301
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Betancur-R R, Arcila D, Vari RP, Hughes LC, Oliveira C, Sabaj MH, Ortí G. Phylogenomic incongruence, hypothesis testing, and taxonomic sampling: The monophyly of characiform fishes. Evolution 2018; 73:329-345. [PMID: 30426469 DOI: 10.1111/evo.13649] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 10/23/2018] [Accepted: 11/05/2018] [Indexed: 11/30/2022]
Abstract
Phylogenomic studies using genome-wide datasets are quickly becoming the state of the art for systematics and comparative studies, but in many cases, they result in strongly supported incongruent results. The extent to which this conflict is real depends on different sources of error potentially affecting big datasets (assembly, stochastic, and systematic error). Here, we apply a recently developed methodology (GGI or gene genealogy interrogation) and data curation to new and published datasets with more than 1000 exons, 500 ultraconserved element (UCE) loci, and transcriptomic sequences that support incongruent hypotheses. The contentious non-monophyly of the order Characiformes proposed by two studies is shown to be a spurious outcome induced by sample contamination in the transcriptomic dataset and an ambiguous result due to poor taxonomic sampling in the UCE dataset. By exploring the effects of number of taxa and loci used for analysis, we show that the power of GGI to discriminate among competing hypotheses is diminished by limited taxonomic sampling, but not equally sensitive to gene sampling. Taken together, our results reinforce the notion that merely increasing the number of genetic loci for a few representative taxa is not a robust strategy to advance phylogenetic knowledge of recalcitrant groups. We leverage the expanded exon capture dataset generated here for Characiformes (206 species in 23 out of 24 families) to produce a comprehensive phylogeny and a revised classification of the order.
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Affiliation(s)
- Ricardo Betancur-R
- Department of Biology, University of Puerto Rico, Río Piedras Campus, San Juan, Puerto Rico, 00931.,Department of Biology, University of Oklahoma, Norman, Oklahoma, 73019.,Department of Vertebrate Zoology, National Museum of Natural History Smithsonian Institution, Washington, DC, 20013
| | - Dahiana Arcila
- Department of Biology, University of Oklahoma, Norman, Oklahoma, 73019.,Department of Vertebrate Zoology, National Museum of Natural History Smithsonian Institution, Washington, DC, 20013.,Sam Noble Oklahoma Museum of Natural History, University of Oklahoma, Norman, Oklahoma, 73019
| | - Richard P Vari
- Sam Noble Oklahoma Museum of Natural History, University of Oklahoma, Norman, Oklahoma, 73019
| | - Lily C Hughes
- Department of Vertebrate Zoology, National Museum of Natural History Smithsonian Institution, Washington, DC, 20013.,Department of Biological Sciences, The George Washington University, Washington, DC, 20052
| | - Claudio Oliveira
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, Brazil
| | - Mark H Sabaj
- Department of Ichthyology, The Academy of Natural Sciences of Drexel University, Philadelphia, Pennsylvania, 19103
| | - Guillermo Ortí
- Department of Vertebrate Zoology, National Museum of Natural History Smithsonian Institution, Washington, DC, 20013.,Department of Biological Sciences, The George Washington University, Washington, DC, 20052
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302
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Jiang W, Qiu Y, Pan X, Zhang Y, Wang X, Lv Y, Bian C, Li J, You X, Chen J, Yang K, Yang J, Sun C, Liu Q, Cheng L, Yang J, Shi Q. Genome Assembly for a Yunnan-Guizhou Plateau "3E" Fish, Anabarilius grahami (Regan), and Its Evolutionary and Genetic Applications. Front Genet 2018; 9:614. [PMID: 30564274 PMCID: PMC6288284 DOI: 10.3389/fgene.2018.00614] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 11/21/2018] [Indexed: 11/26/2022] Open
Abstract
A Yunnan-Guizhou Plateau fish, the Kanglang white minnow (Anabarilius grahami), is a typical “3E” (Endangered, Endemic, and Economic) species in China. Its distribution is limited to Fuxian Lake, the nation’s second deepest lake, with a significant local economic value but a drastically declining wild population. This species has been evaluated as VU (Vulnerable) in the China Species Red List. As one of the “Four Famous Fish” in Yunnan province, the artificial breeding has been achieved since 2003. It has not only re-established its wild natural populations by reintroduction of the artificial breeding stocks, but also brought a wide and popular utilization of this species to the local fish farms. A. grahami has become one of the main native aquaculture species in Yunnan province, and the artificial production has been emerging in steady growth each year. To promote the conservation and sustainable utilization of this fish, we initiated its