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Delicado D, Hauffe T, Wilke T. Fifth mass extinction event triggered the diversification of the largest family of freshwater gastropods (Caenogastropoda: Truncatelloidea: Hydrobiidae). Cladistics 2024; 40:82-96. [PMID: 37712584 DOI: 10.1111/cla.12558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 08/09/2023] [Accepted: 08/21/2023] [Indexed: 09/16/2023] Open
Abstract
The fifth mass extinction event (MEE) at the Cretaceous-Palaeogene (K-Pg) boundary 66 million years ago (Ma) led to massive species loss but also triggered the diversification of higher taxa. Five models have been proposed depending on whether this diversification occurred before, during or after the K-Pg boundary and the rate of species accumulation. While the effects of the K-Pg MEE on vertebrate evolution are relatively well understood, the impact on invertebrates, particularly in freshwater ecosystems, remains controversial. One example is the hyperdiverse Hydrobiidae-the most species-rich family of freshwater gastropods. Whereas some studies place its origin in the Jurassic or even Carboniferous, most fossil records postdate the K-Pg event. We therefore used robustly time-calibrated multi-locus phylogenies of >400 species representing >100 hydrobiid genera to unravel its evolutionary history and patterns of diversification. We found that the family started diversifying shortly after the K-Pg boundary (∼60 Ma; 95% highest posterior density 52-69 Ma). Lineage richness gradually increased to the present and phylogenetic diversity until ∼25 Ma. These findings suggest that diversification was not initially driven by ecological opportunity. Combining the two criteria of timing and rate of diversification, a soft-explosive diversification model of aquatic vertebrates best fits the patterns observed. We also show that most higher hydrobiid taxa (i.e. subfamilies) diversified from the Middle Oligocene to Middle Miocene (i.e. 12-28 Ma). Two of the 15 major clades delimited are described here as new subfamilies (i.e. Bullaregiinae n. subfam. and Pontobelgrandiellinae n. subfam.), whose members are restricted to subterranean waters. Our results are an important contribution to understanding how the fifth MEE has shaped evolution and patterns of biodiversity in continental aquatic systems. Given the high extinction risks faced by many hydrobiids today, they also emphasise the need to study the biodiversity of vulnerable ecosystems.
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Affiliation(s)
- Diana Delicado
- Animal Ecology and Systematics, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32 (IFZ), D-35392, Giessen, Germany
| | - Torsten Hauffe
- Department of Biology, University of Fribourg and Swiss Institute of Bioinformatics, Chemin du Musée 10, CH-1700, Fribourg, Switzerland
| | - Thomas Wilke
- Animal Ecology and Systematics, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32 (IFZ), D-35392, Giessen, Germany
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Duong TY, Pham LTK, Le XTK, Nguyen NTT, Nor AM, Le TH. Mitophylogeny of Pangasiid Catfishes and its Taxonomic Implications for Pangasiidae and the Suborder Siluroidei. Zool Stud 2023; 62:e48. [PMID: 37965298 PMCID: PMC10641430 DOI: 10.6620/zs.2023.62-48] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 07/24/2023] [Indexed: 11/16/2023]
Abstract
Pangasiidae (catfish order: Siluriformes) comprises 30 valid catfish species in four genera: Pangasius, Pangasianodon, Helicophagus, and Pseudolais. Their systematics are frequently revised due to the addition of newly described species. Although Pangasiidae is known to be a monophyletic family, the generic and phylogenetic relationships among the taxa are poorly resolved. This study characterized three newly obtained complete mitogenomes of Mekong River catfishes from Vietnam (Pangasius mekongensis, Pangasius krempfi, and Pangasianodon hypophthalmus), as well as the inter-and intrafamilial relationships of the Pangasiidae and catfish families in Siluroidei. The genomic features of their mitogenomes were similar to those of previously reported pangasiids, including all regulatory elements, extended terminal associated sequences (ETAS), and conserved sequence blocks (CSBs) (CSB-1, CSB-2, CSB-3, and CSBs, A to F) in the control region. A comprehensive phylogeny constructed from datasets of multiple 13 PCG sequences from 117 complete mitogenomes of 32 recognized siluriform families established Pangasiidae as monophyletic and a sister group of Austroglanididae. The [Pangasiidae + Austroglanididae] + (Ictaluridae + Cranoglanididae) + Ariidae] clade is a sister to the "Big Africa" major clade of Siluriformes. Furthermore, both phylogenies constructed from the single barcodes (83 partial cox1 and 80 partial cytB, respectively) clearly indicate genus relationships within Pangasiidae. Pangasianodon was monophyletic and a sister to the (Pangasius + Helicophagus + Pseudolais) group. Within the genus Pangasius, P. mekongensis was placed as a sister taxon to P. pangasius. Pangasius sanitwongsei was found to be related to and grouped with Pangasianodon, but in single-gene phylogenies, it was assigned to the Pangasius + Helicophagus + Pseudolais group. The datasets in this study are useful for studying pangasiid systematics, taxonomy and evolution.
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Affiliation(s)
- Thuy Yen Duong
- College of Aquaculture and Fisheries, Can Tho University, 3/2 street, Can Tho City, Vietnam. E-mail: (Duong)
| | - Linh Thi Khanh Pham
- Immunology Department, Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST). 18. Hoang Quoc Viet Rd., Cau Giay, Hanoi, Vietnam. E-mail: (Le); (Pham); (Kim Le)
- Graduate University of Science and Technology (GUST), Vietnam Academy of Science and Technology (VAST), 18. Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - Xuyen Thi Kim Le
- Immunology Department, Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST). 18. Hoang Quoc Viet Rd., Cau Giay, Hanoi, Vietnam. E-mail: (Le); (Pham); (Kim Le)
- Graduate University of Science and Technology (GUST), Vietnam Academy of Science and Technology (VAST), 18. Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - Ngoc Tran Thi Nguyen
- College of Aquaculture and Fisheries, Can Tho University, 3/2 street, Can Tho City, Vietnam. E-mail: (Duong)
| | - Azizah Mohd Nor
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia. E-mail: (Nor)
| | - Thanh Hoa Le
- Immunology Department, Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST). 18. Hoang Quoc Viet Rd., Cau Giay, Hanoi, Vietnam. E-mail: (Le); (Pham); (Kim Le)
- Graduate University of Science and Technology (GUST), Vietnam Academy of Science and Technology (VAST), 18. Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
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Zheng S, Tao W, Tao H, Yang H, Wu L, Shao F, Wang Z, Jin L, Peng Z, Wang D, Zhang Y. Characterization of the male-specific region containing the candidate sex-determining gene in Amur catfish (Silurus asotus) using third-generation- and pool-sequencing data. Int J Biol Macromol 2023; 248:125908. [PMID: 37482150 DOI: 10.1016/j.ijbiomac.2023.125908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 06/30/2023] [Accepted: 07/11/2023] [Indexed: 07/25/2023]
Abstract
Amur catfish (Silurus asotus) is an ecologically and economically important fish species in Asia. Here, we assembled the female and male Amur catfish genomes, with genome sizes of 757.15 and 755.44 Mb, respectively, at the chromosome level using nanopore and Hi-C technologies. Consistent with the known diploid chromosome count, both genomes contained 29 chromosome-size scaffolds covering 98.80 and 98.73 % of the complete haplotypic assembly with scaffold N50 of 28.87 and 27.29 Mb, respectively. The female (n = 40) and male (n = 40) pools were re-sequenced. Comparative analysis of sequencing and re-sequencing data from both sexes confirmed the presence of an XX/XY sex determination system in Amur catfish and revealed Chr5 as the sex chromosome containing an approximately 400 kb Y-specific region (MSY). Gene annotation revealed a male-specific duplicate of amhr2, namely amhr2y, in MSY, which is male-specific in different wild populations and expressed only in the testes. Amur catfish shared partially syntenic MSY and amhr2y genes with the southern catfish (S. meridionalis, Chr24), which were located on different chromosomes. High sequence divergence between amhr2y and amhr2 and high sequence similarity with amhr2y were observed in both species. These results indicate the common origin of the sex-determining (SD) gene and transition of amhr2y in the two Silurus species. Accumulation of repetitive elements in the MSY of both species may be the main driver of the transition of amhr2y. Overall, our study provides valuable catfish genomic resources. Moreover, determination of amhr2y as the candidate SD gene in Amur catfish provides another example of amhr2 as the SD gene in fish.
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Affiliation(s)
- Shuqing Zheng
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Wenjing Tao
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Hongyan Tao
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Haowen Yang
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Limin Wu
- Engineering Lab of Henan Province for Aquatic Animal Disease Control, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, College of Fisheries, Henan Normal University, Xinxiang 453007, China
| | - Feng Shao
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Zhijian Wang
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Li Jin
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Zuogang Peng
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China.
| | - Deshou Wang
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China.
| | - Yaoguang Zhang
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China.
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Conte M, de Campos DF, Eme J. Effective practices for thermal tolerance polygon experiments using mottled catfish Corydoras paleatus. J Therm Biol 2023; 115:103616. [PMID: 37437371 DOI: 10.1016/j.jtherbio.2023.103616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 06/06/2023] [Accepted: 06/06/2023] [Indexed: 07/14/2023]
Abstract
Temperature is an important environmental factor that affects how organisms allocate metabolic resources to physiological processes. Laboratory experiments that determine absolute thermal limits for representative species are important for understanding how fishes are affected by climate change. Critical Thermal Methodology (CTM) and Chronic Lethal Methodology (CLM) experiments were utilized to construct a complete thermal tolerance polygon for the South American fish species, Mottled catfish (Corydoras paleatus). Mottled catfish showed Chronic Lethal Maxima (CLMax) of 34.9 ± 0.52 °C and Chronic Lethal Minima (CLMin) of 3.8 ± 0.08 °C. Fish were chronically acclimated (∼2 weeks) to 6 temperatures ranging from 7.2 ± 0.05 °C →32.2 ± 0.16 °C (7 °C, 12 °C, 17 °C, 22 °C, 27 °C, and 32 °C), and CTM used to estimate upper and lower acute temperature tolerance. Linear regressions of Critical Thermal Maxima (CTMax) and Minima (CTMin) data with each acclimation temperature were used along with CLMax and CLMin to create a complete thermal tolerance polygon. The highest CTMax was 38.4 ± 0.60 °C for fish acclimated to 32.2 ± 0.16 °C, and the lowest CTMin was 3.36 ± 1.84 °C for fish acclimated to 7.2 ± 0.05 °C. Mottled catfish have a polygon measuring 785.7°C2, and the slope of the linear regressions showed the species gained 0.55 °C and 0.32 °C of upper and lower tolerance per degree of acclimation temperature, respectively. We compared slopes of CTMax or CTMin regression lines to each other using a set of comparisons between 3, 4, 5, or 6 acclimation temperatures. Our data demonstrated that 3 acclimation temperatures were as sufficient as 4 → 6 to pair with estimates of chronic upper and lower thermal limits for accurately determining a complete thermal tolerance polygon. Construction of this species' complete thermal tolerance polygon provides a template for other researchers. The following is sufficient to generate a complete thermal tolerance polygon: Three chronic acclimation temperatures that are spread somewhat evenly across a species' thermal range, include an estimation of CLMax and CLMin, and are followed by CTMax and CTMin measurements.
