当前位置： SCI文献检索 > Genome Biology and Evolution期刊下所有文献 > Genome Assembly of the Common Pheasant Phasianus colchicus: A Model for Speciation and Ecological Genomics.

Genome Assembly of the Common Pheasant Phasianus colchicus: A Model for Speciation and Ecological Genomics.

Abstract：

:The common pheasant (Phasianus colchicus) in the order Galliformes and the family Phasianidae, has 30 subspecies distributed across its native range in the Palearctic realm and has been introduced to Europe, North America, and Australia. It is an important game bird often subjected to wildlife management as well as a model species to study speciation, biogeography, and local adaptation. However, the genomic resources for the common pheasant are generally lacking. We sequenced a male individual of the subspecies torquatus of the common pheasant with the Illumina HiSeq platform. We obtained 94.88 Gb of usable sequences by filtering out low-quality reads of the raw data generated. This resulted in a 1.02 Gb final assembly, which equals the estimated genome size. BUSCO analysis using chicken as a model showed that 93.3% of genes were complete. The contig N50 and scaffold N50 sizes were 178 kb and 10.2 Mb, respectively. All these indicate that we obtained a high-quality genome assembly. We annotated 16,485 protein-coding genes and 123.3 Mb (12.05% of the genome) of repetitive sequences by ab initio and homology-based prediction. Furthermore, we applied a RAD-sequencing approach for another 45 individuals of seven representative subspecies in China and identified 4,376,351 novel single nucleotide polymorphism (SNPs) markers. Using this unprecedented data set, we uncovered the geographic population structure and genetic introgression among common pheasants in China. Our results provide the first high-quality reference genome for the common pheasant and a valuable genome-wide SNP database for studying population genomics and demographic history.

journal_name

Genome Biol Evol

journal_title

Genome biology and evolution

authors

Liu Y,Liu S,Zhang N,Chen,Que P,Liu N,Höglund J,Zhang Z,Wang B

doi

10.1093/gbe/evz249

subject

Has Abstract

pub_date

2019-12-01 00:00:00

pages

3326-3331

issue

12

issn

1759-6653

pii

5622760

journal_volume

11

pub_type

杂志文章

相关文献

Genome Biology and Evolution文献大全
  • Inference of Evolutionary Forces Acting on Human Biological Pathways.

    abstract：:Because natural selection is likely to act on multiple genes underlying a given phenotypic trait, we study here the potential effect of ongoing and past selection on the genetic diversity of human biological pathways. We first show that genes included in gene sets are generally under stronger selective constraints tha...

    journal_title：Genome biology and evolution

    pub_type： 杂志文章

    doi：10.1093/gbe/evv083

    authors： Daub JT,Dupanloup I,Robinson-Rechavi M,Excoffier L

    更新日期：2015-05-13 00:00:00

  • Regulation of Large Number of Weak Targets-New Insights from Twin-microRNAs.

    abstract：:Each animal microRNA (miRNA) targets many genes for repression. Down-regulation of most of these targets is weak and has no detectable individual phenotypic effect. Whether this extensive weak repression is biologically relevant is a central issue in the debate on miRNA functionality. In the "small (target) pool" view...

    journal_title：Genome biology and evolution

    pub_type： 杂志文章

    doi：10.1093/gbe/evy079

    authors： Zhao Y,Lin P,Liufu Z,Yang H,Lyu Y,Shen X,Wu CI,Tang T

    更新日期：2018-04-01 00:00:00

  • Nanopore Sequencing Significantly Improves Genome Assembly of the Protozoan Parasite Trypanosoma cruzi.

    abstract：:Chagas disease was described by Carlos Chagas, who first identified the parasite Trypanosoma cruzi from a 2-year-old girl called Berenice. Many T. cruzi sequencing projects based on short reads have demonstrated that genome assembly and downstream comparative analyses are extremely challenging in this species, given t...

    journal_title：Genome biology and evolution

    pub_type： 杂志文章

    doi：10.1093/gbe/evz129

    authors： Díaz-Viraqué F,Pita S,Greif G,de Souza RCM,Iraola G,Robello C

    更新日期：2019-07-01 00:00:00

  • Draft Genome Sequences of Two Closely Related Aflatoxigenic Aspergillus Species Obtained from the Ivory Coast.

