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Majeed A, Singh A, Choudhary S, Bhardwaj P. RNAseq‐based phylogenetic reconstruction of Taxaceae and Cephalotaxaceae. Cladistics 2018; 35:461-468. [PMID: 34633712 DOI: 10.1111/cla.12362] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/15/2018] [Indexed: 11/29/2022] Open
Affiliation(s)
- Aasim Majeed
- Molecular Genetics Laboratory Department of Plant Sciences Central University of Punjab Mansa Road Bathinda 151001 India
| | - Amandeep Singh
- Molecular Genetics Laboratory Department of Plant Sciences Central University of Punjab Mansa Road Bathinda 151001 India
| | - Shruti Choudhary
- Molecular Genetics Laboratory Department of Plant Sciences Central University of Punjab Mansa Road Bathinda 151001 India
| | - Pankaj Bhardwaj
- Molecular Genetics Laboratory Department of Plant Sciences Central University of Punjab Mansa Road Bathinda 151001 India
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2
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Dai W, Zou M, Yang L, Du K, Chen W, Shen Y, Mayden RL, He S. Phylogenomic Perspective on the Relationships and Evolutionary History of the Major Otocephalan Lineages. Sci Rep 2018; 8:205. [PMID: 29317769 PMCID: PMC5760653 DOI: 10.1038/s41598-017-18432-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 12/11/2017] [Indexed: 12/21/2022] Open
Abstract
The phylogeny of otocephalan fishes is the subject of broad controversy based on morphological and molecular evidence. The primary unresolved issue pertaining to this lineage relates to the origin of Characiphysi, especially the paraphyly of Characiformes. The considerable uncertainty associated with this lineage has precluded a greater understanding of the origin and evolution of the clade. Herein, a phylogenomic approach was applied to resolve this debate. By analyzing 10 sets of transcriptomic data generated in this study and 12 sets of high-throughput data available in public databases, we obtained 1,110 single-copy orthologous genes (935,265 sites for analysis) from 22 actinopterygians, including 14 otocephalan fishes from six orders: Clupeiformes, Gonorynchiformes, Cypriniformes, Siluriformes, Characiformes, and Gymnotiformes. Based on a selection of 125 nuclear genes screened from single-gene maximum likelihood (ML) analyses and sequence bias testing, well-established relationships among Otocephala were reconstructed. We suggested that Gymnotiformes are more closely related to Characiformes than to Siluriformes and Characiformes are possibly paraphyletic. We also estimated that Otocephala originated in the Early-Late Jurassic, which postdates most previous estimations, and hypothesized scenarios of the early historical biogeographies of major otocephalan lineages.
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Affiliation(s)
- Wei Dai
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100039, People's Republic of China
| | - Ming Zou
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Beijing, 430070, People's Republic of China
| | - Liandong Yang
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100039, People's Republic of China
| | - Kang Du
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100039, People's Republic of China
| | - Weitao Chen
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100039, People's Republic of China
| | - Yanjun Shen
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100039, People's Republic of China
| | - Richard L Mayden
- Department of Biology, Saint Louis University, Saint Louis, MO, 63103, USA
| | - Shunping He
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, People's Republic of China.
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Evolution of Shh endoderm enhancers during morphological transition from ventral lungs to dorsal gas bladder. Nat Commun 2017; 8:14300. [PMID: 28155855 PMCID: PMC5296767 DOI: 10.1038/ncomms14300] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 12/16/2016] [Indexed: 11/13/2022] Open
Abstract
Shh signalling plays a crucial role for endoderm development. A Shh endoderm enhancer, MACS1, is well conserved across terrestrial animals with lungs. Here, we first show that eliminating mouse MACS1 causes severe defects in laryngeal development, indicating that MACS1-directed Shh signalling is indispensable for respiratory organogenesis. Extensive phylogenetic analyses revealed that MACS1 emerged prior to the divergence of cartilaginous and bony fishes, and even euteleost fishes have a MACS1 orthologue. Meanwhile, ray-finned fishes evolved a novel conserved non-coding sequence in the neighbouring region. Transgenic assays showed that MACS1 drives reporter expression ventrally in laryngeal epithelium. This activity has been lost in the euteleost lineage, and instead, the conserved non-coding sequence of euteleosts acquired an enhancer activity to elicit dorsal epithelial expression in the posterior pharynx and oesophagus. These results implicate that evolution of these two enhancers is relevant to the morphological transition from ventral lungs to dorsal gas bladder. Endoderm enhancer MACS1 of Sonic Hedgehog is conserved in animals with lungs. Here, the authors show that mouse without MACS1 has defective laryngeal development, and use phylogenetic analyses to show association of evolutionary lung-gas bladder transition with change of the enhancer.