whole genome sequencing project using an Illumina Hiseq2500 platform. The assembled genome size of A. grahami is 1.006 Gb, accounting for 98.63% of the estimated genome size (1.020 Gb), with contig N50 and scaffold N50 values of 26.4 kb and 4.41 Mb, respectively. Approximately about 50.38% of the genome was repetitive. A total of 25,520 protein-coding genes were subsequently predicted. A phylogenetic tree based on 4,580 single-copy genes from A. grahami and 18 other cyprinids revealed three well-supported subclades within the Cyprinidae. This is the first inter-subfamily relationship of cyprinids at genome level, providing a simple yet useful framework for understanding the traditional but popular subfamily classification systems. Interestingly, a further population demography of A. grahami uncovered a historical relationship between this fish and Fuxian Lake, suggesting that range expansion or shrinkage of the habitat has had a remarkable impact on the population size of endemic plateau fishes. Additionally, a total of 33,836 simple sequence repeats (SSR) markers were identified, and 11 loci were evaluated for a preliminary genetic diversity analysis in this study, thus providing another useful genetic resource for studying this “3E” species.
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Affiliation(s)
- Wansheng Jiang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Ying Qiu
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 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, China
| | - Xiaofu Pan
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Yuanwei Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Xiaoai Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Yunyun Lv
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 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, China
| | - Chao Bian
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 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, China
| | - Jia Li
- 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, China
| | - Xinxin You
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 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, China
| | - Jieming Chen
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 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, China
| | - Kunfeng Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | | | - Chao Sun
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Qian Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Le Cheng
- BGI-Yunnan, BGI-Shenzhen, Kunming, China
| | - Junxing Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Qiong Shi
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 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, China
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303
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Huang Y, Wang M, Zhao X, Shi Q. Transcriptome sequencing of the gill and barbel of Southern catfish (Silurus meridionalis) revealed immune responses and novel rhamnose-binding lectins (RBLs). Genomics 2018; 111:222-230. [PMID: 30465915 DOI: 10.1016/j.ygeno.2018.11.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 10/29/2018] [Accepted: 11/09/2018] [Indexed: 11/28/2022]
Abstract
Southern catfish (Silurus meridionalis) is an economically important species widely cultured in China. It is well known for its fast growth, strong resistance to diseases and euryphage. However, little is known about the mechanisms for its powerful immune systems. Our Fish-T1K project has finished its first phase of 200 fish transcriptomes, with sequencing of gills in most examined fishes. In this study, we performed transcriptome sequencing of the gill and the maxillary barbel of Southern catfish, with the latter as a control. High expression of immune-related transcripts were observed in these two tissues. We observed that genes in the T cell receptor signaling pathway had higher transcription values in the gill than in the barbel. In addition, eight new rhamnose-binding lectins (RBLs) were identified and their carbohydrate recognition domains (CRDs) were classified according to the eight conserved cysteine residues and two conserved motifs (-YGR- and -DPC-). This is the first transcriptome report by high-throughput sequencing of the Southern catfish. Our genomic data and discovery of novel RBLs in this project should be able to promote better understandings of the roles of gills in immune responses and disease prevention for further aquaculture.
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Affiliation(s)
- Yu Huang
- 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.
| | - Min Wang
- 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; BGI Zhenjiang Institute of Hydrobiology, Zhenjiang 212000, China.
| | - Xiaomeng Zhao
- 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; Laboratory of Aquatic Genomics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China.