    abstract：:Aspergillus ochraceoroseus and Aspergillus rambellii were isolated from soil detritus in Taï National Park, Ivory Coast, Africa. The Type strain for each species happens to be the only representative ever sampled. Both species secrete copious amounts of aflatoxin B1 and sterigmatocystin, because each of their genomes ...

    journal_title：Genome biology and evolution

    pub_type： 杂志文章

    doi：10.1093/gbe/evv246

    authors： Moore GG,Mack BM,Beltz SB

    更新日期：2015-12-03 00:00:00

  • A trnI_CAU triplication event in the complete chloroplast genome of Paris verticillata M.Bieb. (Melanthiaceae, Liliales).

    abstract：:The chloroplast is an essential plant organelle responsible for photosynthesis. Gene duplication, relocation, and loss in the chloroplast genome (cpDNA) are useful for exploring the evolution and phylogeny of plant species. In this study, the complete chloroplast genome of Paris verticillata was sequenced using the 45...

    journal_title：Genome biology and evolution

    pub_type： 杂志文章

    doi：10.1093/gbe/evu138

    authors： Do HD,Kim JS,Kim JH

    更新日期：2014-06-19 00:00:00

  • Life in an arsenic-containing gold mine: genome and physiology of the autotrophic arsenite-oxidizing bacterium rhizobium sp. NT-26.

    abstract：:Arsenic is widespread in the environment and its presence is a result of natural or anthropogenic activities. Microbes have developed different mechanisms to deal with toxic compounds such as arsenic and this is to resist or metabolize the compound. Here, we present the first reference set of genomic, transcriptomic a...

    journal_title：Genome biology and evolution

    pub_type： 杂志文章

    doi：10.1093/gbe/evt061

    authors： Andres J,Arsène-Ploetze F,Barbe V,Brochier-Armanet C,Cleiss-Arnold J,Coppée JY,Dillies MA,Geist L,Joublin A,Koechler S,Lassalle F,Marchal M,Médigue C,Muller D,Nesme X,Plewniak F,Proux C,Ramírez-Bahena MH,Schenowitz C

    更新日期：2013-01-01 00:00:00

  • Evolution of a bitter taste receptor gene cluster in a New World sparrow.

    abstract：:Bitter taste perception likely evolved as a protective mechanism against the ingestion of harmful compounds in food. The evolution of the taste receptor type 2 (TAS2R) gene family, which encodes the chemoreceptors that are directly responsible for the detection of bitter compounds, has therefore been of considerable i...

    journal_title：Genome biology and evolution

    pub_type： 杂志文章

    doi：10.1093/gbe/evq027

    authors： Davis JK,Lowman JJ,Thomas PJ,ten Hallers BF,Koriabine M,Huynh LY,Maney DL,de Jong PJ,Martin CL,NISC Comparative Sequencing Program.,Thomas JW

    更新日期：2010-07-12 00:00:00

  • The repABC Plasmids with Quorum-Regulated Transfer Systems in Members of the Rhizobiales Divide into Two Structurally and Separately Evolving Groups.

    abstract：:The large repABC plasmids of the order Rhizobiales with Class I quorum-regulated conjugative transfer systems often define the nature of the bacterium that harbors them. These otherwise diverse plasmids contain a core of highly conserved genes for replication and conjugation raising the question of their evolutionary ...

    journal_title：Genome biology and evolution

    pub_type： 杂志文章

    doi：10.1093/gbe/evv227

    authors： Wetzel ME,Olsen GJ,Chakravartty V,Farrand SK

    更新日期：2015-11-19 00:00:00

  • The Role of microRNAs in the Repeated Parallel Diversification of Lineages of Midas Cichlid Fish from Nicaragua.

    abstract：:Cichlid fishes are an ideal model system for studying biological diversification because they provide textbook examples of rapid speciation. To date, there has been little focus on the role of gene regulation during cichlid speciation. However, in recent years, gene regulation has been recognized as a powerful force l...

    journal_title：Genome biology and evolution

    pub_type： 杂志文章

    doi：10.1093/gbe/evw097

    authors： Franchini P,Xiong P,Fruciano C,Meyer A

    更新日期：2016-06-03 00:00:00

  • Gene duplication and environmental adaptation within yeast populations.