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Killen SS, Glazier DS, Rezende EL, Clark TD, Atkinson D, Willener AST, Halsey LG. Ecological Influences and Morphological Correlates of Resting and Maximal Metabolic Rates across Teleost Fish Species. Am Nat 2016; 187:592-606. [PMID: 27104992 DOI: 10.1086/685893] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Rates of aerobic metabolism vary considerably across evolutionary lineages, but little is known about the proximate and ultimate factors that generate and maintain this variability. Using data for 131 teleost fish species, we performed a large-scale phylogenetic comparative analysis of how interspecific variation in resting metabolic rates (RMRs) and maximum metabolic rates (MMRs) is related to several ecological and morphological variables. Mass- and temperature-adjusted RMR and MMR are highly correlated along a continuum spanning a 30- to 40-fold range. Phylogenetic generalized least squares models suggest that RMR and MMR are higher in pelagic species and that species with higher trophic levels exhibit elevated MMR. This variation is mirrored at various levels of structural organization: gill surface area, muscle protein content, and caudal fin aspect ratio (a proxy for activity) are positively related with aerobic capacity. Muscle protein content and caudal fin aspect ratio are also positively correlated with RMR. Hypoxia-tolerant lineages fall at the lower end of the metabolic continuum. Different ecological lifestyles are associated with contrasting levels of aerobic capacity, possibly reflecting the interplay between selection for increased locomotor performance on one hand and tolerance to low resource availability, particularly oxygen, on the other. These results support the aerobic capacity model of the evolution of endothermy, suggesting elevated body temperatures evolved as correlated responses to selection for high activity levels.
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Characterizing the transcriptome and molecular markers information for roach, Rutilus rutilus. J Genet 2016; 95:45-51. [PMID: 27019431 DOI: 10.1007/s12041-015-0597-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Rutilus rutilus (roach) is native to most of Europe and western Asia, and the Irtysh River basin in Sinkiang, northwest China is the marginal area of their natural distribution. The wide distribution and unique characteristic of this species makes it an ideal model for analysing ecological and comparative genomics. However, the limited genome sequences available for this species have hindered these investigations. Transcriptomes from the brains and livers of five individuals collected from the Irtysh River basin were sequenced using Illumina paired-end sequencing technology. A collection of 132,289 unigenes for this species were obtained using a de novo assembly method based on nearly 120 million clean reads encompassing more than 14 Gb data. Approximately 37.5% (49,656), 27.1% (35,867) and 21.2% (27,987) of the transcriptome had homologues deposited in Nt, Nr and Swiss-Prot, respectively; 12.3% (16,328) were assigned to eukaryotic orthologous groups of proteins classifications, and 21.5% (28,429) harboured Interpro domains. On the basis of the assembled transcriptome, we detected 177,493 single-nuc leotide variation resident in 39.3% (52,029) of the sequences and 20.8% (27,497) of the sequences harbouring 36,639 simple sequence repeats. The identified molecular markers are a basis for further ecological analysis, and the transcriptome reported here allows for more extensive evolutionary analyses of the Cyprinidae, the most species-rich family of freshwater fishes.
