers P, von Döhren J, Krämer D, Gibson R, Giribet G, Herrera-Bachiller A, Junoy J, Kajihara H, Kvist S, Kånneby T, Sun SC, Thiel M, Turbeville JM, Strand M. The future of nemertean taxonomy (phylum Nemertea) - a proposal. ZOOL SCR 2016. [DOI: 10.1111/zsc.12182] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Per Sundberg
- University of Gothenburg; Department of Marine Sciences; Gothenburg Sweden
| | - Sónia C. S. Andrade
- Departamento de Genética e Biologia Evolutiva; IB-Universidade de; São Paulo Brazil
| | - Thomas Bartolomaeus
- University of Bonn; Institute of Evolutionary Biology and Animal Ecology; Bonn Germany
| | - Patrick Beckers
- University of Bonn; Institute of Evolutionary Biology and Animal Ecology; Bonn Germany
| | - Jörn von Döhren
- University of Bonn; Institute of Evolutionary Biology and Animal Ecology; Bonn Germany
| | - Daria Krämer
- University of Bonn; Institute of Evolutionary Biology and Animal Ecology; Bonn Germany
| | - Ray Gibson
- 94 Queens Avenue, Meols; Wirral CH47 0NA U.K
| | - Gonzalo Giribet
- Museum of Comparative Zoology; Department of Organismic and Evolutionary Biology; Harvard University; Cambridge MA USA
| | | | - Juan Junoy
- Departamento de Ciencias de la Vida; Universidad de Alcalá; Madrid Spain
| | | | - Sebastian Kvist
- Department of Natural History; Royal Ontario Museum; Toronto Canada
- Department of Ecology and Evolutionary Biology; University of Toronto; Toronto Canada
| | - Tobias Kånneby
- Swedish Museum of Natural History; Department of Zoology; Stockholm Sweden
| | - Shi-Chun Sun
- Institute of Evolution & Marine Biodiversity; Ocean University of China; Qingdao China
| | - Martin Thiel
- Facultad Ciencias del Mar; Centro de Estudios Avanzados en Zonas Áridas (CEAZA); Millennium Nucleus Ecology and Sustainable Management of Oceanic Island (ESMOI); Universidad Católica del Norte; Coquimbo Chile
| | | | - Malin Strand
- Swedish Species Information Centre; The Sven Lovén Centre for Marine Sciences; Strömstad Sweden
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27
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Mesquita FS, Ramos RS, Pugliesi G, Andrade SCS, Van Hoeck V, Langbeen A, Oliveira ML, Gonella-Diaza AM, Gasparin G, Fukumasu H, Pulz LH, Membrive CM, Coutinho LL, Binelli M. Endometrial transcriptional profiling of a bovine fertility model by Next-Generation Sequencing. Genom Data 2016; 7:26-8. [PMID: 26981354 PMCID: PMC4778601 DOI: 10.1016/j.gdata.2015.11.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 11/07/2015] [Indexed: 11/23/2022]
Abstract
Studying the multitude of molecular networks and pathways that are potentially involved in a complex trait such as fertility requires an equally complex and broad strategy. Here, we used Next-Generation Sequencing for the characterization of the transcriptional signature of the bovine endometrial tissue. Periovulatory endocrine environments were manipulated to generate two distinctly different fertility phenotypes. Cycling, non-lactating, multiparous Nelore cows were manipulated to ovulate larger (> 13 mm; LF group; high fertility phenotype) or smaller (< 12 mm; SF group) follicles. As a result, greater proestrus estrogen concentrations, corpora lutea and early diestrus progesterone concentrations were also observed in LF group in comparison to SF group. Endometrial cell proliferation was estimated by the protein marker MKI67 on tissues collected 4 (D4) and 7 (D7) days after induction of ovulation. Total RNA extracts from D7 were sequenced and compared according to the transcriptional profile of each experimental group (LF versus SF). Functional enrichment analysis revealed that LF and SF endometria were asynchronous in regards to their phenotype manifestation. Major findings indicated an LF endometrium that was switching phenotypes earlier than the SF one. More specifically, a proliferating SF endometrium was observed on D7, whereas the LF tissue, which expressed a proliferative phenotype earlier at D4, seemed to have already shifted towards a biosynthetically and metabolically active endometrium on D7. Data on MKI67 support the transcriptomic results. RNA-Seq-derived transcriptional profile of the endometrial tissue indicated a temporal effect of the periovulatory endocrine environment, suggesting that the moment of the endometrial exposure to the ovarian steroids, E2 and P4, regulates the timing of phenotype manifestation. Gene expression profiling revealed molecules that may be targeted to elucidate ovarian steroid-dependent mechanisms that regulate endometrial tissue receptivity. Data was deposited in the SRA database from NCBI (SRA Experiment SRP051330) and are associated with the Bio-Project (PRJNA270391). An overview of the gene expression data has been deposited in NCBI's Gene Expression Omnibus (GEO) and is accessible through GEO Series accession number GSE65450. Further assessment of the data in combination with other data sets exploring the transcriptional profile of the endometrial tissue during early diestrus may potentially identify novel molecular mechanisms and/or markers of the uterine receptivity.