    abstract：:Population-level differences in the number of copies of genes resulting from gene duplication and loss have recently been recognized as an important source of variation in eukaryotes. However, except for a small number of cases, the phenotypic effects of this variation are unknown. Data from the Saccharomyces Genome R...

    journal_title：Genome biology and evolution

    pub_type： 杂志文章

    doi：10.1093/gbe/evq043

    authors： Ames RM,Rash BM,Hentges KE,Robertson DL,Delneri D,Lovell SC

    更新日期：2010-01-01 00:00:00

  • Phylogenomic data support a seventh order of Methylotrophic methanogens and provide insights into the evolution of Methanogenesis.

    abstract：:Increasing evidence from sequence data from various environments, including the human gut, suggests the existence of a previously unknown putative seventh order of methanogens. The first genomic data from members of this lineage, Methanomassiliicoccus luminyensis and "Candidatus Methanomethylophilus alvus," provide in...

    journal_title：Genome biology and evolution

    pub_type： 信件

    doi：10.1093/gbe/evt128

    authors： Borrel G,O'Toole PW,Harris HM,Peyret P,Brugère JF,Gribaldo S

    更新日期：2013-01-01 00:00:00

  • Lineage-Specific Expression Divergence in Grasses Is Associated with Male Reproduction, Host-Pathogen Defense, and Domestication.

    abstract：:Poaceae (grasses) is an agriculturally important and widely distributed family of plants with extraordinary phenotypic diversity, much of which was generated under recent lineage-specific evolution. Yet, little is known about the genes and functional modules involved in the lineage-specific divergence of grasses. Here...

    journal_title：Genome biology and evolution

    pub_type： 信件

    doi：10.1093/gbe/evy245

    authors： Assis R

    更新日期：2019-01-01 00:00:00

  • Predicting the Stability of Homologous Gene Duplications in a Plant RNA Virus.

    abstract：:One of the striking features of many eukaryotes is the apparent amount of redundancy in coding and non-coding elements of their genomes. Despite the possible evolutionary advantages, there are fewer examples of redundant sequences in viral genomes, particularly those with RNA genomes. The factors constraining the main...

    journal_title：Genome biology and evolution

    pub_type： 杂志文章

    doi：10.1093/gbe/evw219

    authors： Willemsen A,Zwart MP,Higueras P,Sardanyés J,Elena SF

    更新日期：2016-10-12 00:00:00

  • Contrasting Patterns of Genomic Diversity Reveal Accelerated Genetic Drift but Reduced Directional Selection on X-Chromosome in Wild and Domestic Sheep Species.

    abstract：:Analyses of genomic diversity along the X chromosome and of its correlation with autosomal diversity can facilitate understanding of evolutionary forces in shaping sex-linked genomic architecture. Strong selective sweeps and accelerated genetic drift on the X-chromosome have been inferred in primates and other model s...

    journal_title：Genome biology and evolution

    pub_type： 杂志文章

    doi：10.1093/gbe/evy085

    authors： Chen ZH,Zhang M,Lv FH,Ren X,Li WR,Liu MJ,Nam K,Bruford MW,Li MH

    更新日期：2018-04-01 00:00:00

  • The Chemosensory Receptor Repertoire of a True Shark Is Dominated by a Single Olfactory Receptor Family.

    abstract：:Throughout the animal kingdom chemical senses are one of the primary means by which organisms make sense of their environment. To achieve perception of complex chemosensory stimuli large repertoires of olfactory and gustatory receptors are employed in bony vertebrates, which are characterized by high evolutionary dyna...

    journal_title：Genome biology and evolution

    pub_type： 信件

    doi：10.1093/gbe/evz002

    authors： Sharma K,Syed AS,Ferrando S,Mazan S,Korsching SI

    更新日期：2019-02-01 00:00:00

  • Transcriptome Differences between Alternative Sex Determining Genotypes in the House Fly, Musca domestica.

    abstract：:Sex determination evolves rapidly, often because of turnover of the genes at the top of the pathway. The house fly, Musca domestica, has a multifactorial sex determination system, allowing us to identify the selective forces responsible for the evolutionary turnover of sex determination in action. There is a male dete...