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Austin CM, Tan MH, Croft LJ, Hammer MP, Gan HM. Whole Genome Sequencing of the Asian Arowana (Scleropages formosus) Provides Insights into the Evolution of Ray-Finned Fishes. Genome Biol Evol 2015; 7:2885-95. [PMID: 26446539 PMCID: PMC4684697 DOI: 10.1093/gbe/evv186] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The Asian arowana (Scleropages formosus) is of commercial importance, conservation concern, and is a representative of one of the oldest lineages of ray-finned fish, the Osteoglossomorpha. To add to genomic knowledge of this species and the evolution of teleosts, the genome of a Malaysian specimen of arowana was sequenced. A draft genome is presented consisting of 42,110 scaffolds with a total size of 708 Mb (2.85% gaps) representing 93.95% of core eukaryotic genes. Using a k-mer-based method, a genome size of 900 Mb was also estimated. We present an update on the phylogenomics of fishes based on a total of 27 species (23 fish species and 4 tetrapods) using 177 orthologous proteins (71,360 amino acid sites), which supports established relationships except that arowana is placed as the sister lineage to all teleost clades (Bayesian posterior probability 1.00, bootstrap replicate 93%), that evolved after the teleost genome duplication event rather than the eels (Elopomorpha). Evolutionary rates are highly heterogeneous across the tree with fishes represented by both slowly and rapidly evolving lineages. A total of 94 putative pigment genes were identified, providing the impetus for development of molecular markers associated with the spectacular colored phenotypes found within this species.
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Affiliation(s)
- Christopher M Austin
- School of Science, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia Monash University Malaysia Genomics Facility, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia
| | - Mun Hua Tan
- School of Science, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia Monash University Malaysia Genomics Facility, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia
| | - Larry J Croft
- School of Science, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia Monash University Malaysia Genomics Facility, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia Malaysian Genomics Resource Centre Berhad, Boulevard Signature Office, Kuala Lumpur, Malaysia
| | - Michael P Hammer
- Museum and Art Gallery of the Northern Territory, Darwin, NT, Australia
| | - Han Ming Gan
- School of Science, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia Monash University Malaysia Genomics Facility, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia
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Lyu MJA, Gowik U, Kelly S, Covshoff S, Mallmann J, Westhoff P, Hibberd JM, Stata M, Sage RF, Lu H, Wei X, Wong GKS, Zhu XG. RNA-Seq based phylogeny recapitulates previous phylogeny of the genus Flaveria (Asteraceae) with some modifications. BMC Evol Biol 2015; 15:116. [PMID: 26084484 PMCID: PMC4472175 DOI: 10.1186/s12862-015-0399-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 05/29/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The genus Flaveria has been extensively used as a model to study the evolution of C4 photosynthesis as it contains C3 and C4 species as well as a number of species that exhibit intermediate types of photosynthesis. The current phylogenetic tree of the genus Flaveria contains 21 of the 23 known Flaveria species and has been previously constructed using a combination of morphological data and three non-coding DNA sequences (nuclear encoded ETS, ITS and chloroplast encoded trnL-F). RESULTS Here we developed a new strategy to update the phylogenetic tree of 16 Flaveria species based on RNA-Seq data. The updated phylogeny is largely congruent with the previously published tree but with some modifications. We propose that the data collection method provided in this study can be used as a generic method for phylogenetic tree reconstruction if the target species has no genomic information. We also showed that a "F. pringlei" genotype recently used in a number of labs may be a hybrid between F. pringlei (C3) and F. angustifolia (C3-C4). CONCLUSIONS We propose that the new strategy of obtaining phylogenetic sequences outlined in this study can be used to construct robust trees in a larger number of taxa. The updated Flaveria phylogenetic tree also supports a hypothesis of stepwise and parallel evolution of C4 photosynthesis in the Flavaria clade.
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Affiliation(s)
- Ming-Ju Amy Lyu
- CAS-MPG Partner Institute and Key Laboratory for Computational Biology, Shanghai Institutes for Biological Sciences, Shanghai, China.
| | - Udo Gowik
- Institute of Plant Molecular and Developmental Biology, Heinrich-Heine-University, Dusseldorf, Germany.
| | - Steve Kelly
- Department of Plant Sciences, University of Oxford, Oxford, UK.
| | - Sarah Covshoff
- Department of Plant Sciences, University of Cambridge, Cambridge, UK.
| | - Julia Mallmann
- Institute of Plant Molecular and Developmental Biology, Heinrich-Heine-University, Dusseldorf, Germany.
| | - Peter Westhoff
- Institute of Plant Molecular and Developmental Biology, Heinrich-Heine-University, Dusseldorf, Germany.
| | - Julian M Hibberd
- Department of Plant Sciences, University of Cambridge, Cambridge, UK.
| | - Matt Stata
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada.
| | - Rowan F Sage
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada.
| | - Haorong Lu
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China.
| | - Xiaofeng Wei
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China.
| | - Gane Ka-Shu Wong
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China.