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Affiliation(s)
- Madison Conte
- Department of Biological Sciences, California State University San Marcos, 333 S. Twin Oaks Blvd., San Marcos, CA, USA.
| | - Derek Felipe de Campos
- Laboratory of Ecophysiology and Molecular Evolution, Biodiversity Coordination, National Institute for the Amazonian Research, Av. Andre Araujo, 2936, Manaus, AM, Brazil.
| | - John Eme
- Department of Biological Sciences, California State University San Marcos, 333 S. Twin Oaks Blvd., San Marcos, CA, USA.
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Pérez-Rodríguez R, Domínguez-Domínguez O, Pedraza-Lara C, Rosas-Valdez R, Pérez-Ponce de León G, García-Andrade AB, Doadrio I. Multi-locus phylogeny of the catfish genus Ictalurus Rafinesque, 1820 (Actinopterygii, Siluriformes) and its systematic and evolutionary implications. BMC Ecol Evol 2023; 23:27. [PMID: 37370016 PMCID: PMC10304232 DOI: 10.1186/s12862-023-02134-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
BACKGROUND Ictalurus is one of the most representative groups of North American freshwater fishes. Although this group has a well-studied fossil record and has been the subject of several morphological and molecular phylogenetic studies, incomplete taxonomic sampling and insufficient taxonomic studies have produced a rather complex classification, along with intricate patterns of evolutionary history in the genus that are considered unresolved and remain under debate. RESULTS Based on four loci and the most comprehensive taxonomic sampling analyzed to date, including currently recognized species, previously synonymized species, undescribed taxa, and poorly studied populations, this study produced a resolved phylogenetic framework that provided plausible species delimitation and an evolutionary time framework for the genus Ictalurus. CONCLUSIONS Our phylogenetic hypothesis revealed that Ictalurus comprises at least 13 evolutionary units, partially corroborating the current classification and identifying populations that emerge as putative undescribed taxa. The divergence times of the species indicate that the diversification of Ictalurus dates to the early Oligocene, confirming its status as one of the oldest genera within the family Ictaluridae.
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Affiliation(s)
- Rodolfo Pérez-Rodríguez
- Laboratorio de Biología Acuática, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Ciudad Universitaria, Morelia, 58000, Michoacán, México
| | - Omar Domínguez-Domínguez
- Laboratorio de Biología Acuática, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Ciudad Universitaria, Morelia, 58000, Michoacán, México
| | - Carlos Pedraza-Lara
- Forensic Science, Medicine School, National Autonomous University of Mexico, Circuito de la investigación científica s/n, Ciudad Universitaria, Coyoacan, 04510, CdMx, Mexico
| | - Rogelio Rosas-Valdez
- Laboratorio de Colecciones Biológicas y Sistemática Molecular, Unidad Académica de Ciencias Biológicas, Universidad Autónoma de Zacatecas, Av. Preparatoria S/N, Campus Universitario II, Col. Agronómica, Zacatecas, C. P. 98066, México
| | - Gerardo Pérez-Ponce de León
- Instituto de Biología, UNAM, Circuito exterior s/n, Ciudad Universitaria, Coyoacán, C.P. 04510, D.F, México
- Escuela Nacional de Estudios Superiores Unidad Mérida, Universidad Nacional Autónoma de México, Km 4.5 Carretera Mérida-Tetiz, Ucú, Yucatán, México
| | - Ana Berenice García-Andrade
- Laboratorio de Biología Acuática, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Ciudad Universitaria, Morelia, 58000, Michoacán, México
- Laboratorio de Macroecología Evolutiva, Red de Biología Evolutiva, Instituto de Ecología, A.C. Carretera antigua a Coatepec 351, El Haya, Xalapa, 91070, Veracruz, México
| | - Ignacio Doadrio
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales, CSIC, c/José Gutiérrez Abascal 2, Madrid, E-28006, España.
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Day JJ, Steell EM, Vigliotta TR, Withey LA, Bills R, Friel JP, Genner MJ, Stiassny MLJ. Exceptional levels of species discovery ameliorate inferences of the biogeography and diversification of an Afrotropical catfish family. Mol Phylogenet Evol 2023; 182:107754. [PMID: 36906193 DOI: 10.1016/j.ympev.2023.107754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 02/24/2023] [Accepted: 03/05/2023] [Indexed: 03/13/2023]
Abstract
Endeavours in species discovery, particularly the characterisation of cryptic species, have been greatly aided by the application of DNA molecular sequence data to phylogenetic reconstruction and inference of evolutionary and biogeographic processes. However, the extent of cryptic and undescribed diversity remains unclear in tropical freshwaters, where biodiversity is declining at alarming rates. To investigate how data on previously undiscovered biodiversity impacts inferences of biogeography and diversification dynamics, we generated a densely sampled species-level family tree of Afrotropical Mochokidae catfishes (220 valid species) that was ca. 70 % complete. This was achieved through extensive continental sampling specifically targeting the genus Chiloglanis a specialist of the relatively unexplored fast-flowing lotic habitat. Applying multiple species-delimitation methods, we report exceptional levels of species discovery for a vertebrate genus, conservatively delimiting a staggering ca. 50 putative new Chiloglanis species, resulting in a near 80 % increase in species richness for the genus. Biogeographic reconstructions of the family identified the Congo Basin as a critical region in the generation of mochokid diversity, and further revealed complex scenarios for the build-up of continental assemblages of the two most species rich mochokid genera, Synodontis and Chiloglanis. While Syndontis showed most divergence events within freshwater ecoregions consistent with largely in situ diversification, Chiloglanis showed much less aggregation of freshwater ecoregions, suggesting dispersal as a key diversification process in this older group. Despite the significant increase in mochokid diversity identified here, diversification rates were best supported by a constant rate model consistent with patterns in many other tropical continental radiations. While our findings highlight fast-flowing lotic freshwaters as potential hotspots for undescribed and cryptic species diversity, a third of all freshwater fishes are currently threatened with extinction, signifying an urgent need to increase exploration of tropical freshwaters to better characterise and conserve its biodiversity.
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Affiliation(s)
- Julia J Day
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK.
| | - Elizabeth M Steell
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Thomas R Vigliotta
- Department of Ichthyology, American Museum of Natural History, New York, NY, USA
| | - Lewis A Withey
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Roger Bills
- South African Institute for Aquatic Biodiversity, Private Bag, 1015, 6140 Grahamstown, South Africa
| | - John P Friel
- Alabama Museum of Natural History, The University of Alabama, Box 870340, 35487-0340 Tuscaloosa, AL, USA
| | - Martin J Genner
- School of Biological Sciences, University of Bristol, Life Sciences Building, 24, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Melanie L J Stiassny
- Department of Ichthyology, American Museum of Natural History, New York, NY, USA
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Janzen FH, Pérez-Rodríguez R, Domínguez-Domínguez O, Hendrickson DA, Sabaj MH, Blouin-Demers G. Phylogenetic relationships of the North American catfishes (Ictaluridae, Siluriformes): Investigating the origins and parallel evolution of the troglobitic species. Mol Phylogenet Evol 2023; 182:107746. [PMID: 36849094 DOI: 10.1016/j.ympev.2023.107746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 02/09/2023] [Accepted: 02/22/2023] [Indexed: 02/27/2023]
Abstract
Insular habitats have played an important role in developing evolutionary theory, including natural selection and island biogeography. Caves are insular habitats that place extreme selective pressures on organisms due to the absence of light and food scarcity. Therefore, cave organisms present an excellent opportunity for studying colonization and speciation in response to the unique abiotic conditions that require extreme adaptations. One vertebrate family, the North American catfishes (Ictaluridae), includes four troglobitic species that inhabit the karst region bordering the western Gulf of Mexico. The phylogenetic relationships of these species have been contentious, and conflicting hypotheses have been proposed to explain their origins. The purpose of our study was to construct a time-calibrated phylogeny of Ictaluridae using first-occurrence fossil data and the largest molecular dataset on the group to date. We test the hypothesis that troglobitic ictalurids have evolved in parallel, thus resulting from repeated cave colonization events. We found that Prietella lundbergi is sister to surface-dwelling Ictalurus and that Prietella phreatophila + Trogloglanis pattersoni are sister to surface-dwelling Ameiurus, suggesting that ictalurids colonized subterranean habitats at least twice in evolutionary history. The sister relationship between Prietella phreatophila and Trogloglanis pattersoni may indicate that these two species diverged from a common ancestor following a subterranean dispersal event between Texas and Coahuila aquifers. We recovered Prietella as a polyphyletic genus and recommend P. lundbergi be removed from this genus. With respect to Ameiurus, we found evidence for a potentially undescribed species sister to A. platycephalus, which warrants further investigation of Atlantic and Gulf slope Ameiurus species. In Ictalurus, we identified shallow divergence between I. dugesii and I. ochoterenai, I. australis and I. mexicanus, and I. furcatus and I. meridionalis, indicating a need to reexamine the validity of each species. Lastly, we propose minor revisions to the intrageneric classification of Noturus including the restriction of subgenus Schilbeodes to N. gyrinus (type species), N. lachneri, N. leptacanthus, and N. nocturnus.