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Affiliation(s)
- F S Mesquita
- Universidade Federal do Pampa, Curso de Medicina Veterinária, Uruguaiana, RS, Brazil
| | - R S Ramos
- Universidade de São Paulo, Faculdade de Medicina Veterinária e Zootecnia, Departamento de Reprodução Animal, Pirassununga, SP, Brazil
| | - G Pugliesi
- Universidade de São Paulo, Faculdade de Medicina Veterinária e Zootecnia, Departamento de Reprodução Animal, Pirassununga, SP, Brazil
| | - S C S Andrade
- Universidade de São Paulo, Faculdade de Medicina Veterinária e Zootecnia, Departamento de Reprodução Animal, Pirassununga, SP, Brazil; Universidade de São Paulo, Escola Superior de Agricultura "Luiz de Queiroz", Departamento de Zootecnia, Piracicaba, SP, Brazil
| | - V Van Hoeck
- Universidade de São Paulo, Faculdade de Medicina Veterinária e Zootecnia, Departamento de Reprodução Animal, Pirassununga, SP, Brazil
| | - A Langbeen
- University of Antwerp, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, Wilrijk, Belgium
| | - M L Oliveira
- Universidade de São Paulo, Faculdade de Medicina Veterinária e Zootecnia, Departamento de Reprodução Animal, Pirassununga, SP, Brazil
| | - A M Gonella-Diaza
- Universidade de São Paulo, Faculdade de Medicina Veterinária e Zootecnia, Departamento de Reprodução Animal, Pirassununga, SP, Brazil
| | - G Gasparin
- Universidade de São Paulo, Escola Superior de Agricultura "Luiz de Queiroz", Departamento de Zootecnia, Piracicaba, SP, Brazil
| | - H Fukumasu
- Universidade de São Paulo, Faculdade de Zootecnia e Engenharia de Alimentos, Pirassununga, SP, Brazil
| | - L H Pulz
- Universidade de São Paulo, Faculdade de Zootecnia e Engenharia de Alimentos, Pirassununga, SP, Brazil
| | - C M Membrive
- Universidade Estadual Paulista "Júlio de Mesquita Filho", Campus Experimental de Dracena, Dracena, SP, Brazil
| | - L L Coutinho
- Universidade de São Paulo, Escola Superior de Agricultura "Luiz de Queiroz", Departamento de Zootecnia, Piracicaba, SP, Brazil
| | - M Binelli
- Universidade de São Paulo, Faculdade de Medicina Veterinária e Zootecnia, Departamento de Reprodução Animal, Pirassununga, SP, Brazil
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Novo M, Fernández R, Andrade SCS, Marchán DF, Cunha L, Díaz Cosín DJ. Phylogenomic analyses of a Mediterranean earthworm family (Annelida: Hormogastridae). Mol Phylogenet Evol 2015; 94:473-478. [PMID: 26522608 DOI: 10.1016/j.ympev.2015.10.026] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 10/19/2015] [Accepted: 10/24/2015] [Indexed: 10/22/2022]
Abstract
Earthworm taxonomy and evolutionary biology remain a challenge because of their scarce distinct morphological characters of taxonomic value, the morphological convergence by adaptation to the uniformity of the soil where they inhabit, and their high plasticity when challenged with stressful or new environmental conditions. Here we present a phylogenomic study of the family Hormogastridae, representing also the first piece of work of this type within earthworms. We included seven transcriptomes of the group representing the main lineages as previously-described, analysed in a final matrix that includes twelve earthworms and eleven outgroups. While there is a high degree of gene conflict in the generated trees that obscure some of the internal relationships, the origin of the family is well resolved: the hormogastrid Hemigastrodrilus appears as the most ancestral group, followed by the ailoscolecid Ailoscolex, therefore rejecting the validity of the family Ailoscolecidae. Our results place the origin of hormogastrids in Southern France, as previously hypothesised.
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Affiliation(s)
- Marta Novo
- Cardiff School of Biosciences, Cardiff University, BIOSI 1, Museum Avenue, Cardiff CF10 3AT, UK; Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA; Departamento de Zoología y Antropología Física, Facultad de Biología, Universidad Complutense de Madrid, C/ José Antonio Nováis 2, 28040 Madrid, Spain.