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada.
- Department of Medicine, University of Alberta, Edmonton, AB, T6G 2E1, Canada.
| | - Xin-Guang Zhu
- CAS-MPG Partner Institute and Key Laboratory for Computational Biology, Shanghai Institutes for Biological Sciences, Shanghai, China.
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Grimholt U, Tsukamoto K, Azuma T, Leong J, Koop BF, Dijkstra JM. A comprehensive analysis of teleost MHC class I sequences. BMC Evol Biol 2015; 15:32. [PMID: 25888517 PMCID: PMC4364491 DOI: 10.1186/s12862-015-0309-1] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 02/16/2015] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND MHC class I (MHCI) molecules are the key presenters of peptides generated through the intracellular pathway to CD8-positive T-cells. In fish, MHCI genes were first identified in the early 1990's, but we still know little about their functional relevance. The expansion and presumed sub-functionalization of cod MHCI and access to many published fish genome sequences provide us with the incentive to undertake a comprehensive study of deduced teleost fish MHCI molecules. RESULTS We expand the known MHCI lineages in teleosts to five with identification of a new lineage defined as P. The two lineages U and Z, which both include presumed peptide binding classical/typical molecules besides more derived molecules, are present in all teleosts analyzed. The U lineage displays two modes of evolution, most pronouncedly observed in classical-type alpha 1 domains; cod and stickleback have expanded on one of at least eight ancient alpha 1 domain lineages as opposed to many other teleosts that preserved a number of these ancient lineages. The Z lineage comes in a typical format present in all analyzed ray-finned fish species as well as lungfish. The typical Z format displays an unprecedented conservation of almost all 37 residues predicted to make up the peptide binding groove. However, also co-existing atypical Z sub-lineage molecules, which lost the presumed peptide binding motif, are found in some fish like carps and cavefish. The remaining three lineages, L, S and P, are not predicted to bind peptides and are lost in some species. CONCLUSIONS Much like tetrapods, teleosts have polymorphic classical peptide binding MHCI molecules, a number of classical-similar non-classical MHCI molecules, and some members of more diverged MHCI lineages. Different from tetrapods, however, is that in some teleosts the classical MHCI polymorphism incorporates multiple ancient MHCI domain lineages. Also different from tetrapods is that teleosts have typical Z molecules, in which the residues that presumably form the peptide binding groove have been almost completely conserved for over 400 million years. The reasons for the uniquely teleost evolution modes of peptide binding MHCI molecules remain an enigma.
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Affiliation(s)
| | - Kentaro Tsukamoto
- Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi, 470-1192, Japan.
| | - Teruo Azuma
- Fisheries Technology Division, National Research Institute of Fisheries Engineering, 7620-7, Hasaki, Kamisu-shi, Ibaraki, Japan.
| | - Jong Leong
- Centre for Biomedical Research, Department of Biology, University of Victoria, PO Box 3020 STN CSC, Victoria, Canada.
| | - Ben F Koop
- Centre for Biomedical Research, Department of Biology, University of Victoria, PO Box 3020 STN CSC, Victoria, Canada.
| | - Johannes M Dijkstra
- Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi, 470-1192, Japan.