    journal_title：Genome biology and evolution

    pub_type： 杂志文章

    doi：10.1093/gbe/evv128

    authors： Meisel RP,Scott JG,Clark AG

    更新日期：2015-07-02 00:00:00

  • Long-term asymmetrical acceleration of protein evolution after gene duplication.

    abstract：:Rapid divergence of gene copies after duplication is thought to determine the fate of the copies and evolution of novel protein functions. However, data on how long the gene copies continue to experience an elevated rate of evolution remain scarce. Standard theory of gene duplications based on some level of genetic re...

    journal_title：Genome biology and evolution

    pub_type： 杂志文章

    doi：10.1093/gbe/evu159

    authors： Pich I Roselló O,Kondrashov FA

    更新日期：2014-07-28 00:00:00

  • The Huperzia selago Shoot Tip Transcriptome Sheds New Light on the Evolution of Leaves.

    abstract：:Lycopodiophyta-consisting of three orders, Lycopodiales, Isoetales and Selaginellales, with different types of shoot apical meristems (SAMs)-form the earliest branch among the extant vascular plants. They represent a sister group to all other vascular plants, from which they differ in that their leaves are microphylls...

    journal_title：Genome biology and evolution

    pub_type： 杂志文章

    doi：10.1093/gbe/evx169

    authors： Evkaikina AI,Berke L,Romanova MA,Proux-Wéra E,Ivanova AN,Rydin C,Pawlowski K,Voitsekhovskaja OV

    更新日期：2017-09-01 00:00:00

  • Day and Night: Metabolic Profiles and Evolutionary Relationships of Six Axenic Non-Marine Cyanobacteria.

    abstract：:Cyanobacteria are dominant primary producers of various ecosystems and they colonize marine as well as freshwater and terrestrial habitats. On the basis of their oxygenic photosynthesis they are known to synthesize a high number of secondary metabolites, which makes them promising for biotechnological applications. St...

    journal_title：Genome biology and evolution

    pub_type： 杂志文章

    doi：10.1093/gbe/evy275

    authors： Will SE,Henke P,Boedeker C,Huang S,Brinkmann H,Rohde M,Jarek M,Friedl T,Seufert S,Schumacher M,Overmann J,Neumann-Schaal M,Petersen J

    更新日期：2019-01-01 00:00:00

  • Sex-Biased Gene Expression and Dosage Compensation on the Artemia franciscana Z-Chromosome.

    abstract：:Males and females of Artemia franciscana, a crustacean commonly used in the aquarium trade, are highly dimorphic. Sex is determined by a pair of ZW chromosomes, but the nature and extent of differentiation of these chromosomes is unknown. Here, we characterize the Z chromosome by detecting genomic regions that show lo...

    journal_title：Genome biology and evolution

    pub_type： 杂志文章

    doi：10.1093/gbe/evz053

    authors： Huylmans AK,Toups MA,Macon A,Gammerdinger WJ,Vicoso B

    更新日期：2019-04-01 00:00:00

  • Evolution of Sphingomonad Gene Clusters Related to Pesticide Catabolism Revealed by Genome Sequence and Mobilomics of Sphingobium herbicidovorans MH.

    abstract：:Bacterial degraders of chlorophenoxy herbicides have been isolated from various ecosystems, including pristine environments. Among these degraders, the sphingomonads constitute a prominent group that displays versatile xenobiotic-degradation capabilities. Four separate sequencing strategies were required to provide th...

    journal_title：Genome biology and evolution

    pub_type： 杂志文章

    doi：10.1093/gbe/evx185

    authors： Nielsen TK,Rasmussen M,Demanèche S,Cecillon S,Vogel TM,Hansen LH

    更新日期：2017-09-01 00:00:00

  • Transcriptional Mutagenesis Prevents Ribosomal DNA Deterioration: The Role of Duplications and Deletions.

    abstract：:Clashes between transcription and replication complexes can cause point mutations and chromosome rearrangements on heavily transcribed genes. In eukaryotic ribosomal RNA genes, the system that prevents transcription-replication conflicts also causes frequent copy number variation. Such fast mutational dynamics do not ...