| | - Rosa Fernández
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Sónia C S Andrade
- Departamento de Genética e Biologia Evolutiva, IB-USP, São Paulo, CEP 05508-090, Brazil
| | - Daniel F Marchán
- Departamento de Zoología y Antropología Física, Facultad de Biología, Universidad Complutense de Madrid, C/ José Antonio Nováis 2, 28040 Madrid, Spain
| | - Luis Cunha
- Cardiff School of Biosciences, Cardiff University, BIOSI 1, Museum Avenue, Cardiff CF10 3AT, UK
| | - Darío J Díaz Cosín
- Departamento de Zoología y Antropología Física, Facultad de Biología, Universidad Complutense de Madrid, C/ José Antonio Nováis 2, 28040 Madrid, Spain
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González VL, Andrade SCS, Bieler R, Collins TM, Dunn CW, Mikkelsen PM, Taylor JD, Giribet G. A phylogenetic backbone for Bivalvia: an RNA-seq approach. Proc Biol Sci 2015; 282:20142332. [PMID: 25589608 PMCID: PMC4308999 DOI: 10.1098/rspb.2014.2332] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Bivalves are an ancient and ubiquitous group of aquatic invertebrates with an estimated 10 000–20 000 living species. They are economically significant as a human food source, and ecologically important given their biomass and effects on communities. Their phylogenetic relationships have been studied for decades, and their unparalleled fossil record extends from the Cambrian to the Recent. Nevertheless, a robustly supported phylogeny of the deepest nodes, needed to fully exploit the bivalves as a model for testing macroevolutionary theories, is lacking. Here, we present the first phylogenomic approach for this important group of molluscs, including novel transcriptomic data for 31 bivalves obtained through an RNA-seq approach, and analyse these data with published genomes and transcriptomes of other bivalves plus outgroups. Our results provide a well-resolved, robust phylogenetic backbone for Bivalvia with all major lineages delineated, addressing long-standing questions about the monophyly of Protobranchia and Heterodonta, and resolving the position of particular groups such as Palaeoheterodonta, Archiheterodonta and Anomalodesmata. This now fully resolved backbone demonstrates that genomic approaches using hundreds of genes are feasible for resolving phylogenetic questions in bivalves and other animals.
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Affiliation(s)
- Vanessa L González
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Sónia C S Andrade
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Rüdiger Bieler
- Integrative Research Center, Field Museum of Natural History, Chicago, IL 60605, USA
| | - Timothy M Collins
- Department of Biological Sciences, Florida International University, Miami, FL 33199, USA
| | - Casey W Dunn
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI 02912, USA
| | - Paula M Mikkelsen
- Paleontological Research Institution and Department of Earth and Atmospheric Sciences, Cornell University, Ithaca, NY 14850, USA
| | - John D Taylor
- Department of Life Sciences, The Natural History Museum, London SW7 5BD, UK
| | - Gonzalo Giribet
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
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Mesquita FS, Ramos RS, Pugliesi G, Andrade SCS, Van Hoeck V, Langbeen A, Oliveira ML, Gonella-Diaza AM, Gasparin G, Fukumasu H, Pulz LH, Membrive CM, Coutinho LL, Binelli M. The Receptive Endometrial Transcriptomic Signature Indicates an Earlier Shift from Proliferation to Metabolism at Early Diestrus in the Cow. Biol Reprod 2015; 93:52. [PMID: 26178716 DOI: 10.1095/biolreprod.115.129031] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 06/19/2015] [Indexed: 01/23/2023] Open
Abstract
This study aimed to characterize the endometrial transcriptome and functional pathways overrepresented in the endometrium of cows treated to ovulate larger (≥13 mm) versus smaller (≤12 mm) follicles. Nelore cows were presynchronized prior to receiving cloprostenol (large follicle [LF] group) or not (small follicle [SF] group), along with a progesterone (P4) device on Day (D) -10. Devices were withdrawn and cloprostenol administered 42-60 h (LF) or 30-36 h (SF) before GnRH agonist treatment (D0). Tissues were collected on D4 (experiment [Exp.] 1; n = 24) or D7 (Exp. 2; n = 60). Endometrial transcriptome was obtained by RNA-Seq, whereas proliferation and apoptosis were assessed by immunohistochemistry. Overall, LF cows developed larger follicles and corpora lutea, and produced greater amounts of estradiol (D-1, Exp. 1, SF: 0.7 ± 0.2; LF: 2.4 ± 0.2 pg/ml; D-1, Exp. 2, SF: 0.5 ± 0.1; LF: 2.3 ± 0.6 pg/ml) and P4 (D4, Exp. 1, SF: 0.8 ± 0.1; LF: 1.4 ± 0.2 ng/ml; D7, Exp. 2, SF: 2.5 ± 0.4; LF: 3.7 ± 0.4 ng/ml). Functional enrichment indicated that biosynthetic and metabolic processes were enriched in LF endometrium, whereas SF endometrium transcriptome was biased toward cell proliferation. Data also suggested reorganization of the extracellular matrix toward a proliferation-permissive phenotype in SF endometrium. LF endometrium showed an earlier onset of proliferative activity, whereas SF endometrium expressed a delayed increase in glandular epithelium proliferation. In conclusion, the periovulatory endocrine milieu regulates bovine endometrial transcriptome and seems to determine the transition from a proliferation-permissive to a biosynthetic and metabolically active endometrial phenotype, which may be associated with the preparation of an optimally receptive uterine environment.