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Fine mapping and evolution of the major sex determining region in turbot (Scophthalmus maximus). G3-GENES GENOMES GENETICS 2014; 4:1871-80. [PMID: 25106948 PMCID: PMC4199694 DOI: 10.1534/g3.114.012328] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Fish sex determination (SD) systems are varied, suggesting evolutionary changes including either multiple evolution origins of genetic SD from nongenetic systems (such as environmental SD) and/or turnover events replacing one genetic system by another. When genetic SD is found, cytological differentiation between the two members of the sex chromosome pair is often minor or undetectable. The turbot (Scophthalmus maximus), a valuable commercial flatfish, has a ZZ/ZW system and a major SD region on linkage group 5 (LG5), but there are also other minor genetic and environmental influences. We here report refined mapping of the turbot SD region, supported by comparative mapping with model fish species, to identify the turbot master SD gene. Six genes were located to the SD region, two of them associated with gonad development (sox2 and dnajc19). All showed a high association with sex within families (P = 0), but not at the population level, so they are probably partially sex-linked genes, but not SD gene itself. Analysis of crossovers in LG5 using two families confirmed a ZZ/ZW system in turbot and suggested a revised map position for the master gene. Genetic diversity and differentiation for 25 LG5 genetic markers showed no differences between males and females sampled from a wild population, suggesting a recent origin of the SD region in turbot. We also analyzed associations with markers of the most relevant sex-related linkage groups in brill (S. rhombus), a closely related species to turbot; the data suggest that an ancient XX/XY system in brill changed to a ZZ/ZW mechanism in turbot.
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Rondeau EB, Minkley DR, Leong JS, Messmer AM, Jantzen JR, von Schalburg KR, Lemon C, Bird NH, Koop BF. The genome and linkage map of the northern pike (Esox lucius): conserved synteny revealed between the salmonid sister group and the Neoteleostei. PLoS One 2014; 9:e102089. [PMID: 25069045 PMCID: PMC4113312 DOI: 10.1371/journal.pone.0102089] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 06/14/2014] [Indexed: 11/19/2022] Open
Abstract
The northern pike is the most frequently studied member of the Esociformes, the closest order to the diverse and economically important Salmoniformes. The ancestor of all salmonids purportedly experienced a whole-genome duplication (WGD) event, making salmonid species ideal for studying the early impacts of genome duplication while complicating their use in wider analyses of teleost evolution. Studies suggest that the Esociformes diverged from the salmonid lineage prior to the WGD, supporting the use of northern pike as a pre-duplication outgroup. Here we present the first genome assembly, reference transcriptome and linkage map for northern pike, and evaluate the suitability of this species to provide a representative pre-duplication genome for future studies of salmonid and teleost evolution. The northern pike genome sequence is composed of 94,267 contigs (N50 = 16,909 bp) contained in 5,688 scaffolds (N50 = 700,535 bp); the total scaffolded genome size is 878 million bases. Multiple lines of evidence suggest that over 96% of the protein-coding genome is present in the genome assembly. The reference transcriptome was constructed from 13 tissues and contains 38,696 transcripts, which are accompanied by normalized expression data in all tissues. Gene-prediction analysis produced a total of 19,601 northern pike-specific gene models. The first-generation linkage map identifies 25 linkage groups, in agreement with northern pike's diploid karyotype of 2N = 50, and facilitates the placement of 46% of assembled bases onto linkage groups. Analyses reveal a high degree of conserved synteny between northern pike and other model teleost genomes. While conservation of gene order is limited to smaller syntenic blocks, the wider conservation of genome organization implies the northern pike exhibits a suitable approximation of a non-duplicated Protacanthopterygiian genome. This dataset will facilitate future studies of esocid biology and empower ongoing examinations of the Atlantic salmon and rainbow trout genomes by facilitating their comparison with other major teleost groups.