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304
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Straube N, Li C, Mertzen M, Yuan H, Moritz T. A phylogenomic approach to reconstruct interrelationships of main clupeocephalan lineages with a critical discussion of morphological apomorphies. BMC Evol Biol 2018; 18:158. [PMID: 30352561 PMCID: PMC6199709 DOI: 10.1186/s12862-018-1267-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Accepted: 09/26/2018] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Previous molecular studies on the phylogeny and classification of clupeocephalan fishes revealed numerous new taxonomic entities. For re-analysing these taxa, we perform target gene capturing and subsequent next generation sequencing of putative ortholog exons of major clupeocephalan lineages. Sequence information for the RNA bait design was derived from publicly available genomes of bony fishes. Newly acquired sequence data comprising > 800 exon sequences was subsequently used for phylogenetic reconstructions. RESULTS Our results support monophyletic Otomorpha comprising Alepocephaliformes. Within Ostariophysi, Gonorynchiformes are sister to a clade comprising Cypriniformes, Characiformes, Siluriformes and Gymnotiformes, where the interrelationships of Characiformes, Siluriformes and Gymnotiformes remain enigmatic. Euteleosts comprise four major clades: Lepidogalaxiiformes, Protacanthopterygii, Stomiatii, and Galaxiiformes plus Neoteleostei. The monotypic Lepidogalaxiiformes form the sister-group to all remaining euteleosts. Protacanthopterygii, comprising Argentini-, Esoci- and Salmoniformes, is sister to Stomiatii (Osmeriformes and Stomiatiformes) and Galaxiiformes plus Neoteleostei. CONCLUSIONS Several proposed monophyla defined by morphological apomorphies within the Clupeocephalan phylogeny are confirmed by the phylogenetic estimates presented herein. However, other morphologically described groups cannot be reconciled with molecular phylogenies. Thus, numerous morphological apomoprhies of supposed monophyla are called into question. The interpretation of suggested morphological synapomorphies of otomorph fishes is strongly affected by the inclusion of deep-sea inhabiting, and to that effect morphologically adapted Alepocephaliformes. Our revision of these potential synapomorphies, in the context that Alepocephaliformes are otomorph fishes, reveals that only a single character of the total nine characters proposed as synapomorphic for the group is clearly valid for all otomorphs. Three further characters remain possible apomorphies since their status remains unclear in the deep-sea adapted Alepocephaliformes showing developmental lag and lacking a swim bladder. Further, our analysis places Galaxiiformes as sister group to neoteleosts, which contradicts some previous molecular phylogenetic studies. This needs further investigation from a morphological perspective, as suggested synapomophies for several euteleostean lineages are challenged or still lacking. For the verification of results presented herein, a denser phylogenomic-level taxon sampling should be applied.
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Affiliation(s)
- Nicolas Straube
- Institut für Zoologie & Evolutionsbiologie, Friedrich-Schiller-Universität Jena, Erbertstraße 1, 07743 Jena, Germany
- Zoologische Staatssammlung München, Staatliche Naturwissenschaftliche Sammlungen Bayerns, Münchhausenstraße 21, 81247 Munich, Germany
| | - Chenhong Li
- Key Laboratory of Exploration and Utilization of Aquatic, Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, 201306 China
| | - Matthias Mertzen
- Institut für Zoologie & Evolutionsbiologie, Friedrich-Schiller-Universität Jena, Erbertstraße 1, 07743 Jena, Germany
- Deutsches Meeresmuseum, Katharinenberg 14-20, 18439 Stralsund, Germany
| | - Hao Yuan
- Key Laboratory of Exploration and Utilization of Aquatic, Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, 201306 China
| | - Timo Moritz
- Institut für Zoologie & Evolutionsbiologie, Friedrich-Schiller-Universität Jena, Erbertstraße 1, 07743 Jena, Germany