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Affiliation(s)
- Francesco H Janzen
- Department of Biology, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada.
| | | | | | - Dean A Hendrickson
- Biodiversity Center, Texas Natural History Collections, University of Texas at Austin, Austin, TX 78758, United States
| | - Mark H Sabaj
- The Academy of Natural Sciences of Drexel University, Philadelphia, PA 19103, United States
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8
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Kundu S, De Alwis PS, Binarao JD, Lee SR, Kim AR, Gietbong FZ, Yi M, Kim HW. Mitochondrial DNA Corroborates the Genetic Variability of Clarias Catfishes (Siluriformes, Clariidae) from Cameroon. Life (Basel) 2023; 13:life13051068. [PMID: 37240713 DOI: 10.3390/life13051068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 04/07/2023] [Accepted: 04/21/2023] [Indexed: 05/28/2023] Open
Abstract
The airbreathing walking catfish (Clariidae: Clarias) comprises 32 species that are endemic to African freshwater systems. The species-level identification of this group is challenging due to their complex taxonomy and polymorphism. Prior to this study, the biological and ecological studies were restricted to a single species, Clarias gariepinus, resulting in a biased view of their genetic diversity in African waters. Here, we generated the 63-mitochondrial Cytochrome c oxidase subunit 1 (COI) gene sequences of Clarias camerunensis and Clarias gariepinus from the Nyong River in Cameroon. Both C. camerunensis and C. gariepinus species maintained adequate intra-species (2.7% and 2.31%) and inter-species (6.9% to 16.8% and 11.4% to 15.1%) genetic distances with other Clarias congeners distributed in African and Asian/Southeast Asian drainages. The mtCOI sequences revealed 13 and 20 unique haplotypes of C. camerunensis and C. gariepinus, respectively. The TCS networks revealed distinct haplotypes of C. camerunensis and shared haplotypes of C. gariepinus in African waters. The multiple species delimitation approaches (ABGD and PTP) revealed a total of 20 and 22 molecular operational taxonomic units (MOTUs), respectively. Among the two Clarias species examined, we found more than one MOTU in C. camerunensis, which is consistent with population structure and tree topology results. The phylogeny generated through Bayesian Inference analysis clearly separated C. camerunensis and C. gariepinus from other Clarias species with high posterior probability supports. The present study elucidates the occurrence of possible cryptic diversity and allopatric speciation of C. camerunensis in African drainages. Further, the present study confirms the reduced genetic diversity of C. gariepinus across its native and introduced range, which might have been induced by unscientific aquaculture practices. The study recommends a similar approach to the same and related species from different river basins to illuminate the true diversity of Clarias species in Africa and other countries.
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Affiliation(s)
- Shantanu Kundu
- Department of Marine Biology, Pukyong National University, Busan 48513, Republic of Korea
| | - Piyumi S De Alwis
- Department of Marine Biology, Pukyong National University, Busan 48513, Republic of Korea
| | - Jerome D Binarao
- Department of Marine Biology, Pukyong National University, Busan 48513, Republic of Korea
| | - Soo-Rin Lee
- Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan 48513, Republic of Korea
| | - Ah Ran Kim
- Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan 48513, Republic of Korea
| | | | - Myunggi Yi
- Department of Biomedical Engineering, Pukyong National University, Busan 48513, Republic of Korea
| | - Hyun-Woo Kim
- Department of Marine Biology, Pukyong National University, Busan 48513, Republic of Korea
- Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan 48513, Republic of Korea
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Mitochondriomics of Clarias Fishes (Siluriformes: Clariidae) with a New Assembly of Clarias camerunensis: Insights into the Genetic Characterization and Diversification. Life (Basel) 2023; 13:life13020482. [PMID: 36836839 PMCID: PMC9960581 DOI: 10.3390/life13020482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/06/2023] [Accepted: 02/08/2023] [Indexed: 02/12/2023] Open
Abstract
The mitogenome of an endemic catfish Clarias camerunensis was determined from the Cameroon water. This circular mitogenome was 16,511 bp in length and comprised 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and a single AT-rich control region. The heavy strand accommodates 28 genes, whereas the light strand is constituted by ND6 and eight transfer RNA (tRNA) genes. The C. camerunensis mitochondrial genome is AT biased (56.89%), as showcased in other Clarias species. The comparative analyses revealed that most of the Clarias species have 6 overlapping and 11 intergenic spacer regions. Most of the PCGs were initiated and terminated with the ATG start codon and TAA stop codon, respectively. The tRNAs of C. camerunensis folded into the distinctive cloverleaf secondary structure, except trnS1. The placement of the conserved domains in the control region was similar in all the Clarias species with highly variable nucleotides in CSB-I. Both maximum likelihood and Bayesian-based matrilineal phylogenies distinctly separated all Clarias species into five clades on the basis of their known distributions (South China, Sundaland, Indochina, India, and Africa). The TimeTree analysis revealed that the two major clades (Indo-Africa and Asia) of Clarias species might have diverged during the Paleogene (≈28.66 MYA). Our findings revealed the separation of Indian species (C. dussumieri) and African species (C. camerunensis and Clarias gariepinus) took place during the Paleogene, as well as the South Chinese species (Clarias fuscus) and Sundaland species (Clarias batrachus) splits from the Indochinese species (Clarias macrocephalus) during the Neogene through independent colonization. This pattern of biotic relationships highlights the influence of topography and geological events in determining the evolutionary history of Clarias species. The enrichment of mitogenomic data and multiple nuclear loci from their native range or type locality will confirm the true diversification of Clarias species in African and Asian countries.
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10
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Conith MR, Ringo D, Conith AJ, Deleon A, Wagner M, McMenamin S, Cason C, Cooper WJ. The Evolution of Feeding Mechanics in the Danioninae, or Why Giant Danios Don't Suck Like Zebrafish. Integr Org Biol 2022; 4:obac049. [PMID: 36518182 PMCID: PMC9730500 DOI: 10.1093/iob/obac049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 09/11/2022] [Accepted: 11/11/2022] [Indexed: 08/24/2023] Open
Abstract
By linking anatomical structure to mechanical performance we can improve our understanding of how selection shapes morphology. Here we examined the functional morphology of feeding in fishes of the subfamily Danioninae (order Cypriniformes) to determine aspects of cranial evolution connected with their trophic diversification. The Danioninae comprise three major lineages and each employs a different feeding strategy. We gathered data on skull form and function from species in each clade, then assessed their evolutionary dynamics using phylogenetic-comparative methods. Differences between clades are strongly associated with differences in jaw protrusion. The paedomorphic Danionella clade does not use jaw protrusion at all, members of the Danio clade use jaw protrusion for suction production and prey capture, and members of the sister clade to Danio (e.g., Devario and Microdevario) use jaw protrusion to retain prey after capture. The shape of the premaxillary bone is a major determinant of protrusion ability, and premaxilla morphology in each of these lineages is consistent with their protrusion strategies. Premaxilla shapes have evolved rapidly, which indicates that they have been subjected to strong selection. We compared premaxilla development in giant danio (Devario aequipinnatus) and zebrafish (Danio rerio) and discuss a developmental mechanism that could shift danionine fishes between the feeding strategies employed by these species and their respective clades. We also identified a highly integrated evolutionary module that has been an important factor in the evolution of trophic mechanics within the Danioninae.
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Affiliation(s)
- M R Conith
- Department of Biology, Western Washington University, Bellingham, WA 98225, USA
| | - D Ringo
- Department of Biology, Western Washington University, Bellingham, WA 98225, USA
| | - A J Conith
- Department of Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - A Deleon
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
| | - M Wagner
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
| | - S McMenamin
- Biology Department, Boston College, Chestnut Hill, MA 02467, USA
| | - C Cason
- Marine and Coastal Science, Western Washington University, Bellingham, WA 98225, USA
| | - W J Cooper
- Department of Biology, Western Washington University, Bellingham, WA 98225, USA
- Marine and Coastal Science, Western Washington University, Bellingham, WA 98225, USA
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11
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Zhu C, Liu H, Pan Z, Cheng L, Sun Y, Wang H, Chang G, Wu N, Ding H, Zhao H, Zhang L, Yu X. Insights into chromosomal evolution and sex determination of Pseudobagrus ussuriensis (Bagridae, Siluriformes) based on a chromosome-level genome. DNA Res 2022; 29:6647841. [PMID: 35861402 PMCID: PMC9358014 DOI: 10.1093/dnares/dsac028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 07/20/2022] [Indexed: 12/01/2022] Open
Abstract
Pseudobagrus ussuriensis is an aquaculture catfish with significant sexual dimorphism. In this study, a chromosome-level genome with a size of 741.97 Mb was assembled for female P. ussuriensis. A total of 26 chromosome-level contigs covering 97.34% of the whole-genome assembly were obtained with an N50 of 28.53 Mb and an L50 of 11. A total of 24,075 protein-coding genes were identified, with 91.54% (22,039) genes being functionally annotated. Based on the genome assembly, four chromosome evolution clusters of catfishes were identified and the formation process of P. ussuriensis chromosomes was predicted. A total of 55 sex-related quantitative trait loci (QTLs) with a phenotypic variance explained value of 100% were located on chromosome 8 (chr08). The QTLs and other previously identified sex-specific markers were located in a sex-determining region of 16.83 Mb (from 6.90 to 23.73 Mb) on chr08, which was predicted as the X chromosome. The sex-determining region comprised 554 genes, with 135 of which being differently expressed between males and females/pseudofemales, and 16 candidate sex-determining genes were screened out. The results of this study provided a useful chromosome-level genome for genetic, genomic and evolutionary studies of P. ussuriensis, and also be useful for further studies on sex-determination mechanism analysis and sex-control breeding of this fish.
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Affiliation(s)
- Chuankun Zhu
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University , Huai’an 223300, China
| | - Haiyang Liu
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences , Guangzhou 510380, China
| | - Zhengjun Pan
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University , Huai’an 223300, China
| | - Lei Cheng
- Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Heilongjiang Fisheries Research Institute, Chinese Academy of Fishery Sciences , Harbin 150070, China
| | - Yanhong Sun
- Wuhan Aquaculture Science Research Institute , Wuhan 430207, China
| | - Hui Wang
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University , Huai’an 223300, China
| | - Guoliang Chang
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University , Huai’an 223300, China
| | - Nan Wu
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University , Huai’an 223300, China
| | - Huaiyu Ding
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University , Huai’an 223300, China
| | - Haitao Zhao
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University , Huai’an 223300, China
| | - Lei Zhang
- Key Laboratory of Fishery Sustainable Development and Water Environment Protection of Huai’an City, Huai’an Sub Center of the Institute of Hydrobiology, Chinese Academy of Sciences , Huai’an 223002, China
| | - Xiangsheng Yu
- Huai’an Fisheries Technical Guidance Station , Huai’an 223001, China
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12
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Schedel FDB, Chakona A, Sidlauskas BL, Popoola MO, Usimesa Wingi N, Neumann D, Vreven EJWMN, Schliewen UK. New phylogenetic insights into the African catfish families Mochokidae and Austroglanididae. JOURNAL OF FISH BIOLOGY 2022; 100:1171-1186. [PMID: 35184288 PMCID: PMC9310817 DOI: 10.1111/jfb.15014] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 01/20/2022] [Accepted: 02/16/2022] [Indexed: 06/14/2023]
Abstract
Several hundred catfish species (order: Siluriformes) belonging to 11 families inhabit Africa, of which at least six families are endemic to the continent. Although four of those families are well-known to belong to the 'Big-Africa clade', no previous study has addressed the phylogenetic placement of the endemic African catfish family Austroglanididae in a comprehensive framework with molecular data. Furthermore, interrelationships within the 'Big-Africa clade', including the most diverse family Mochokidae, remain unclear. This study was therefore designed to help reconstruct inter- and intrarelationships of all currently valid mochokid genera, to infer their position within the 'Big Africa clade' and to establish a first molecular phylogenetic hypothesis of the relationships of the enigmatic Austroglanididae within the Siluriformes. We assembled a comprehensive mitogenomic dataset comprising all protein coding genes and representing almost all recognized catfish families (N = 33 of 39) with carefully selected species (N = 239). We recovered the monophyly of the previously identified multifamily clades 'Big Asia' and 'Big Africa' and determined Austroglanididae to be closely related to Pangasiidae, Ictaluroidea and Ariidae. Mochokidae was recovered as the sister group to a clade encompassing Auchenoglanididae, Claroteidae, Malapteruridae and the African Schilbeidae, albeit with low statistical support. The two mochokid subfamilies Mochokinae and Chiloglanidinae as well as the chiloglanid tribe Atopochilini were recovered as reciprocally monophyletic. The genus Acanthocleithron forms the sister group of all remaining Mochokinae, although with low support. The genus Atopodontus is the sister group of all remaining Atopochilini. In contrast to morphological reconstructions, the monophyly of the genus Chiloglanis was strongly supported in our analysis, with Chiloglanis macropterus nested within a Chiloglanis sublineage encompassing only other taxa from the Congo drainage. This is an important result because the phylogenetic relationships of C. macropterus have been controversial in the past, and because we and other researchers assumed that this species would be resolved as sister to most or all other members of Chiloglanis. The apparent paraphyly of Synodontis with respect to Microsynodontis provided an additional surprise, with Synodontis punu turning out to be the sister group of the latter genus.