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Affiliation(s)
- F S Mesquita
- Universidade Federal do Pampa, Curso de Medicina Veterinária, Uruguaiana, Rio Grande do Sul, Brazil
| | - R S Ramos
- Universidade de São Paulo, Faculdade de Medicina Veterinária e Zootecnia, Departamento de Reprodução Animal, Pirassununga, São Paulo, Brazil
| | - G Pugliesi
- Universidade de São Paulo, Faculdade de Medicina Veterinária e Zootecnia, Departamento de Reprodução Animal, Pirassununga, São Paulo, Brazil
| | - S C S Andrade
- Universidade de São Paulo, Faculdade de Medicina Veterinária e Zootecnia, Departamento de Reprodução Animal, Pirassununga, São Paulo, Brazil Universidade de São Paulo, Escola Superior de Agricultura "Luiz de Queiroz", Departamento de Zootecnia, Piracicaba, São Paulo, Brazil
| | - V Van Hoeck
- Universidade de São Paulo, Faculdade de Medicina Veterinária e Zootecnia, Departamento de Reprodução Animal, Pirassununga, São Paulo, Brazil
| | - A Langbeen
- University of Antwerp, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, Wilrijk, Belgium
| | - M L Oliveira
- Universidade de São Paulo, Faculdade de Medicina Veterinária e Zootecnia, Departamento de Reprodução Animal, Pirassununga, São Paulo, Brazil
| | - A M Gonella-Diaza
- Universidade de São Paulo, Faculdade de Medicina Veterinária e Zootecnia, Departamento de Reprodução Animal, Pirassununga, São Paulo, Brazil
| | - G Gasparin
- Universidade de São Paulo, Escola Superior de Agricultura "Luiz de Queiroz", Departamento de Zootecnia, Piracicaba, São Paulo, Brazil
| | - H Fukumasu
- Universidade de São Paulo, Faculdade de Zootecnia e Engenharia de Alimentos, Pirassununga, São Paulo, Brazil
| | - L H Pulz
- Universidade de São Paulo, Faculdade de Zootecnia e Engenharia de Alimentos, Pirassununga, São Paulo, Brazil
| | - C M Membrive
- Universidade Estadual Paulista "Júlio de Mesquita Filho", Campus Experimental de Dracena, Dracena, São Paulo, Brazil
| | - L L Coutinho
- Universidade de São Paulo, Escola Superior de Agricultura "Luiz de Queiroz", Departamento de Zootecnia, Piracicaba, São Paulo, Brazil
| | - M Binelli
- Universidade de São Paulo, Faculdade de Medicina Veterinária e Zootecnia, Departamento de Reprodução Animal, Pirassununga, São Paulo, Brazil
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Zapata F, Wilson NG, Howison M, Andrade SCS, Jörger KM, Schrödl M, Goetz FE, Giribet G, Dunn CW. Phylogenomic analyses of deep gastropod relationships reject Orthogastropoda. Proc Biol Sci 2015; 281:20141739. [PMID: 25232139 DOI: 10.1098/rspb.2014.1739] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Gastropods are a highly diverse clade of molluscs that includes many familiar animals, such as limpets, snails, slugs and sea slugs. It is one of the most abundant groups of animals in the sea and the only molluscan lineage that has successfully colonized land. Yet the relationships among and within its constituent clades have remained in flux for over a century of morphological, anatomical and molecular study. Here, we re-evaluate gastropod phylogenetic relationships by collecting new transcriptome data for 40 species and analysing them in combination with publicly available genomes and transcriptomes. Our datasets include all five main gastropod clades: Patellogastropoda, Vetigastropoda, Neritimorpha, Caenogastropoda and Heterobranchia. We use two different methods to assign orthology, subsample each of these matrices into three increasingly dense subsets, and analyse all six of these supermatrices with two different models of molecular evolution. All 12 analyses yield the same unrooted network connecting the five major gastropod lineages. This reduces deep gastropod phylogeny to three alternative rooting hypotheses. These results reject the prevalent hypothesis of gastropod phylogeny, Orthogastropoda. Our dated tree is congruent with a possible end-Permian recovery of some gastropod clades, namely Caenogastropoda and some Heterobranchia subclades.