- Deutsches Meeresmuseum, Katharinenberg 14-20, 18439 Stralsund, Germany
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305
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Lopes-Marques M, Kabeya N, Qian Y, Ruivo R, Santos MM, Venkatesh B, Tocher DR, Castro LFC, Monroig Ó. Retention of fatty acyl desaturase 1 (fads1) in Elopomorpha and Cyclostomata provides novel insights into the evolution of long-chain polyunsaturated fatty acid biosynthesis in vertebrates. BMC Evol Biol 2018; 18:157. [PMID: 30340454 PMCID: PMC6194568 DOI: 10.1186/s12862-018-1271-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 10/02/2018] [Indexed: 12/22/2022] Open
Abstract
Background Provision of long-chain polyunsaturated fatty acids (LC-PUFA) in vertebrates occurs through the diet or via endogenous production from C18 precursors through consecutive elongations and desaturations. It has been postulated that the abundance of LC-PUFA in the marine environment has remarkably modulated the gene complement and function of Fads in marine teleosts. In vertebrates two fatty acyl desaturases, namely Fads1 and Fads2, encode ∆5 and ∆6 desaturases, respectively. To fully clarify the evolutionary history of LC-PUFA biosynthesis in vertebrates, we investigated the gene repertoire and function of Fads from species placed at key evolutionary nodes. Results We demonstrate that functional Fads1Δ5 and Fads2∆6 arose from a tandem gene duplication in the ancestor of vertebrates, since they are present in the Arctic lamprey. Additionally, we show that a similar condition was retained in ray-finned fish such as the Senegal bichir and spotted gar, with the identification of fads1 genes in these lineages. Functional characterisation of the isolated desaturases reveals the first case of a Fads1 enzyme with ∆5 desaturase activity in the Teleostei lineage, the Elopomorpha. In contrast, in Osteoglossomorpha genomes, while no fads1 was identified, two separate fads2 duplicates with ∆6 and ∆5 desaturase activities respectively were uncovered. Conclusions We conclude that, while the essential genetic components involved LC-PUFA biosynthesis evolved in the vertebrate ancestor, the full completion of the LC-PUFA biosynthesis pathway arose uniquely in gnathostomes. Electronic supplementary material The online version of this article (10.1186/s12862-018-1271-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mónica Lopes-Marques
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), U. Porto - University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Matosinhos, Portugal.,Laboratory of Histology and Embryology, Department of Microscopy, Institute of Biomedical Sciences Abel Salazar (ICBAS), U.Porto - University of Porto, Rua Jorge Viterbo Ferreira 228, P 4050-313, Porto, Portugal
| | - Naoki Kabeya
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yu Qian
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, FK9 4LA, Scotland, UK
| | - Raquel Ruivo
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), U. Porto - University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Matosinhos, Portugal
| | - Miguel M Santos
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), U. Porto - University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Matosinhos, Portugal.,Faculty of Sciences (FCUP), Department of Biology, U.Porto - University of Porto, Rua do Campo Alegre, P 4169-007, Porto, Portugal
| | - Byrappa Venkatesh
- Comparative Genomics Laboratory, Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Biopolis, Singapore, 138673, Singapore
| | - Douglas R Tocher
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, FK9 4LA, Scotland, UK
| | - L Filipe C Castro
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), U. Porto - University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Matosinhos, Portugal. .,Faculty of Sciences (FCUP), Department of Biology, U.Porto - University of Porto, Rua do Campo Alegre, P 4169-007, Porto, Portugal.
| | - Óscar Monroig
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, FK9 4LA, Scotland, UK. .,Instituto de Acuicultura Torre de la Sal (IATS-CSIC), Ribera de Cabanes, 12595, Castellón, Spain.