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Affiliation(s)
- Frederic D. B. Schedel
- Zoological InstituteUniversity of BaselBaselSwitzerland
- Department of IchthyologySNSB‐Bavarian State Collection of ZoologyMunichGermany
- Faculty of BiologyLMU MunichMunichGermany
| | | | - Brian L. Sidlauskas
- Department of Fisheries, Wildlife and Conservation SciencesOregon State UniversityCorvallisOregonUSA
| | | | | | - Dirk Neumann
- Department of IchthyologySNSB‐Bavarian State Collection of ZoologyMunichGermany
| | - Emmanuel J. W. M. N. Vreven
- Vertebrate Section, Royal Museum for Central AfricaTervurenBelgium
- KU Leuven, Laboratory of Biodiversity and Evolutionary GenomicsLeuvenBelgium
| | - Ulrich K. Schliewen
- Department of IchthyologySNSB‐Bavarian State Collection of ZoologyMunichGermany
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13
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Wen M, Pan Q, Jouanno E, Montfort J, Zahm M, Cabau C, Klopp C, Iampietro C, Roques C, Bouchez O, Castinel A, Donnadieu C, Parrinello H, Poncet C, Belmonte E, Gautier V, Avarre J, Dugue R, Gustiano R, Hà TTT, Campet M, Sriphairoj K, Ribolli J, de Almeida FL, Desvignes T, Postlethwait JH, Floi Bucao C, Robinson‐Rechavi M, Bobe J, Herpin A, Guiguen Y. An ancient truncated duplication of the anti‐Mullerian hormone receptor type 2 gene is a potential conserved master sex determinant in the Pangasiidae catfish family. Mol Ecol Resour 2022; 22:2411-2428. [PMID: 35429227 PMCID: PMC9555307 DOI: 10.1111/1755-0998.13620] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/29/2022] [Accepted: 04/11/2022] [Indexed: 11/30/2022]
Abstract
The evolution of sex determination (SD) in teleosts is amazingly dynamic, as reflected by the variety of different master sex-determining genes identified. Pangasiids are economically important catfishes in South Asian countries, but little is known about their SD system. Here, we generated novel genomic resources for 12 Pangasiids and characterized their SD system. Based on a Pangasianodon hypophthalmus chromosome-scale genome assembly, we identified an anti-Müllerian hormone receptor type Ⅱ gene (amhr2) duplication, which was further characterized as being sex-linked in males and expressed only in testes. These results point to a Y chromosome male-specific duplication (amhr2by) of the autosomal amhr2a. Sequence annotation revealed that the P. hypophthalmus Amhr2by is truncated in its N-terminal domain, lacking the cysteine-rich extracellular part of the receptor that is crucial for ligand binding, suggesting a potential route for its neofunctionalization. Reference-guided assembly of 11 additional Pangasiids, along with sex-linkage studies, revealed that this truncated amhr2by duplication is a male-specific conserved gene in Pangasiids. Reconstructions of the amhr2 phylogeny suggested that amhr2by arose from an ancient duplication/insertion event at the root of the Siluroidei radiation that is dated to ~100 million years ago. Together these results bring multiple lines of evidence supporting that amhr2by is an ancient and conserved master sex-determining gene in Pangasiids, a finding that highlights the recurrent use of the transforming growth factor β pathway, which is often used for the recruitment of teleost master SD genes, and provides another empirical case towards firther understanding of dynamics of SD systems.
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Affiliation(s)
- Ming Wen
- State Key Laboratory of Developmental Biology of Freshwater Fish College of Life Science Hunan Normal University Changsha China
- INRAE LPGP 35000 Rennes France
| | - Qiaowei Pan
- INRAE LPGP 35000 Rennes France
- Department of Ecology and Evolution University of Lausanne Lausanne Switzerland
| | | | | | - Margot Zahm
- Plate‐forme bio‐informatique Genotoul Mathématiques et Informatique Appliquées de Toulouse INRAE Castanet Tolosan France
| | - Cédric Cabau
- SIGENAE, GenPhySE Université de Toulouse INRAE ENVT Castanet Tolosan France
| | - Christophe Klopp
- Plate‐forme bio‐informatique Genotoul Mathématiques et Informatique Appliquées de Toulouse INRAE Castanet Tolosan France
- SIGENAE, GenPhySE Université de Toulouse INRAE ENVT Castanet Tolosan France
| | | | - Céline Roques
- INRAE, US 1426, GeT‐PlaGe Genotoul, Castanet‐Tolosan France
| | | | | | | | - Hugues Parrinello
- Montpellier GenomiX (MGX), c/o Institut de Génomique Fonctionnelle 141 rue de la Cardonille 34094 Montpellier Cedex France
| | - Charles Poncet
- GDEC Gentyane INRAE Université Clermont Auvergne Clermont‐Ferrand France
| | - Elodie Belmonte
- GDEC Gentyane INRAE Université Clermont Auvergne Clermont‐Ferrand France
| | - Véronique Gautier
- GDEC Gentyane INRAE Université Clermont Auvergne Clermont‐Ferrand France
| | | | - Remi Dugue
- ISEM Univ Montpellier CNRS IRD Montpellier France
| | - Rudhy Gustiano
- Research Institute of Freshwater Fisheries (CRIFI‐RIFF) Instalasi Penelitian Perikanan Air Tawar Jalan Ragunan‐Pasar Minggu P.O. Box 7220/jkspm Jakarta 12540 Indonesia
| | - Trần Thị Thúy Hà
- Research Institute for Aquaculture No.1. Dinh Bang Tu Son, Bac Ninh Viet Nam
| | | | - Kednapat Sriphairoj
- Faculty of Natural Resources and Agro‐Industry Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus Sakon Nakhon Thailand
| | - Josiane Ribolli
- Laboratório de Biologia e Cultivo de Peixes de Água Doce Universidade Federal de Santa Catarina Florianópolis SC Brasil
| | | | - Thomas Desvignes
- Institute of Neuroscience University of Oregon Eugene OR 97403 USA
| | | | - Christabel Floi Bucao
- Department of Ecology and Evolution University of Lausanne Lausanne Switzerland
- SIB Swiss Institute of Bioinformatics 1015 Lausanne Switzerland
| | - Marc Robinson‐Rechavi
- Department of Ecology and Evolution University of Lausanne Lausanne Switzerland
- SIB Swiss Institute of Bioinformatics 1015 Lausanne Switzerland
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14
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Craig JM, Kumar S, Hedges SB. Limitations of phylogenomic data can drive inferred speciation rate shifts. Mol Biol Evol 2022; 39:6528856. [PMID: 35166841 PMCID: PMC8896619 DOI: 10.1093/molbev/msac038] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Biodiversity analyses of phylogenomic timetrees have produced many high-profile examples of shifts in the rate of speciation across the tree of life. Temporally correlated events in ecology, climate, and biogeography are frequently invoked to explain these rate shifts. In a re-examination of 15 genomic timetrees and 25 major published studies of the pattern of speciation through time, we observed an unexpected correlation between the timing of reported rate shifts and the information content of sequence alignments. Here, we show that the paucity of sequence variation and insufficient species sampling in phylogenomic datasets are the likely drivers of many inferred speciation rate shifts, rather than the proposed biological explanations. Therefore, data limitations can produce predictable but spurious signals of rate shifts even when speciation rates may be similar across taxa and time. Our results suggest that the reliable detection of speciation rate shifts requires the acquisition and assembly of long phylogenomic alignments with near-complete species sampling and accurate estimates of species richness for the clades of study.
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Affiliation(s)
- Jack M Craig
- Center for Biodiversity, Temple University, Philadelphia, United States.,Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, United States.,Department of Biology, Temple University, Philadelphia, United States
| | - Sudhir Kumar
- Center for Biodiversity, Temple University, Philadelphia, United States.,Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, United States.,Department of Biology, Temple University, Philadelphia, United States.,Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - S Blair Hedges
- Center for Biodiversity, Temple University, Philadelphia, United States.,Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, United States.,Department of Biology, Temple University, Philadelphia, United States
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15
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Gao Z, You X, Zhang X, Chen J, Xu T, Huang Y, Lin X, Xu J, Bian C, Shi Q. A chromosome-level genome assembly of the striped catfish (Pangasianodon hypophthalmus). Genomics 2021; 113:3349-3356. [PMID: 34343676 DOI: 10.1016/j.ygeno.2021.07.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 07/13/2021] [Accepted: 07/28/2021] [Indexed: 12/15/2022]
Abstract
Striped catfish (Pangasianodon hypophthalmus), belonging to the Pangasiidae family, has become an economically important fish with wide cultivation in Southeast Asia. Owing to the high-fat trait, it is always considered as an oily fish. In our present study, a high-quality genome assembly of the striped catfish was generated by integration of Illumina short reads, Nanopore long reads and Hi-C data. A 731.7-Mb genome assembly was finally obtained, with a contig N50 of 3.5 Mb, a scaffold N50 of 29.5 Mb, and anchoring of 98.46% of the assembly onto 30 pseudochromosomes. The genome contained 36.9% repeat sequences, and a total 18,895 protein-coding genes were predicted. Interestingly, we identified a tandem triplication of fatty acid binding protein 1 gene (fabp1; thereby named as fabp1-1, fabp1-2 and fabp1-3 respectively), which may be related to the high fat content in striped catfish. Meanwhile, the FABP1-2 and -3 isoforms differed from FABP1-1 by several missense mutations including R126T, which may affect the fatty acid binding properties. In summary, we report a high-quality chromosome-level genome assembly of the striped catfish, which provides a valuable genetic resource for biomedical studies on the high-fat trait, and lays a solid foundation for practical aquaculture and molecular breeding of this international teleost species.