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Affiliation(s)
- Felipe Zapata
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI 02906, USA
| | | | - Mark Howison
- Center for Computation and Visualization, Brown University, Providence, RI 02906, USA
| | - Sónia C S Andrade
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Katharina M Jörger
- SNSB-Bavarian State Collection of Zoology, Munich 81247, Germany Department Biology II, BioZentrum, Ludwig-Maximilians-Universität, Planegg-Martinsried 82152, Germany
| | - Michael Schrödl
- SNSB-Bavarian State Collection of Zoology, Munich 81247, Germany Department Biology II, BioZentrum, Ludwig-Maximilians-Universität, Planegg-Martinsried 82152, Germany
| | - Freya E Goetz
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI 02906, USA
| | - Gonzalo Giribet
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Casey W Dunn
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI 02906, USA
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Binelli M, Scolari SC, Pugliesi G, Van Hoeck V, Gonella-Diaza AM, Andrade SCS, Gasparin GR, Coutinho LL. The transcriptome signature of the receptive bovine uterus determined at early gestation. PLoS One 2015; 10:e0122874. [PMID: 25849079 PMCID: PMC4388694 DOI: 10.1371/journal.pone.0122874] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 02/24/2015] [Indexed: 11/19/2022] Open
Abstract
Pregnancy success is critical to the profitability of cattle operations. However, the molecular events driving the uterine tissue towards embryo receptivity are poorly understood. This study aimed to characterize the uterine transcriptome profiles of pregnant (P) versus non-pregnant (NP) cows during early pregnancy and attempted to define a potential set of marker genes that can be valuable for predicting pregnancy outcome. Therefore, beef cows were synchronized (n=51) and artificially inseminated (n=36) at detected estrus. Six days after AI (D6), jugular blood samples and a biopsy from the uterine horn contralateral to the ovary containing the corpus luteum were collected. Based on pregnancy outcome on D30, samples were retrospectively allocated to the following groups: P (n=6) and NP (n=5). Both groups had similar plasma progesterone concentrations on D6. Uterine biopsies were submitted to RNA-Seq analysis in a Illumina platform. The 272,685,768 million filtered reads were mapped to the Bos Taurus reference genome and 14,654 genes were analyzed for differential expression between groups. Transcriptome data showed that 216 genes are differently expressed when comparing NP versus P uterine tissue (Padj ≤ 0.1). More specifically, 36 genes were up-regulated in P cows and 180 are up-regulated in NP cows. Functional enrichment and pathway analyses revealed enriched expression of genes associated with extracellular matrix remodeling in the NP cows and nucleotide binding, microsome and vesicular fraction in the P cows. From the 40 top-ranked genes, the transcript levels of nine genes were re-evaluated using qRT-PCR. In conclusion, this study characterized a unique set of genes, expressed in the uterus 6 days after insemination, that indicate a receptive state leading to pregnancy success. Furthermore, expression of such genes can be used as potential markers to efficiently predict pregnancy success.
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Affiliation(s)
- Mario Binelli
- Laboratório de Fisiologia e Endocrinologia Molecular, Department of Animal Reproduction, FMVZ-USP, Pirassununga, Sao Paulo, Brazil
- * E-mail:
| | - Saara C. Scolari
- Laboratório de Fisiologia e Endocrinologia Molecular, Department of Animal Reproduction, FMVZ-USP, Pirassununga, Sao Paulo, Brazil
| | - Guilherme Pugliesi
- Laboratório de Fisiologia e Endocrinologia Molecular, Department of Animal Reproduction, FMVZ-USP, Pirassununga, Sao Paulo, Brazil
| | - Veerle Van Hoeck
- Laboratório de Fisiologia e Endocrinologia Molecular, Department of Animal Reproduction, FMVZ-USP, Pirassununga, Sao Paulo, Brazil
| | - Angela M. Gonella-Diaza
- Laboratório de Fisiologia e Endocrinologia Molecular, Department of Animal Reproduction, FMVZ-USP, Pirassununga, Sao Paulo, Brazil
| | - Sónia C. S. Andrade
- Laboratório de Fisiologia e Endocrinologia Molecular, Department of Animal Reproduction, FMVZ-USP, Pirassununga, Sao Paulo, Brazil
| | - Gustavo R. Gasparin
- Laboratório de Genética Animal, Departamento de Zootecnia, ESALQ-USP, Pirassununga, Sao Paulo, Brazil
| | - Luiz L. Coutinho
- Laboratório de Genética Animal, Departamento de Zootecnia, ESALQ-USP, Pirassununga, Sao Paulo, Brazil
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Zapata F, Wilson NG, Howison M, Andrade SCS, Jörger KM, Schrödl M, Goetz FE, Giribet G, Dunn CW. Correction to Phylogenomic analyses of deep gastropod relationships reject Orthogastropoda. Proc Biol Sci 2015. [DOI: 10.1098/rspb.2014.2941] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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34
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Godoy TF, Moreira GCM, Boschiero C, Gheyas AA, Gasparin G, Paduan M, Andrade SCS, Montenegro H, Burt DW, Ledur MC, Coutinho LL. SNP and INDEL detection in a QTL region on chicken chromosome 2 associated with muscle deposition. Anim Genet 2015; 46:158-63. [PMID: 25690762 DOI: 10.1111/age.12271] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/09/2014] [Indexed: 11/28/2022]
Abstract
Genetic improvement is important for the poultry industry, contributing to increased efficiency of meat production and quality. Because breast muscle is the most valuable part of the chicken carcass, knowledge of polymorphisms influencing this trait can help breeding programs. Therefore, the complete genome of 18 chickens from two different experimental lines (broiler and layer) from EMBRAPA was sequenced, and SNPs and INDELs were detected in a QTL region for breast muscle deposition on chicken chromosome 2 between microsatellite markers MCW0185 and MCW0264 (105,849-112,649 kb). Initially, 94,674 unique SNPs and 10,448 unique INDELs were identified in the target region. After quality filtration, 77% of the SNPs (85,765) and 60% of the INDELs (7828) were retained. The studied region contains 66 genes, and functional annotation of the filtered variants identified 517 SNPs and three INDELs in exonic regions. Of these, 357 SNPs were classified as synonymous, 153 as non-synonymous, three as stopgain, four INDELs as frameshift and three INDELs as non-frameshift. These exonic mutations were identified in 37 of the 66 genes from the target region, three of which are related to muscle development (DTNA, RB1CC1 and MOS). Fifteen non-tolerated SNPs were detected in several genes (MEP1B, PRKDC, NSMAF, TRAPPC8, SDR16C5, CHD7, ST18 and RB1CC1). These loss-of-function and exonic variants present in genes related to muscle development can be considered candidate variants for further studies in chickens. Further association studies should be performed with these candidate mutations as should validation in commercial populations to allow a better explanation of QTL effects.