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306
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Capobianco A, Friedman M. Vicariance and dispersal in southern hemisphere freshwater fish clades: a palaeontological perspective. Biol Rev Camb Philos Soc 2018; 94:662-699. [DOI: 10.1111/brv.12473] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 09/17/2018] [Accepted: 09/19/2018] [Indexed: 02/07/2023]
Affiliation(s)
- Alessio Capobianco
- Museum of Paleontology and Department of Earth and Environmental Sciences; University of Michigan; 1105 N. University Ave, Ann Arbor MI 48109-1079 U.S.A
| | - Matt Friedman
- Museum of Paleontology and Department of Earth and Environmental Sciences; University of Michigan; 1105 N. University Ave, Ann Arbor MI 48109-1079 U.S.A
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307
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Hilton EJ, Lavoué S. A review of the systematic biology of fossil and living bony-tongue fishes, Osteoglossomorpha (Actinopterygii: Teleostei). NEOTROPICAL ICHTHYOLOGY 2018. [DOI: 10.1590/1982-0224-20180031] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
ABSTRACT The bony-tongue fishes, Osteoglossomorpha, have been the focus of a great deal of morphological, systematic, and evolutionary study, due in part to their basal position among extant teleostean fishes. This group includes the mooneyes (Hiodontidae), knifefishes (Notopteridae), the abu (Gymnarchidae), elephantfishes (Mormyridae), arawanas and pirarucu (Osteoglossidae), and the African butterfly fish (Pantodontidae). This morphologically heterogeneous group also has a long and diverse fossil record, including taxa from all continents and both freshwater and marine deposits. The phylogenetic relationships among most extant osteoglossomorph families are widely agreed upon. However, there is still much to discover about the systematic biology of these fishes, particularly with regard to the phylogenetic affinities of several fossil taxa, within Mormyridae, and the position of Pantodon. In this paper we review the state of knowledge for osteoglossomorph fishes. We first provide an overview of the diversity of Osteoglossomorpha, and then discuss studies of the phylogeny of Osteoglossomorpha from both morphological and molecular perspectives, as well as biogeographic analyses of the group. Finally, we offer our perspectives on future needs for research on the systematic biology of Osteoglossomorpha.
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Affiliation(s)
| | - Sébastien Lavoué
- National Taiwan University, Taiwan; Universiti Sains Malaysia, Malaysia
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308
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Machado AM, Tørresen OK, Kabeya N, Couto A, Petersen B, Felício M, Campos PF, Fonseca E, Bandarra N, Lopes-Marques M, Ferraz R, Ruivo R, Fonseca MM, Jentoft S, Monroig Ó, da Fonseca RR, C Castro LF. " Out of the Can": A Draft Genome Assembly, Liver Transcriptome, and Nutrigenomics of the European Sardine, Sardina pilchardus. Genes (Basel) 2018; 9:E485. [PMID: 30304855 PMCID: PMC6210256 DOI: 10.3390/genes9100485] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 10/01/2018] [Accepted: 10/02/2018] [Indexed: 12/30/2022] Open
Abstract
Clupeiformes, such as sardines and herrings, represent an important share of worldwide fisheries. Among those, the European sardine (Sardina pilchardus, Walbaum 1792) exhibits significant commercial relevance. While the last decade showed a steady and sharp decline in capture levels, recent advances in culture husbandry represent promising research avenues. Yet, the complete absence of genomic resources from sardine imposes a severe bottleneck to understand its physiological and ecological requirements. We generated 69 Gbp of paired-end reads using Illumina HiSeq X Ten and assembled a draft genome assembly with an N50 scaffold length of 25,579 bp and BUSCO completeness of 82.1% (Actinopterygii). The estimated size of the genome ranges between 655 and 850 Mb. Additionally, we generated a relatively high-level liver transcriptome. To deliver a proof of principle of the value of this dataset, we established the presence and function of enzymes (Elovl2, Elovl5, and Fads2) that have pivotal roles in the biosynthesis of long chain polyunsaturated fatty acids, essential nutrients particularly abundant in oily fish such as sardines. Our study provides the first omics dataset from a valuable economic marine teleost species, the European sardine, representing an essential resource for their effective conservation, management, and sustainable exploitation.
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Affiliation(s)
- André M Machado
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, 4450-208 Matosinhos, Portugal.
| | - Ole K Tørresen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, 0371 Oslo, Norway.
| | - Naoki Kabeya
- Department of Aquatic Bioscience, The University of Tokyo, Tokyo 113-8654, Japan.
| | - Alvarina Couto
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, 4450-208 Matosinhos, Portugal.