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Affiliation(s)
- Zijian Gao
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China; Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China
| | - Xinxin You
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China; Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China
| | - Xinhui Zhang
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China
| | - Jieming Chen
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China; Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China
| | - Tengfei Xu
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China
| | - Yu Huang
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China
| | - Xueqiang Lin
- BGI Marine-Hainan, BGI Marine, BGI, Wenchang 571327, China
| | - Junmin Xu
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China
| | - Chao Bian
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China; Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China
| | - Qiong Shi
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China; Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.
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16
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Sequencing an F1 hybrid of Silurus asotus and S. meridionalis enabled the assembly of high-quality parental genomes. Sci Rep 2021; 11:13797. [PMID: 34226617 PMCID: PMC8257616 DOI: 10.1038/s41598-021-93257-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 06/16/2021] [Indexed: 01/27/2023] Open
Abstract
Genome complexity such as heterozygosity may heavily influence its de novo assembly. Sequencing somatic cells of the F1 hybrids harboring two sets of genetic materials from both of the paternal and maternal species may avoid alleles discrimination during assembly. However, the feasibility of this strategy needs further assessments. We sequenced and assembled the genome of an F1 hybrid between Silurus asotus and S. meridionalis using the SequelII platform and Hi-C scaffolding technologies. More than 300 Gb raw data were generated, and the final assembly obtained 2344 scaffolds composed of 3017 contigs. The N50 length of scaffolds and contigs was 28.55 Mb and 7.49 Mb, respectively. Based on the mapping results of short reads generated for the paternal and maternal species, each of the 29 chromosomes originating from S. asotus and S. meridionalis was recognized. We recovered nearly 94% and 96% of the total length of S. asotus and S. meridionalis. BUSCO assessments and mapping analyses suggested that both genomes had high completeness and accuracy. Further analyses demonstrated the high collinearity between S. asotus, S. meridionalis, and the related Pelteobagrus fulvidraco. Comparison of the two genomes with that assembled only using the short reads from non-hybrid parental species detected a small portion of sequences that may be incorrectly assigned to the different species. We supposed that at least part of these situations may have resulted from mitotic recombination. The strategy of sequencing the F1 hybrid genome can recover the vast majority of the parental genomes and may improve the assembly of complex genomes.
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17
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Characterization of the complete mitochondrial genome of Macrotocinclus affinis (Siluriformes; Loricariidae) and phylogenetic studies of Siluriformes. Mol Biol Rep 2021; 48:677-689. [PMID: 33442829 DOI: 10.1007/s11033-020-06120-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 12/22/2020] [Indexed: 10/22/2022]
Abstract
The vertebrate mitochondrial genome is typically circular molecules made up of 14,000 to 16,000 bp, including 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (12 s rRNA and 16 s rRNA) and a control region. Compared with nuclear DNA, mitochondrial DNA has a higher mutation rate, so it is one of the most effective and reliable molecular markers in fish phylogeny. Macrotocinclus affinis was the only species in Macrotocinclus (it was classified as Otocinclus in the past) and currently lacks genetic information. Most of the current researches are based on the mitochondrial Cytb gene and RAG1 and RAG2 nuclear genes to study the phylogenetic analysis of Siluriformes. So, the study provides the characteristic features of the Macrotocinclus affinis mitochondrial genome and this is the first time that the phylogenetic relationship of Siluriformes has been reconstructed based on COI. We aimed to sequence the entire mitochondrial genome of Macrotocinclus affinis using conventional PCR techniques and to clarify its phylogenetic status in Siluriformes by using the COI sequence of mitochondria. In this study, we sequenced the whole mitochondrial genome of this species yielding a 16,632 bp circular assembly composed of the typical vertebrate mitochondrial features. It contains 13 protein-coding genes, two rRNA genes, 22 tRNA genes, a putative control region, and one origin of replication on the light-strand. The overall base composition includes A (30.07%), T (24.43%), C (29.43%) and G (16.01%). The genome composition is A + T biased (54.5%), and exhibits AT-skew (0.1036) and GC-skew (-0.2962). Moreover, the 13 PCGs encode 3850 amino acids in total. The result of the phylogenetic tree supports Macrotocinclus affinis has a closest relationship with Otocinclus cf. hoppei far. These results will help to understand the characteristics of the mitochondrial genome of Macrotocinclus affinis and provide molecular basis for the evolutionary relationship of Loricariidae.
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18
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Scholz T, Barčák D, Waeschenbach A, McAllister CT, Choudhury A. Tapeworms (Cestoda) of Ictalurid Catfishes (Siluriformes) in North America: Redescription of Type Species of Two Genera and Proposal of Essexiellinae n. Subfam. J Parasitol 2021; 106:444-463. [PMID: 32294216 DOI: 10.1645/20-12] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Ictalurid catfishes (Siluriformes) in North America harbor proteocephalid tapeworms of the subfamily Corallobothriinae. Type species of 2 of 3 genera of these tapeworms from ictalurids are redescribed, based on museum and newly collected material. Essexiella fimbriata (Essex, 1928) is typified mainly by a wide, umbrella-shaped scolex with a metascolex formed by numerous folds of tissue, anteriorly directed suckers without sphincters, vitellarium bent inwards posteriorly, "flower-shaped" uterus (with anterior, lateral, and posterior diverticula), and a conspicuously pre-equatorial genital atrium. Verified host records of this cestode are only from 3 species of Ictalurus Rafinesque, 1820. Megathylacoides giganteum (Essex, 1928), which seems to be specific to the channel catfish (Ictalurus punctatus), possesses a globular scolex, with a weakly developed metascolex formed by tissue folds posterior to the suckers, anterolaterally directed suckers with large semilunar sphincters, proglottids that are widest at the level of the genital atrium at the anterior third of the proglottid, and uterine diverticula that do not reach the vitelline follicles laterally. A new subfamily, Essexiellinae Scholz and Barčák, is proposed to accommodate species of EssexiellaScholz, de Chambrier, Mariaux and Kuchta, 2011 (type genus), MegathylacoidesJones, Kerley and Sneed, 1956, and CorallotaeniaFreze, 1965 from ictalurid catfishes in the Nearctic Region. These tapeworms possess a metascolex, medullary genital organs, uterus lined with numerous chromophilic cells, pre-equatorial genital atrium, and uterine development of type 2. The new subfamily was monophyletic in all molecular phylogenetic analyses, being most closely related to 3 Neotropical proteocephalids from the redtail catfish, Phractocephalus hemioliopterus (Bloch and Schneider, 1801), but distant from all remaining proteocephalid tapeworms from freshwater fishes in North America.
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Affiliation(s)
- Tomáš Scholz
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Daniel Barčák
- Institute of Parasitology, Slovak Academy of Sciences, Hlinkova 3, 040 01 Košice, Slovakia
| | - Andrea Waeschenbach
- Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, United Kingdom
| | - Chris T McAllister
- Division of Science and Mathematics, Eastern Oklahoma State College, Idabel, Oklahoma 74745
| | - Anindo Choudhury
- Division of Natural Sciences, St. Norbert College, De Pere, Wisconsin 54115
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19
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Ferreira M, de Jesus IS, Viana PF, Garcia C, Matoso DA, Cioffi MB, Bertollo LAC, Feldberg E. Chromosomal Evolution in Aspredinidae (Teleostei, Siluriformes): Insights on Intra- and Interspecific Relationships with Related Groups. Cytogenet Genome Res 2020; 160:539-553. [PMID: 33227787 DOI: 10.1159/000511125] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 07/22/2020] [Indexed: 11/19/2022] Open
Abstract
The family Aspredinidae comprises a clade of complex systematic relationships, both from molecular and morphological approaches. In this study, conventional and molecular cytogenetic studies coupled with nucleotide sequencing were performed in 6 Aspredininae species (Amaralia hypsiura, Bunocephalus cf. aloikae, Bunocephalus amaurus, Bunocephalus aff. coracoideus, Bunocephalus verrucosus, and Platystacus cotylephorus) from different locations of the Amazon hydrographic basin. Our results showed highly divergent diploid numbers (2n) among the species, ranging from 49 to 74, including the occurrence of an XX/X0 sex chromosome system. A neighbor-joining phylogram based on the cytochrome c oxidase I (COI) showed that Bunocephalus coracoideus is not a monophyletic clade, but closely related to B. verrucosus. The karyotypic data associated with COI suggest an ancestral karyotype for Aspredinidae with a reduced 2n, composed of bi-armed chromosomes and a trend toward chromosomal fissions resulting in higher diploid number karyotypes, mainly composed of acrocentric chromosomes. Evolutionary relationships were discussed under a phylogenetic context with related species from different Siluriformes families. The karyotype features and chromosomal diversity of Aspredinidae show an amazing differentiation, making this family a remarkable model for investigating the evolutionary dynamics in siluriforms as well as in fish as a whole.
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Affiliation(s)
- Milena Ferreira
- Laboratório de Genética Animal, Programa de Pó-graduação em Genética, Conservação e Biologia Evolutiva, Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil.,Secretaria de Estado de Educação e Qualidade do Ensino (SEDUC), Manaus, Brazil
| | - Isac S de Jesus
- Laboratório de Fisiologia Comportamental e Evolução, Programa de Pó-graduação em Genética, Conservação e Biologia Evolutiva, Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
| | - Patrik F Viana
- Laboratório de Genética Animal, Programa de Pó-graduação em Genética, Conservação e Biologia Evolutiva, Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
| | - Caroline Garcia
- Laboratório de Citogenética, Departamento de Ciências Biológicas, Universidade Estadual do Sudoeste da Bahia, Jequié, Brazil
| | - Daniele A Matoso
- Departamento de Genética, Instituto de Ciências Biológicas, Universidade Federal do Amazonas, Manaus, Brazil
| | - Marcelo B Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil,
| | - Luiz A C Bertollo
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Eliana Feldberg
- Laboratório de Genética Animal, Programa de Pó-graduação em Genética, Conservação e Biologia Evolutiva, Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
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20
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Ditcharoen S, Sassi FDMC, Bertollo LAC, Molina WF, Liehr T, Saenjundaeng P, Tanomtong A, Supiwong W, Suwannapoom C, Cioffi MDB. Comparative chromosomal mapping of microsatellite repeats reveals divergent patterns of accumulation in 12 Siluridae (Teleostei: Siluriformes) species. Genet Mol Biol 2020; 43:e20200091. [PMID: 33156890 PMCID: PMC7654372 DOI: 10.1590/1678-4685-gmb-2020-0091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 09/03/2020] [Indexed: 01/08/2023] Open
Abstract
The freshwater family Siluridae occurs in Eurasia and is especially speciose in South and Southeast Asia, representing an important aquaculture and fishery targets. However, despite the restricted cytogenetic data, a high diploid number variation (from 2n=40 to 92) characterizes this fish group. Considering the large genomic divergence among its species, silurid genomes have experienced an enormous diversification throughout their evolutionary history. Here, we aim to investigate the chromosomal distribution of several microsatellite repeats in 12 Siluridae species and infer about their possible roles in the karyotype evolution that occurred in this group. Our results indicate divergent patterns of microsatellite distribution and accumulation among the analyzed species. Indeed, they are especially present in significant chromosome locations, such as the centromeric and telomeric regions, precisely the ones associated with several kinds of chromosomal rearrangements. Our data provide pieces of evidence that repetitive DNAs played a direct role in fostering the chromosomal differentiation and biodiversity in this fish family.