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Affiliation(s)
- Eric B. Rondeau
- Department of Biology, Centre for Biomedical Research, University of Victoria, Victoria, British Columbia, Canada
| | - David R. Minkley
- Department of Biology, Centre for Biomedical Research, University of Victoria, Victoria, British Columbia, Canada
| | - Jong S. Leong
- Department of Biology, Centre for Biomedical Research, University of Victoria, Victoria, British Columbia, Canada
| | - Amber M. Messmer
- Department of Biology, Centre for Biomedical Research, University of Victoria, Victoria, British Columbia, Canada
| | - Johanna R. Jantzen
- Department of Biology, Centre for Biomedical Research, University of Victoria, Victoria, British Columbia, Canada
| | - Kristian R. von Schalburg
- Department of Biology, Centre for Biomedical Research, University of Victoria, Victoria, British Columbia, Canada
| | - Craig Lemon
- The Charles O. Hayford Hackettstown State Fish Hatchery, Hackettstown, New Jersey, United States of America
| | - Nathan H. Bird
- Department of Biology, Centre for Biomedical Research, University of Victoria, Victoria, British Columbia, Canada
| | - Ben F. Koop
- Department of Biology, Centre for Biomedical Research, University of Victoria, Victoria, British Columbia, Canada
- * E-mail:
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11
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Faircloth BC, Sorenson L, Santini F, Alfaro ME. A Phylogenomic Perspective on the Radiation of Ray-Finned Fishes Based upon Targeted Sequencing of Ultraconserved Elements (UCEs). PLoS One 2013; 8:e65923. [PMID: 23824177 PMCID: PMC3688804 DOI: 10.1371/journal.pone.0065923] [Citation(s) in RCA: 199] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 05/01/2013] [Indexed: 11/19/2022] Open
Abstract
Ray-finned fishes constitute the dominant radiation of vertebrates with over 32,000 species. Although molecular phylogenetics has begun to disentangle major evolutionary relationships within this vast section of the Tree of Life, there is no widely available approach for efficiently collecting phylogenomic data within fishes, leaving much of the enormous potential of massively parallel sequencing technologies for resolving major radiations in ray-finned fishes unrealized. Here, we provide a genomic perspective on longstanding questions regarding the diversification of major groups of ray-finned fishes through targeted enrichment of ultraconserved nuclear DNA elements (UCEs) and their flanking sequence. Our workflow efficiently and economically generates data sets that are orders of magnitude larger than those produced by traditional approaches and is well-suited to working with museum specimens. Analysis of the UCE data set recovers a well-supported phylogeny at both shallow and deep time-scales that supports a monophyletic relationship between Amia and Lepisosteus (Holostei) and reveals elopomorphs and then osteoglossomorphs to be the earliest diverging teleost lineages. Our approach additionally reveals that sequence capture of UCE regions and their flanking sequence offers enormous potential for resolving phylogenetic relationships within ray-finned fishes.
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Affiliation(s)
- Brant C. Faircloth
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, California, United States of America
| | - Laurie Sorenson
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, California, United States of America
| | - Francesco Santini
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, California, United States of America
| | - Michael E. Alfaro
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, California, United States of America
- * E-mail:
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12
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Broughton RE, Betancur-R R, Li C, Arratia G, Ortí G. Multi-locus phylogenetic analysis reveals the pattern and tempo of bony fish evolution. PLOS CURRENTS 2013; 5:ecurrents.tol.2ca8041495ffafd0c92756e75247483e. [PMID: 23788273 PMCID: PMC3682800 DOI: 10.1371/currents.tol.2ca8041495ffafd0c92756e75247483e] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Over half of all vertebrates are "fishes", which exhibit enormous diversity in morphology, physiology, behavior, reproductive biology, and ecology. Investigation of fundamental areas of vertebrate biology depend critically on a robust phylogeny of fishes, yet evolutionary relationships among the major actinopterygian and sarcopterygian lineages have not been conclusively resolved. Although a consensus phylogeny of teleosts has been emerging recently, it has been based on analyses of various subsets of actinopterygian taxa, but not on a full sample of all bony fishes. Here we conducted a comprehensive phylogenetic study on a broad taxonomic sample of 61 actinopterygian and sarcopterygian lineages (with a chondrichthyan outgroup) using a molecular data set of 21 independent loci. These data yielded a resolved phylogenetic hypothesis for extant Osteichthyes, including 1) reciprocally monophyletic Sarcopterygii and Actinopterygii, as currently understood, with polypteriforms as the first diverging lineage within Actinopterygii; 2) a monophyletic group containing gars and bowfin (= Holostei) as sister group to teleosts; and 3) the earliest diverging lineage among teleosts being Elopomorpha, rather than Osteoglossomorpha. Relaxed-clock dating analysis employing a set of 24 newly applied fossil calibrations reveals divergence times that are more consistent with paleontological estimates than previous studies. Establishing a new phylogenetic pattern with accurate divergence dates for bony fishes illustrates several areas where the fossil record is incomplete and provides critical new insights on diversification of this important vertebrate group.
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