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark.
| | - Bent Petersen
- Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
- Centre of Excellence for Omics-Driven Computational Biodiscovery, Faculty of Applied Sciences, Asian Institute of Medicine, Science and Technology, Kedah 08000, Malaysia.
| | - Mónica Felício
- Portuguese Institute for the Sea and Atmosphere, (IPMA), 1749-077 Lisbon, Portugal.
| | - Paula F Campos
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, 4450-208 Matosinhos, Portugal.
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark.
| | - Elza Fonseca
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, 4450-208 Matosinhos, Portugal.
- Department of Biology, Faculty of Sciences, University of Porto, 4099-022 Porto, Portugal.
| | - Narcisa Bandarra
- Portuguese Institute for the Sea and Atmosphere, (IPMA), 1749-077 Lisbon, Portugal.
| | - Mónica Lopes-Marques
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, 4450-208 Matosinhos, Portugal.
| | - Renato Ferraz
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, 4450-208 Matosinhos, Portugal.
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4099-022 Porto, Portugal.
| | - Raquel Ruivo
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, 4450-208 Matosinhos, Portugal.
| | - Miguel M Fonseca
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, 4450-208 Matosinhos, Portugal.
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, 0371 Oslo, Norway.
- Centre for Coastal Research, Department of Natural Sciences, University of Agder, 4630 Kristiansand, Norway.
| | - Óscar Monroig
- Instituto de Acuicultura Torre de la Sal, Consejo Superior de Investigaciones Científicas (IATS-CSIC), 12595 Ribera de Cabanes, Spain.
| | - Rute R da Fonseca
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark.
- Center for Macroecology, Evolution, and Climate, Natural History Museum of Denmark, University of Copenhagen, DK-2100 Copenhagen, Denmark.
| | - L Filipe C Castro
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, 4450-208 Matosinhos, Portugal.
- Department of Biology, Faculty of Sciences, University of Porto, 4099-022 Porto, Portugal.
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Vialle RA, de Souza JES, Lopes KDP, Teixeira DG, Alves Sobrinho PDA, Ribeiro-dos-Santos AM, Furtado C, Sakamoto T, Oliveira Silva FA, Herculano Corrêa de Oliveira E, Hamoy IG, Assumpção PP, Ribeiro-dos-Santos Â, Santos Lima JPM, Seuánez HN, de Souza SJ, Santos S. Whole Genome Sequencing of the Pirarucu (Arapaima gigas) Supports Independent Emergence of Major Teleost Clades. Genome Biol Evol 2018; 10:2366-2379. [PMID: 29982381 PMCID: PMC6143160 DOI: 10.1093/gbe/evy130] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/30/2018] [Indexed: 01/14/2023] Open
Abstract
The Pirarucu (Arapaima gigas) is one of the world's largest freshwater fishes and member of the superorder Osteoglossomorpha (bonytongues), one of the oldest lineages of ray-finned fishes. This species is an obligate air-breather found in the basin of the Amazon River with an attractive potential for aquaculture. Its phylogenetic position among bony fishes makes the Pirarucu a relevant subject for evolutionary studies of early teleost diversification. Here, we present, for the first time, a draft genome version of the A. gigas genome, providing useful information for further functional and evolutionary studies. The A. gigas genome was assembled with 103-Gb raw reads sequenced in an Illumina platform. The final draft genome assembly was ∼661 Mb, with a contig N50 equal to 51.23 kb and scaffold N50 of 668 kb. Repeat sequences accounted for 21.69% of the whole genome, and a total of 24,655 protein-coding genes were predicted from the genome assembly, with an average of nine exons per gene. Phylogenomic analysis based on 24 fish species supported the postulation that Osteoglossomorpha and Elopomorpha (eels, tarpons, and bonefishes) are sister groups, both forming a sister lineage with respect to Clupeocephala (remaining teleosts). Divergence time estimations suggested that Osteoglossomorpha and Elopomorpha lineages emerged independently in a period of ∼30 Myr in the Jurassic. The draft genome of A. gigas provides a valuable genetic resource for further investigations of evolutionary studies and may also offer a valuable data for economic applications.