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Affiliation(s)
- Sukhonthip Ditcharoen
- Khon Kaen UniversityKhon Kaen UniversityDepartment of BiologyMuangKhon KaenThailandKhon Kaen University, Faculty of Science, Department of
Biology, Toxic Substances in Livestock and Aquatic Animals Research Group, Muang, Khon Kaen,
Thailand.
| | - Francisco de Menezes Cavalcante Sassi
- Universidade Federal de São Carlos
(UFSCar)Universidade Federal de São Carlos (UFSCar)Departamento de Genética e
EvoluçãoSão CarlosSPBrazilUniversidade Federal de São Carlos (UFSCar),
Departamento de Genética e Evolução, São Carlos, SP,
Brazil.
| | - Luiz Antonio Carlos Bertollo
- Universidade Federal de São Carlos
(UFSCar)Universidade Federal de São Carlos (UFSCar)Departamento de Genética e
EvoluçãoSão CarlosSPBrazilUniversidade Federal de São Carlos (UFSCar),
Departamento de Genética e Evolução, São Carlos, SP,
Brazil.
| | - Wagner Franco Molina
- Universidade Federal do Rio Grande do NorteUniversidade Federal do Rio Grande do NorteDepartamento de Biologia Celular e GenéticaNatalRNBrazilUniversidade Federal do Rio Grande do Norte (UFRN), Centro de
Biociências, Departamento de Biologia Celular e Genética, Natal, RN,
Brazil.
| | - Thomas Liehr
- University Hospital JenaUniversity Hospital JenaInstitute of Human GeneticsJenaGermanyUniversity Hospital Jena, Institute of Human Genetics, Jena,
Germany.
| | - Pasakorn Saenjundaeng
- Khon Kaen UniversityKhon Kaen UniversityFaculty of Applied Science and EngineeringMuangNong KhaiThailandKhon Kaen University, Faculty of Applied Science and
Engineering, Nong Khai Campus, Muang, Nong Khai, Thailand.
| | - Alongklod Tanomtong
- Khon Kaen UniversityKhon Kaen UniversityDepartment of BiologyMuangKhon KaenThailandKhon Kaen University, Faculty of Science, Department of
Biology, Toxic Substances in Livestock and Aquatic Animals Research Group, Muang, Khon Kaen,
Thailand.
| | - Weerayuth Supiwong
- Khon Kaen UniversityKhon Kaen UniversityFaculty of Applied Science and EngineeringMuangNong KhaiThailandKhon Kaen University, Faculty of Applied Science and
Engineering, Nong Khai Campus, Muang, Nong Khai, Thailand.
| | - Chatmongkon Suwannapoom
- University of PhayaoUniversity of PhayaoDepartment of FisherySchool of Agriculture and Natural ResourcesMuang PhayaoThailandUniversity of Phayao, School of Agriculture and Natural
Resources, Department of Fishery, Muang Phayao, Thailand.
| | - Marcelo de Bello Cioffi
- Universidade Federal de São Carlos
(UFSCar)Universidade Federal de São Carlos (UFSCar)Departamento de Genética e
EvoluçãoSão CarlosSPBrazilUniversidade Federal de São Carlos (UFSCar),
Departamento de Genética e Evolução, São Carlos, SP,
Brazil.
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21
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Draft Genome Assembly of the Freshwater Apex Predator Wels Catfish ( Silurus glanis) Using Linked-Read Sequencing. G3-GENES GENOMES GENETICS 2020; 10:3897-3906. [PMID: 32917720 PMCID: PMC7642921 DOI: 10.1534/g3.120.401711] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The wels catfish (Silurus glanis) is one of the largest freshwater fish species in the world. This top predator plays a key role in ecosystem stability, and represents an iconic trophy-fish for recreational fishermen. S. glanis is also a highly valued species for its high-quality boneless flesh, and has been cultivated for over 100 years in Eastern and Central Europe. The interest in rearing S. glanis continues to grow; the aquaculture production of this species has almost doubled during the last decade. However, despite its high ecological, cultural and economic importance, the available genomic resources for S. glanis are very limited. To fulfill this gap we report a de novo assembly and annotation of the whole genome sequence of a female S. glanis. The linked-read based technology with 10X Genomics Chromium chemistry and Supernova assembler produced a highly continuous draft genome of S. glanis: ∼0.8Gb assembly (scaffold N50 = 3.2 Mb; longest individual scaffold = 13.9 Mb; BUSCO completeness = 84.2%), which included 313.3 Mb of putative repeated sequences. In total, 21,316 protein-coding genes were predicted, of which 96% were annotated functionally from either sequence homology or protein signature searches. The highly continuous genome assembly will be an invaluable resource for aquaculture genomics, genetics, conservation, and breeding research of S. glanis.
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22
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Barrios-de Pedro S, Osuna A, Buscalioni ÁD. Helminth eggs from early cretaceous faeces. Sci Rep 2020; 10:18747. [PMID: 33127992 PMCID: PMC7599231 DOI: 10.1038/s41598-020-75757-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 10/20/2020] [Indexed: 11/09/2022] Open
Abstract
The exceptional fossil site of Las Hoyas (upper Barremian, Cuenca, Spain) yields abundant small to medium vertebrate coprolites, hindering the search for parasites. We studied the contents of 29 coprolites that were previously classified into distinct morphotypes. Several parasitic eggs were retrieved from two of these coprolites, confirming the second record of digenea trematode eggs and nematode (ascaridid) eggs from an Early Cretaceous locality. The cylindrical coprolite containing anisakid eggs was likely produced by a crocodylomorph as the parasite host, whereas the bump-headed lace coprolite indicates the role of a fish as an intermediary or definitive host of the trematodes and ascaridids. These trace and body fossils show that the Las Hoyas 126-129 Ma lacustrine ecosystem documents the early connection between basal Gonorynchiformes fish and digenetic trematodes.
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Affiliation(s)
- Sandra Barrios-de Pedro
- Unidad de Paleontología and Centro para la Integración en Paleobiología (CIPb), Departamento de Biología, Edificio de Biología, Universidad Autónoma de Madrid, Calle Darwin 2, Cantoblanco, 28049, Madrid, Spain.
| | - Antonio Osuna
- Departamento de Parasitología, Facultad de Ciencias, Universidad de Granada, Granada, 18071, Granada, Spain.,Instituto Universitario de Biotecnología, Granada, 18071, Granada, Spain
| | - Ángela D Buscalioni
- Unidad de Paleontología and Centro para la Integración en Paleobiología (CIPb), Departamento de Biología, Edificio de Biología, Universidad Autónoma de Madrid, Calle Darwin 2, Cantoblanco, 28049, Madrid, Spain
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23
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Boeger WA, Kritsky DC, Patella L, Bueno‐Silva M. Phylogenetic status and historical origins of the oviparous and viviparous gyrodactylids (Monogenoidea, Gyrodactylidea). ZOOL SCR 2020. [DOI: 10.1111/zsc.12455] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Walter A. Boeger
- Laboratory of Biological Interactions Universidade Federal do Paraná Curitiba Brazil
- Conselho Nacional de Desenvolvimento Científico e Tecnológico, CNPq Brasília Brazil
| | - Delane C. Kritsky
- Department of Community & Public Health College of Health Professions Idaho State University Pocatello ID USA
| | - Luciana Patella
- Laboratory of Biological Interactions Universidade Federal do Paraná Curitiba Brazil
- Conselho Nacional de Desenvolvimento Científico e Tecnológico, CNPq Brasília Brazil
| | - Marlus Bueno‐Silva
- Laboratory of Biological Interactions Universidade Federal do Paraná Curitiba Brazil
- Conselho Nacional de Desenvolvimento Científico e Tecnológico, CNPq Brasília Brazil
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24
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Afriyie G, Wang Z, Dong Z, Ayisi Larbi C, Asiedu B, Guo Y. Complete mitochondrial genome and assembled DNA barcoding analysis of Lutjanus fulgens (Valenciennes, 1830) and its comparison with other Lutjanus species. Ecol Evol 2020; 10:7971-7980. [PMID: 32788954 PMCID: PMC7417232 DOI: 10.1002/ece3.6542] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 06/07/2020] [Accepted: 06/11/2020] [Indexed: 11/10/2022] Open
Abstract
Lutjanus fulgens (Valenciennes, 1830) is a teleost species classified under the family Lutjanidae which is a native of the Eastern Atlantic Ocean. Though highly commercialized due to its abundance and good taste, the production output has declined in recent years. This is an indication of the need for effective management and conservation measures. However, accurate species identification will ensure strategic management and conservation measure. DNA-based species identification has proven its reliability in this regard via precise species identification. Several researchers have confirmed the accuracy of DNAbarcode as a species identification tool as well as species phylogeny analysis based on both the complete mitogenome and COI gene. Currently, nine specimens of L. fulgens were sampled from Ghana and subjected to DNA-based analysis, namely, complete mitochondrial DNAand COI gene (DNA barcoding) analyses. The mitogenomic result revealed that L. fulgens is made up of a 16,500 base pairs (bp) mtDNA which consists of 22 transfer RNAs, 13 protein-coding genes, and two ribosomal RNAs (GenBank Accession Number: MN398650). Furthermore, a sequence polymorphism analysis of the COIgene (MN986442-MN986450) detected two haplotypes. These haplotypes were both collected from the same fish landing site which suggests a possible cryptic linage diversity in the L. fulgens population at Vodza. According to the phylogeny examination, a close taxonomic relationship exists between L. fulgens and Lutjanus buccanella caused by a recent evolution termed as sympatric speciation. This study serves as a novel study for this species, building the foundation for future molecular-based study for this species and as a DNA barcode reference data.