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Affiliation(s)
- T F Godoy
- Departamento de Zootecnia, ESALQ/USP, Av. Pádua Dias 11, Piracicaba, São Paulo, 13419-900, Brazil
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Moreira GCM, Godoy TF, Boschiero C, Gheyas A, Gasparin G, Andrade SCS, Paduan M, Montenegro H, Burt DW, Ledur MC, Coutinho LL. Variant discovery in a QTL region on chromosome 3 associated with fatness in chickens. Anim Genet 2015; 46:141-7. [PMID: 25643900 DOI: 10.1111/age.12263] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/01/2014] [Indexed: 12/17/2022]
Abstract
Abdominal fat content is an economically important trait in commercially bred chickens. Although many quantitative trait loci (QTL) related to fat deposition have been detected, the resolution for these regions is low and functional variants are still unknown. The current study was conducted aiming at increasing resolution for a region previously shown to have a QTL associated with fat deposition, to detect novel variants from this region and to annotate those variants to delineate potentially functional ones as candidates for future studies. To achieve this, 18 chickens from a parental generation used in a reciprocal cross between broiler and layer lines were sequenced using the Illumina next-generation platform with an initial coverage of 18X/chicken. The discovery of genetic variants was performed in a QTL region located on chromosome 3 between microsatellite markers LEI0161 and ADL0371 (33,595,706-42,632,651 bp). A total of 136,054 unique SNPs and 15,496 unique INDELs were detected in this region, and after quality filtering, 123,985 SNPs and 11,298 INDELs were retained. Of these variants, 386 SNPs and 15 INDELs were located in coding regions of genes related to important metabolic pathways. Loss-of-function variants were identified in several genes, and six of those, namely LOC771163, EGLN1, GNPAT, FAM120B, THBS2 and GGPS1, were related to fat deposition. Therefore, these loss-of-function variants are candidate mutations for conducting further studies on this important trait in chickens.
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Affiliation(s)
- G C M Moreira
- Departamento de Zootecnia, USP/ESALQ, Piracicaba, SP, 13418-900, Brazil
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Lemer S, Kawauchi GY, Andrade SCS, González VL, Boyle MJ, Giribet G. Re-evaluating the phylogeny of Sipuncula through transcriptomics. Mol Phylogenet Evol 2014; 83:174-83. [PMID: 25450098 DOI: 10.1016/j.ympev.2014.10.019] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 10/17/2014] [Accepted: 10/23/2014] [Indexed: 01/28/2023]
Abstract
Sipunculans (also known as peanut worms) are an ancient group of exclusively marine worms with a global distribution and a fossil record that dates back to the Early Cambrian. The systematics of sipunculans, now considered a distinct subclade of Annelida, has been studied for decades using morphological and molecular characters, and has reached the limits of Sanger-based approaches. Here, we reevaluate their family-level phylogeny by comparative transcriptomic analysis of eight species representing all known families within Sipuncula. Two data matrices with alternative gene occupancy levels (large matrix with 675 genes and 62% missing data; reduced matrix with 141 genes and 23% missing data) were analysed using concatenation and gene-tree methods, yielding congruent results and resolving each internal node with maximum support. We thus corroborate prior phylogenetic work based on molecular data, resolve outstanding issues with respect to the familial relationships of Aspidosiphonidae, Antillesomatidae and Phascolosomatidae, and highlight the next area of focus for sipunculan systematics.
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Affiliation(s)
- Sarah Lemer
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA.