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Affiliation(s)
- Ricardo Assunção Vialle
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brazil
| | | | - Katia de Paiva Lopes
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brazil
| | - Diego Gomes Teixeira
- Bioinformatics Multidisciplinary Environment – BioME, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil
| | | | - André M Ribeiro-dos-Santos
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brazil
- Departmento de Genética, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil
| | - Carolina Furtado
- Programa de Genética, Instituto Nacional de Câncer (INCA), Rio de Janeiro, RJ, Brazil
| | - Tetsu Sakamoto
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | | | | | - Igor Guerreiro Hamoy
- Laboratório de Genética Aplicada, Universidade Federal Rural da Amazônia, Belém, PA, Brazil
| | | | - Ândrea Ribeiro-dos-Santos
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brazil
- Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém, PA, Brazil
| | - João Paulo Matos Santos Lima
- Bioinformatics Multidisciplinary Environment – BioME, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil
- Departamento de Bioquímica, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil
| | - Héctor N Seuánez
- Programa de Genética, Instituto Nacional de Câncer (INCA), Rio de Janeiro, RJ, Brazil
- Departamento de Genética, Universidade Federal do Rio de Janeiro, RJ, Brazil
| | - Sandro José de Souza
- Bioinformatics Multidisciplinary Environment – BioME, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil
- Instituto do Cérebro, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil
| | - Sidney Santos
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brazil
- Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém, PA, Brazil
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310
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Anoop VK, Dahanukar N, Philip S, Thomas L, Raghavan R. Phylogeny of the hillstream loach genus Mesonoemacheilus reveals widespread diversification through ancient drainage connections in the Western Ghats Biodiversity Hotspot. Mol Phylogenet Evol 2018; 129:77-84. [PMID: 30153500 DOI: 10.1016/j.ympev.2018.08.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 08/09/2018] [Accepted: 08/22/2018] [Indexed: 11/16/2022]
Abstract
Rivers draining the Western Ghats (WG) mountain ranges in peninsular India harbor an exceptionally diverse, unique and evolutionarily distinct assemblage of lower vertebrates with high levels of endemism, attributed to their evolution and potentially long history of isolation during the Late Cretaceous or Early Tertiary. A molecular phylogeny of hillstream loaches of the genus Mesonoemacheilus endemic to the WG revealed the presence of four clades which we designate as 'species groups'. A consensus of various species delimitation methods indicates the likelihood of 'at least' seven more undescribed species within Mesonoemacheilus. Molecular clock analysis dates the basal clade around 38 mya in the Paleogene, and subsequent diversification in the Neogene and Quaternary periods resulting in the current genetic diversity. Biogeographic analysis suggests that vicariance events which separated the rivers on either side of the two geological barriers/gaps, the Palghat and Shencottah, in the Neogene, as well as range contractions and cladogenetic events contributed to the current patterns of diversity and distribution of this genus. Our results also provide preliminary indications on the interconnections and faunal exchange between historical river drainages in the WG region.
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Affiliation(s)
- V K Anoop
- School of Ocean Science and Technology, Kerala University of Fisheries and Ocean Studies (KUFOS), Kochi 682 506, Kerala, India
| | - Neelesh Dahanukar
- Indian Institute of Science Education and Research (IISER), G1 Block, Dr. Homi Bhabha Road, Pashan, Pune 411 008, Maharashtra, India
| | - Siby Philip
- Department of Zoology, Nirmalagiri College, Kannur 670 701, Kerala, India
| | - Liju Thomas
- School of Ocean Science and Technology, Kerala University of Fisheries and Ocean Studies (KUFOS), Kochi 682 506, Kerala, India; Department of Zoology, Nirmalagiri College, Kannur 670 701, Kerala, India
| | - Rajeev Raghavan
- Department of Fisheries Resource Management, Kerala University of Fisheries and Ocean Studies (KUFOS), Kochi 682 506, Kerala, India.
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