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Affiliation(s)
- Gyamfua Afriyie
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education InstitutesFisheries CollegeGuangdong Ocean UniversityZhanjiangChina
| | - Zhongduo Wang
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education InstitutesFisheries CollegeGuangdong Ocean UniversityZhanjiangChina
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic AnimalsFisheries CollegeGuangdong Ocean UniversityZhanjiangChina
| | - Zhongdian Dong
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education InstitutesFisheries CollegeGuangdong Ocean UniversityZhanjiangChina
| | - Christian Ayisi Larbi
- Department of Fisheries and Aquatic Resources ManagementUniversity for Development StudiesTamaleGhana
| | - Berchie Asiedu
- Department of Fisheries and AquacultureUniversity of Energy and Natural ResourcesSunyaniGhana
| | - Yusong Guo
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education InstitutesFisheries CollegeGuangdong Ocean UniversityZhanjiangChina
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25
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Trinigyrus spp. (Monogenea: Dactylogyridae) from Brazilian catfishes: new species, molecular data and new morphological contributions to the genus. J Helminthol 2020; 94:e126. [PMID: 32077391 DOI: 10.1017/s0022149x20000097] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
This study describes two new species, Trinigyrus anthus n. sp. and Trinigyrus carvalhoi n. sp., from gills of Hypostomus spp. from the Upper Paraná River basin, Brazil. Trinigyrus peregrinus is redescribed based on examination of its holotype, paratypes and new material of specimens parasitizing Pterygoplichthys ambrosettii, also from the Upper Paraná River basin, Brazil. New morphological features were included in the diagnosis of the genus, such as the presence of a sclerotized border on the anchor base, and a weakly sclerotized fringe on the base of the male copulatory organ (MCO). Trinigyrus anthus n. sp. differs from other congeners by the shape of the MCO, presenting an enlarged base with sclerotized fringes resembling flower petals. Trinigyrus carvalhoi n. sp. and T. peregrinus are similar but can be differentiated from each other mainly by the sclerotization of the vagina (absent in the new species), and the morphology of the MCO (C-shaped versus one counterclockwise circle, respectively). For the first time, gene sequences of Trinigyrus spp. from Brazil were obtained (partial ribosomal 28S and mitochondrial cytochrome c oxidase I (mtCOI)). The genetic divergences among the new species and T. peregrinus varied from 2 to 3% (6‒18 pb) based on sequences of 28S ribosomal DNA (rDNA), and 6-7% (83‒92 pb) using mtCOI. Phylogenetic analyses based on partial 28S rDNA revealed that Trinigyrus, Heteropriapulus and Unilatus formed a monophyletic and well-supported clade of monogeneans from Neotropical freshwater loricariids, suggesting a closer relationship among these dactylogyrids and their hosts.
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Abstract
Abstract
The Afrotropics house a diverse freshwater ichthyofauna with > 3000 species, almost all of which are endemic. Recent progress in dated phylogenetics and palaeontology of several groups of Afrotropical freshwater fishes (AFFs) has allowed the testing of palaeoecology- and palaeogeography-based hypotheses explaining their early presence in Africa. Seven hypotheses were tested for 37 most-inclusive monophyletic groups of AFFs. Results indicated that ten lineages originated from direct, but asynchronous, marine-to-freshwater shifts. These lineages contribute < 2% to the current AFF species richness. Eleven lineages colonized the Afrotropics from the Orient after the Afro-Arabian plate collided with Eurasia in the early Oligocene. These lineages contribute ~20% to the total diversity. There are seven sister relationships between Afrotropical and Neotropical taxa. For only three of them (4% of the species diversity), the continental drift vicariance hypothesis was not rejected. Distributions of the other four younger trans-Atlantic lineages are better explained by post-drifting long-distance dispersal. In those cases, I discuss the possibility of dispersal through the Northern Hemisphere as an alternative to direct trans-Atlantic dispersal. The origins of ten AFF lineages, including the most species-rich Pseudocrenilabrinae (> 1100 species), are not yet established with confidence.
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Affiliation(s)
- Sébastien Lavoué
- School of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia
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27
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Ditcharoen S, Antonio Carlos Bertollo L, Ráb P, Hnátková E, Franco Molina W, Liehr T, Tanomtong A, Triantaphyllidis C, Ozouf-Costaz C, Tongnunui S, Pengseng P, Supiwong W, Aroutiounian R, de Bello Cioffi M. Genomic Organization of Repetitive DNA Elements and Extensive Karyotype Diversity of Silurid Catfishes (Teleostei: Siluriformes): A Comparative Cytogenetic Approach. Int J Mol Sci 2019; 20:E3545. [PMID: 31331072 PMCID: PMC6678683 DOI: 10.3390/ijms20143545] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Revised: 07/03/2019] [Accepted: 07/16/2019] [Indexed: 11/30/2022] Open
Abstract
The catfish family Siluridae contains 107 described species distributed in Asia, but with some distributed in Europe. In this study, karyotypes and other chromosomal characteristics of 15 species from eight genera were examined using conventional and molecular cytogenetic protocols. Our results showed the diploid number (2n) to be highly divergent among species, ranging from 2n = 40 to 92, with the modal frequency comprising 56 to 64 chromosomes. Accordingly, the ratio of uni- and bi-armed chromosomes is also highly variable, thus suggesting extensive chromosomal rearrangements. Only one chromosome pair bearing major rDNA sites occurs in most species, except for Wallago micropogon, Ompok siluroides, and Kryptoterus giminus with two; and Silurichthys phaiosoma with five such pairs. In contrast, chromosomes bearing 5S rDNA sites range from one to as high as nine pairs among the species. Comparative genomic hybridization (CGH) experiments evidenced large genomic divergence, even between congeneric species. As a whole, we conclude that karyotype features and chromosomal diversity of the silurid catfishes are unusually extensive, but parallel some other catfish lineages and primary freshwater fish groups, thus making silurids an important model for investigating the evolutionary dynamics of fish chromosomes.
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Affiliation(s)
- Sukhonthip Ditcharoen
- Toxic Substances in Livestock and Aquatic Animals Research Group, Department of Biology, Faculty of Science, Khon Kaen University, Muang, Khon Kaen 40002, Thailand
| | - Luiz Antonio Carlos Bertollo
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos, SP 13565-905, Brazil
| | - Petr Ráb
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Liběchov 277 21, Czech Republic
| | - Eva Hnátková
- Department of Zoology and Fisheries, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Kamýcká 129, Prague 165 00, Czech Republic
| | - Wagner Franco Molina
- Departamento de Biologia Celular e Genética, Centro de Biociências, Universidade Federal do Rio Grande do Norte (UFRN), Natal, RN 59078970, Brazil
| | - Thomas Liehr
- Institute of Human Genetics, University Hospital Jena, Jena 07747, Germany
| | - Alongklod Tanomtong
- Toxic Substances in Livestock and Aquatic Animals Research Group, Department of Biology, Faculty of Science, Khon Kaen University, Muang, Khon Kaen 40002, Thailand
| | - Costas Triantaphyllidis
- Department of Genetics, Development and Molecular Biology, Faculty of Sciences, School of Biology, Aristotle University of Thessaloniki, University Campus, Thessaloniki 54124, Greece
| | - Catherine Ozouf-Costaz
- Laboratorie Evolution Paris Seine, Institut de Biologie Paris Seine (IBPS), Sorbonne Universités, Case 5, 7 Quai St Bernard, Paris, 75952 Paris CEDEX 05, France
| | - Sampan Tongnunui
- Department of Conservation Biology, Mahidol University, Kanchanaburi Campus, Sai Yok, Kanchanaburi Province 71150, Thailand
| | - Puan Pengseng
- School of Agricultural of Technology, Walailak University, Thasala, Nakhon Si Thammarat 80160, Thailand
| | - Weerayuth Supiwong
- Faculty of Applied Science and Engineering, Khon Kaen University, Nong Khai Campus, Muang, Nong Khai 43000, Thailand
| | - Rouben Aroutiounian
- Department of Genetics and Cytology, Yerevan State University, Yerevan 0025, Armenia
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos, SP 13565-905, Brazil.
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28
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Kim OTP, Nguyen PT, Shoguchi E, Hisata K, Vo TTB, Inoue J, Shinzato C, Le BTN, Nishitsuji K, Kanda M, Nguyen VH, Nong HV, Satoh N. A draft genome of the striped catfish, Pangasianodon hypophthalmus, for comparative analysis of genes relevant to development and a resource for aquaculture improvement. BMC Genomics 2018; 19:733. [PMID: 30290758 PMCID: PMC6173838 DOI: 10.1186/s12864-018-5079-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 09/14/2018] [Indexed: 11/22/2022] Open
Abstract
Background The striped catfish, Pangasianodon hypophthalmus, is a freshwater and benthopelagic fish common in the Mekong River delta. Catfish constitute a valuable source of dietary protein. Therefore, they are cultured worldwide, and P. hypophthalmus is a food staple in the Mekong area. However, genetic information about the culture stock, is unavailable for breeding improvement, although genetics of the channel catfish, Ictalurus punctatus, has been reported. To acquire genome sequence data as a useful resource for marker-assisted breeding, we decoded a draft genome of P. hypophthalmus and performed comparative analyses. Results Using the Illumina platform, we obtained both nuclear and mitochondrial DNA sequences. Molecular phylogeny using the mitochondrial genome confirmed that P. hypophthalmus is a member of the family Pangasiidae and is nested within a clade including the families Cranoglanididae and Ictaluridae. The nuclear genome was estimated at approximately 700 Mb, assembled into 568 scaffolds with an N50 of 14.29 Mbp, and was estimated to contain ~ 28,600 protein-coding genes, comparable to those of channel catfish and zebrafish. Interestingly, zebrafish produce gadusol, but genes for biosynthesis of this sunscreen compound have been lost from catfish genomes. The differences in gene contents between these two catfishes were found in genes for vitamin D-binding protein and cytosolic phospholipase A2, which have lost only in channel catfish. The Hox cluster in catfish genomes comprised seven paralogous groups, similar to that of zebrafish, and comparative analysis clarified catfish lineage-specific losses of A5a, B10a, and A11a. Genes for insulin-like growth factor (IGF) signaling were conserved between the two catfish genomes. In addition to identification of MHC class I and sex determination-related gene loci, the hypothetical chromosomes by comparison with the channel catfish demonstrated the usefulness of the striped catfish genome as a marker resource. Conclusions We developed genomic resources for the striped catfish. Possible conservation of genes for development and marker candidates were confirmed by comparing the assembled genome to that of a model fish, Danio rerio, and to channel catfish. Since the catfish genomic constituent resembles that of zebrafish, it is likely that zebrafish data for gene functions is applicable to striped catfish as well. Electronic supplementary material The online version of this article (10.1186/s12864-018-5079-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Oanh T P Kim
- Institute of Genome Research, Vietnam Academy of Science and Technology, Cau Giay, Hanoi, Vietnam.
| | - Phuong T Nguyen
- Institute of Genome Research, Vietnam Academy of Science and Technology, Cau Giay, Hanoi, Vietnam
| | - Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Kanako Hisata
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Thuy T B Vo
- Institute of Genome Research, Vietnam Academy of Science and Technology, Cau Giay, Hanoi, Vietnam
| | - Jun Inoue
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Chuya Shinzato
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan.,Present address: Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, 277-8564, Japan
| | - Binh T N Le
- Institute of Genome Research, Vietnam Academy of Science and Technology, Cau Giay, Hanoi, Vietnam
| | - Koki Nishitsuji
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Miyuki Kanda
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Vu H Nguyen
- Institute of Genome Research, Vietnam Academy of Science and Technology, Cau Giay, Hanoi, Vietnam
| | - Hai V Nong
- Institute of Genome Research, Vietnam Academy of Science and Technology, Cau Giay, Hanoi, Vietnam
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan.