| | - Gisele Y Kawauchi
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA; CEBIMar, Universidade de São Paulo, Praia do Cabelo Gordo, São Sebastião, São Paulo, Brazil
| | - Sónia C S Andrade
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA; Departamento de Zootecnia, ESALQ-USP, Piracicaba, São Paulo, Brazil
| | - Vanessa L González
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA; Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA
| | - Michael J Boyle
- Smithsonian Tropical Research Institute (STRI), Naos Marine Laboratories, Panama 0843/03092, Panama
| | - Gonzalo Giribet
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
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Andrade SCS, Montenegro H, Strand M, Schwartz ML, Kajihara H, Norenburg JL, Turbeville JM, Sundberg P, Giribet G. A Transcriptomic Approach to Ribbon Worm Systematics (Nemertea): Resolving the Pilidiophora Problem. Mol Biol Evol 2014; 31:3206-15. [DOI: 10.1093/molbev/msu253] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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Taboada S, Junoy J, Andrade SCS, Giribet G, Cristobo J, Avila C. On the identity of two Antarctic brooding nemerteans: redescription of Antarctonemertes valida (Bürger, 1893) and description of a new species in the genus Antarctonemertes Friedrich, 1955 (Nemertea, Hoplonemertea). Polar Biol 2013. [DOI: 10.1007/s00300-013-1360-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Riesgo A, Andrade SCS, Sharma PP, Novo M, Pérez-Porro AR, Vahtera V, González VL, Kawauchi GY, Giribet G. Comparative description of ten transcriptomes of newly sequenced invertebrates and efficiency estimation of genomic sampling in non-model taxa. Front Zool 2012; 9:33. [PMID: 23190771 PMCID: PMC3538665 DOI: 10.1186/1742-9994-9-33] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Accepted: 11/08/2012] [Indexed: 12/28/2022] Open
Abstract
UNLABELLED INTRODUCTION Traditionally, genomic or transcriptomic data have been restricted to a few model or emerging model organisms, and to a handful of species of medical and/or environmental importance. Next-generation sequencing techniques have the capability of yielding massive amounts of gene sequence data for virtually any species at a modest cost. Here we provide a comparative analysis of de novo assembled transcriptomic data for ten non-model species of previously understudied animal taxa. RESULTS cDNA libraries of ten species belonging to five animal phyla (2 Annelida [including Sipuncula], 2 Arthropoda, 2 Mollusca, 2 Nemertea, and 2 Porifera) were sequenced in different batches with an Illumina Genome Analyzer II (read length 100 or 150 bp), rendering between ca. 25 and 52 million reads per species. Read thinning, trimming, and de novo assembly were performed under different parameters to optimize output. Between 67,423 and 207,559 contigs were obtained across the ten species, post-optimization. Of those, 9,069 to 25,681 contigs retrieved blast hits against the NCBI non-redundant database, and approximately 50% of these were assigned with Gene Ontology terms, covering all major categories, and with similar percentages in all species. Local blasts against our datasets, using selected genes from major signaling pathways and housekeeping genes, revealed high efficiency in gene recovery compared to available genomes of closely related species. Intriguingly, our transcriptomic datasets detected multiple paralogues in all phyla and in nearly all gene pathways, including housekeeping genes that are traditionally used in phylogenetic applications for their purported single-copy nature. CONCLUSIONS We generated the first study of comparative transcriptomics across multiple animal phyla (comparing two species per phylum in most cases), established the first Illumina-based transcriptomic datasets for sponge, nemertean, and sipunculan species, and generated a tractable catalogue of annotated genes (or gene fragments) and protein families for ten newly sequenced non-model organisms, some of commercial importance (i.e., Octopus vulgaris). These comprehensive sets of genes can be readily used for phylogenetic analysis, gene expression profiling, developmental analysis, and can also be a powerful resource for gene discovery. The characterization of the transcriptomes of such a diverse array of animal species permitted the comparison of sequencing depth, functional annotation, and efficiency of genomic sampling using the same pipelines, which proved to be similar for all considered species. In addition, the datasets revealed their potential as a resource for paralogue detection, a recurrent concern in various aspects of biological inquiry, including phylogenetics, molecular evolution, development, and cellular biochemistry.
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Affiliation(s)
- Ana Riesgo
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
- Centro de Estudios Avanzados de Blanes, CSIC, c/ Accés a la Cala St. Francesc 14, Blanes, Girona, 17300, Spain
| | - Sónia C S Andrade
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
| | - Prashant P Sharma
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
| | - Marta Novo
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
- Current address: Cardiff School of Biosciences, Cardiff University, BIOSI 1, Museum Avenue, Cardiff, CF10 3TL, UK
| | - Alicia R Pérez-Porro
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
- Centro de Estudios Avanzados de Blanes, CSIC, c/ Accés a la Cala St. Francesc 14, Blanes, Girona, 17300, Spain
| | - Varpu Vahtera
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
- Current address: Finnish Museum of Natural History, Zoology Unit, Pohjoinen Rautatiekatu 13, 00014 University of Helsinki, Helsinki, Finland
| | - Vanessa L González
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
| | - Gisele Y Kawauchi
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
| | - Gonzalo Giribet
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
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Andrade SCS, Strand M, Schwartz M, Chen H, Kajihara H, von Döhren J, Sun S, Junoy J, Thiel M, Norenburg JL, Turbeville JM, Giribet G, Sundberg P. Disentangling ribbon worm relationships: multi-locus analysis supports traditional classification of the phylum Nemertea. Cladistics 2011; 28:141-159. [DOI: 10.1111/j.1096-0031.2011.00376.x] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
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Abstract
The hoplonemertean Vieitezia luzmurubeae, gen. et sp. nov. is described from specimens collected in a national park on the north-west Iberian Peninsula, the Parque Nacional Marítimo-Terrestre das Illas Atlánticas de Galicia. The species, previously mistaken as the Mediterranean species Tetrastemma vittigerum (Bürger, 1904), is frequently associated with two common species of sea squirt, Phallusia mamillata (Cuvier, 1815) and Ciona intestinalis (Linnaeus, 1767), inside which the nemertean completes its life cycle. Some of the specimens examined were protandrous hermaphrodites. Data on morphology and anatomy are provided with illustrations. Sequences of the nuclear ribosomal gene 18S rRNA and the mitochondrial gene cytochrome c oxidase subunit I were compared with those of other hoplonemertean species and all phylogenetic analyses suggested that Vieitezia is sister to the genus Gononemertes, which parasitises ascidians, within a clade also containing the genera Oerstedia and Nemertellina. In contrast, the morphologically similar genus Tetrastemma appears in a separate clade. This study stresses the need for combining molecular and morphological data when studying nemertean biodiversity.