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29
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Mitochondrial genome of the yellow catfish Pelteobagrus fulvidraco and insights into Bagridae phylogenetics. Genomics 2018; 111:1258-1265. [PMID: 30118781 DOI: 10.1016/j.ygeno.2018.08.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 08/02/2018] [Accepted: 08/13/2018] [Indexed: 11/21/2022]
Abstract
The mitochondrial genome (mitogenome) can provide important information for understanding phylogenetic analysis and molecular evolution. Herein, we amplified the complete mitogenome sequence of Pelteobagrus fulvidraco. The mitogenome was 16,526 bp in length and included 13 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes and a non-coding control region (D-loop). Both the organization and location of genes in the mitogenome were consistent with those from Siluriformes fishes previously published in GenBank. The phylogenetic relationships based on Bayesian inference (BI) and Maximum likelihood (ML) methods showed that P. fulvidraco has close relationships with Pelteobagrus eupogon and Tachysurus intermedius, suggesting that P. fulvidraco belongs to Tachysurus. This study provides evidence that Tachysurus, Pseudobagrus and Leiocassis do not form monophyly, but that these three genera form a monophyletic group. Our results provide reference for further phylogenetic research of the Bagridae species.
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30
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Chakrabarty P, Faircloth BC, Alda F, Ludt WB, Mcmahan CD, Near TJ, Dornburg A, Albert JS, Arroyave J, Stiassny MLJ, Sorenson L, Alfaro ME. Phylogenomic Systematics of Ostariophysan Fishes: Ultraconserved Elements Support the Surprising Non-Monophyly of Characiformes. Syst Biol 2018; 66:881-895. [PMID: 28334176 DOI: 10.1093/sysbio/syx038] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 02/24/2016] [Indexed: 12/30/2022] Open
Abstract
Ostariophysi is a superorder of bony fishes including more than 10,300 species in 1100 genera and 70 families. This superorder is traditionally divided into five major groups (orders): Gonorynchiformes (milkfishes and sandfishes), Cypriniformes (carps and minnows), Characiformes (tetras and their allies), Siluriformes (catfishes), and Gymnotiformes (electric knifefishes). Unambiguous resolution of the relationships among these lineages remains elusive, with previous molecular and morphological analyses failing to produce a consensus phylogeny. In this study, we use over 350 ultraconserved element (UCEs) loci comprising 5 million base pairs collected across 35 representative ostariophysan species to compile one of the most data-rich phylogenies of fishes to date. We use these data to infer higher level (interordinal) relationships among ostariophysan fishes, focusing on the monophyly of the Characiformes-one of the most contentiously debated groups in fish systematics. As with most previous molecular studies, we recover a non-monophyletic Characiformes with the two monophyletic suborders, Citharinoidei and Characoidei, more closely related to other ostariophysan clades than to each other. We also explore incongruence between results from different UCE data sets, issues of orthology, and the use of morphological characters in combination with our molecular data. [Conserved sequence; ichthyology; massively parallel sequencing; morphology; next-generation sequencing; UCEs.].
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Affiliation(s)
- Prosanta Chakrabarty
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, 119 Foster Hall, Baton Rouge, LA 70803, USA
| | - Brant C Faircloth
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, 119 Foster Hall, Baton Rouge, LA 70803, USA
| | - Fernando Alda
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, 119 Foster Hall, Baton Rouge, LA 70803, USA
| | - William B Ludt
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, 119 Foster Hall, Baton Rouge, LA 70803, USA
| | - Caleb D Mcmahan
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, 119 Foster Hall, Baton Rouge, LA 70803, USA.,The Field Museum of Natural History, 1400 S Lake Shore Dr, Chicago, IL 60605, USA
| | - Thomas J Near
- Department of Ecology and Evolutionary Biology, and Peabody Museum of Natural History, Yale University, New Haven, CT 06520, USA
| | - Alex Dornburg
- North Carolina Museum of Natural Sciences, Raleigh, NC 27601, USA
| | - James S Albert
- Department of Biology, University of Louisiana, Lafayette, LA 70504, USA
| | - Jairo Arroyave
- Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Melanie L J Stiassny
- Department of Ichthyology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
| | - Laurie Sorenson
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, 119 Foster Hall, Baton Rouge, LA 70803, USA.,Department of Ecology and Evolutionary Biology, University of California Los Angeles, 610 Yound Drive South, Los Angeles, CA 90095, USA
| | - Michael E Alfaro
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, 610 Yound Drive South, Los Angeles, CA 90095, USA
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31
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Barman AS, Singh M, Pandey PK. Complete mitochondrial genome of near threatened butter Catfish Ompok bimaculatus (Siluriformes: Siluridae). Mitochondrial DNA B Resour 2017; 2:313-314. [PMID: 33473811 PMCID: PMC7799613 DOI: 10.1080/23802359.2017.1334520] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The complete mitochondrial genome of Ompok bimaculatus was obtained, using illumina high-throughput NextSeq 500 with 2 × 150 bp sequencing of mitochondrial DNA. The genome of O. bimaculatus was 16,482 bp in length (GenBank Accession No. KY887474) comprised of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and a control region i.e. D-loop. In present mitogenome, 9 SSR were identified and validated in silico and secondary structures of all the 22 tRNA were predicted. The arrangement of genes was found identical to other siluriformes fish mitogenomes available in NCBI database. Phylogenetic relationship with closely related species were established which provide useful insights into taxonomic status of the species.
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Affiliation(s)
- Anindya Sundar Barman
- College of Fisheries, Central Agricultural University (I), Lembucherra, Tripura, India
| | - Mamta Singh
- College of Fisheries, Central Agricultural University (I), Lembucherra, Tripura, India
| | - Pramod Kumar Pandey
- College of Fisheries, Central Agricultural University (I), Lembucherra, Tripura, India
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Moreira DA, Buckup PA, Furtado C, Val AL, Schama R, Parente TE. Reducing the information gap on Loricarioidei (Siluriformes) mitochondrial genomics. BMC Genomics 2017; 18:345. [PMID: 28472937 PMCID: PMC5418769 DOI: 10.1186/s12864-017-3709-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 04/19/2017] [Indexed: 01/11/2023] Open
Abstract
Background The genetic diversity of Neotropical fish fauna is underrepresented in public databases. This distortion is evident for the order Siluriformes, in which the suborders Siluroidei and Loricarioidei share equivalent proportion of species, although far less is known about the genetics of the latter clade, endemic to the Neotropical Region. Recently, this information gap was evident in a study about the structural diversity of fish mitochondrial genomes, and hampered a precise chronological resolution of Siluriformes. It has also prevented molecular ecology investigations about these catfishes, their interactions with the environment, responses to anthropogenic changes and potential uses. Results Using high-throughput sequencing, we provide the nearly complete mitochondrial genomes for 26 Loricariidae and one Callichthyidae species. Structural features were highly conserved. A notable exception was identified in the monophyletic clade comprising species of the Hemiancistrus, Hypostomini and Peckoltia-clades, a ~60 nucleotide-long deletion encompassing the seven nucleotides at the 3′ end of the Conserved Sequence Block (CSB) D of the control region. The expression of mitochondrial genes followed the usual punctuation pattern. Heteroplasmic sites were identified in most species. The retrieved phylogeny strongly corroborates the currently accepted tree, although bringing to debate the relationship between Schizolecis guntheri and Pareiorhaphis garbei, and highlighting the low genetic variability within the Peckoltia-clade, an eco-morphologically diverse and taxonomically problematic group. Conclusions Herein we have launched the use of high-throughput mitochondrial genomics in the studies of the Loricarioidei species. The new genomic resources reduce the information gap on the molecular diversity of Neotropical fish fauna, impacting the capacity to investigate a variety of aspects of the molecular ecology and evolution of these fishes. Additionally, the species showing the partial CSB-D are candidate models to study the replication and transcription of vertebrate mitochondrial genome. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3709-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daniel Andrade Moreira
- Laboratório de Toxicologia Ambiental, Escola Nacional de Saúde Pública (ENSP), Fundação Oswaldo Cruz (FIOCRUZ), Av. Brasil, 4036, Rio de Janeiro, Brasil.,Laboratório de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (FIOCRUZ), Av. Brasil, 4365, Rio de Janeiro, Brasil
| | - Paulo Andreas Buckup
- Departamento de Vertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro (UFRJ), Quinta da Boa Vista, Rio de Janeiro, RJ, Brasil
| | - Carolina Furtado
- Unidade de Genômica, Instituto Nacional do Câncer (INCA), Rua André Cavalcanti, 37, Rio de Janeiro, Brasil
| | - Adalberto Luis Val
- Laboratório de Ecofisiologia e Evolução Molecular, Instituto Nacional de Pesquisas da Amazônia (INPA), Av. André Araújo, 2936, Manaus, Brasil
| | - Renata Schama
- Laboratório de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (FIOCRUZ), Av. Brasil, 4365, Rio de Janeiro, Brasil
| | - Thiago Estevam Parente
- Laboratório de Toxicologia Ambiental, Escola Nacional de Saúde Pública (ENSP), Fundação Oswaldo Cruz (FIOCRUZ), Av. Brasil, 4036, Rio de Janeiro, Brasil. .,Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (FIOCRUZ), Av. Brasil, 4365, Rio de Janeiro, Brasil.
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33
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The complete mitochondrial genome of the surubim Pseudoplatystoma corruscans (Siluriformes: Pimelodidae) and mitochondrial phylogenomics of catfishes confirm monophyly of Siluriformes families. CONSERV GENET RESOUR 2017. [DOI: 10.1007/s12686-017-0717-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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