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Moraes EM, Abreu AG, Andrade SCS, Sene FM, Solferini VN. Population genetic structure of two columnar cacti with a patchy distribution in eastern Brazil. Genetica 2006; 125:311-23. [PMID: 16247702 DOI: 10.1007/s10709-005-0716-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2005] [Accepted: 07/08/2005] [Indexed: 10/25/2022]
Abstract
The genetic variability and population genetic structure of six populations of Praecereus euchlorus and Pilosocereus machrisii were investigated. The genetic variability in single populations of Pilosocereus vilaboensis, Pilosocereus aureispinus, and Facheiroa squamosa was also examined. All of these cacti species have a patchy geographic distribution in which they are restricted to small areas of xeric habitats in eastern Brazil. An analysis of genetic structure was used to gain insights into the historical mechanisms responsible for the patchy distribution of P. euchlorus and P. machrisii. High genetic variability was found at the populational level in all species (P=58.9-92.8%, A(p)=2.34-3.33, H(e)=0.266-0.401), and did not support our expectations of low variability based on the small population size. Substantial inbreeding was detected within populations (F(IS)=0.370-0.623). In agreement with their insular distribution patterns, P. euchlorus and P. machrisii had a high genetic differentiation (F(ST)=0.484 and F(ST)=0.281, respectively), with no evidence of isolation by distance. Accordingly, estimates of gene flow (N(m)) calculated from F(ST) and private alleles were below the level of N(m)=1 in P. machrisii and P. euchlorus. These results favored historical fragmentation as the mechanism responsible for the patchy distribution of these two species. The genetic distance between P. machrisii and P. vilaboensis was not compatible with their taxonomic distinction, indicating a possible local speciation event in this genus, or the occurrence of introgression events.
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Affiliation(s)
- Evandro M Moraes
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto, São Paulo, Brazil.
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Andrade SCS, Solferini VN. THE INFLUENCE OF SIZE ON THE RADULA OF LITTORARIA ANGULIFERA (GASTROPODA: LITTORINIDAE). Malacologia 2006. [DOI: 10.4002/1543-8120-49.1.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Castro AV, Nascimento-Carvalho CM, Ney-Oliveria F, Araújo-Neto CA, Andrade SCS, Loureiro LLS, Luz PO. Additional markers to refine the World Health Organization algorithm for diagnosis of pneumonia. Indian Pediatr 2005; 42:773-81. [PMID: 16141478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
INTRODUCTION WHO guidelines for primary care of children with tachypnea indicate that all should receive antibiotics for presumed pneumonia. These guidelines have led to excessive antibiotic use. OBJECTIVE To examine the value of history of previous respiratory distress, chest indrawing and fever, and response to bronchodilator(BD) to refine these guidelines. DESIGN Prospective study. SETTING Urban tertiary care hospital. SUBJECTS Children, between the ages of 6 and 59 months, presenting with cough and tachypnea. METHODS 182 children were enrolled. Each child had a chest X-ray that was read by two blinded, independent radiologists. Discordance between the two radiologists led to excluding 17 patients. The remaining 165 children were examined for fever and/or chest indrawing, and if they had a history of previous respiratory distress, challenge with a BD. The association of persistent tachypnea after BD and presence of pulmonary infiltrates was recorded. RESULTS The median age was 22 months (mean 25.1 +- 14.5 mo) and 75.8% were aged greater than 1 year. There were 58.8% males. Previous respiratory distress occurred in 65.0% and 79.2% of children aged less than 1 year and 1 year, respectively. Pneumonia was radiologically diagnosed in 26/165 (15.8%). 2/40 (5 %) of children without a history of previous respiratory distress had pneumonia diagnosed. Of 125 children with history of previous respiratory distress, pneumonia was identified in 24 (19.2 %). Persistence of tachypnea after BD was associated with pulmonary infiltrate in 14/24 (58.3%), whereas, tachypnea persisted in 32/101 (31.7%) children without pulmonary infiltrates (P = 0.02). The negative predictive value of resolution of tachypnea was 87.3% (95% CI 77.5 93.4). BD non-response was most useful in children without fever and/or with chest indrawing to indicate pneumonia as the cause of the tachypnea. CONCLUSION This study indicates that by adding the simple procedures of a history of previous respiratory distress, recording of fever and chest indrawing, and observing the response to bronchodilators, pneumonia can be reliably identified in children presenting with tachypnea and cough. It is probable that this approach to management of children with cough and tachypnea could reduce unnecessary use of antibiotics.
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Affiliation(s)
- A V Castro
- Departments of Pediatrics and Radiodiagnosis, Federal University of Bahia and the Emergency Department, Jorge Valente Hospital, Salvador, Bahia, Brazil
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