    journal_title：Genome biology and evolution

    pub_type： 杂志文章

    doi：10.1093/gbe/evz235

    authors： Colizzi ES,Hogeweg P

    更新日期：2019-11-01 00:00:00

  • Fine-Scale Characterization of Genomic Structural Variation in the Human Genome Reveals Adaptive and Biomedically Relevant Hotspots.

    abstract：:Genomic structural variants (SVs) are distributed nonrandomly across the human genome. The "hotspots" of SVs have been implicated in evolutionary innovations, as well as medical conditions. However, the evolutionary and biomedical features of these hotspots remain incompletely understood. Here, we analyzed data from 2...

    journal_title：Genome biology and evolution

    pub_type： 杂志文章

    doi：10.1093/gbe/evz058

    authors： Lin YL,Gokcumen O

    更新日期：2019-04-01 00:00:00

  • On the Function of Trans-Splicing: No Evidence for Widespread Proteome Diversification in Trypanosomes.

    abstract：:A long-standing mystery of genomic/transcriptomic structure involves spliced leader trans-splicing (SLTS), in which short RNA "tags" transcribed from a distinct genomic locus is added near the 5' end of RNA transcripts by the spliceosome. SLTS has been observed in diverse eukaryotes in a phylogenetic pattern implying ...

    journal_title：Genome biology and evolution

    pub_type： 杂志文章

    doi：10.1093/gbe/evz217

    authors： Soulette CM,Oliverio O,Roy SW

    更新日期：2019-10-01 00:00:00

  • Gene Duplication and Gain in the Trematode Atriophallophorus Winterbourni Contributes to Adaptation to Parasitism.

    abstract：:Gene duplications and novel genes have been shown to play a major role in helminth adaptation to a parasitic lifestyle because they provide the novelty necessary for adaptation to a changing environment, such as living in multiple hosts. Here we present the de novo sequenced and annotated genome of the parasitic trema...

    journal_title：Genome biology and evolution

    pub_type： 杂志文章

    doi：10.1093/gbe/evab010

    authors： Zajac N,Zoller S,Seppälä K,Moi D,Dessimoz C,Jokela J,Hartikainen H,Glover N

    更新日期：2021-01-23 00:00:00

  • Male Mutation Bias Is the Main Force Shaping Chromosomal Substitution Rates in Monotreme Mammals.

    abstract：:In many species, spermatogenesis involves more cell divisions than oogenesis, and the male germline, therefore, accumulates more DNA replication errors, a phenomenon known as male mutation bias. The extent of male mutation bias (α) is estimated by comparing substitution rates of the X, Y, and autosomal chromosomes, as...

    journal_title：Genome biology and evolution

    pub_type： 杂志文章

    doi：10.1093/gbe/evx155

    authors： Link V,Aguilar-Gómez D,Ramírez-Suástegui C,Hurst LD,Cortez D

    更新日期：2017-09-01 00:00:00

  • Toward genome-wide identification of Bateson-Dobzhansky-Muller incompatibilities in yeast: a simulation study.

    abstract：:The Bateson-Dobzhansky-Muller (BDM) model of reproductive isolation by genetic incompatibility is a widely accepted model of speciation. Because of the exceptionally rich biological information about the budding yeast Saccharomyces cerevisiae, the identification of BDM incompatibilities in yeast would greatly deepen o...

    journal_title：Genome biology and evolution

    pub_type： 杂志文章

    doi：10.1093/gbe/evt091

    authors： Li C,Wang Z,Zhang J

    更新日期：2013-01-01 00:00:00

  • A Lineage-Specific Paralog of Oma1 Evolved into a Gene Family from Which a Suppressor of Male Sterility-Inducing Mitochondria Emerged in Plants.

    abstract：:Cytoplasmic male sterility (MS) in plants is caused by MS-inducing mitochondria, which have emerged frequently during plant evolution. Nuclear restorer-of-fertility (Rf)genes can suppress their cognate MS-inducing mitochondria. Whereas many Rfs encode a class of RNA-binding protein, the sugar beet (Caryophyllales) Rf ...

    journal_title：Genome biology and evolution

    pub_type： 杂志文章

    doi：10.1093/gbe/evaa186

    authors： Arakawa T,Kagami H,Katsuyama T,Kitazaki K,Kubo T

    更新日期：2020-12-06 00:00:00

  • OASes and STING: adaptive evolution in concert.

    abstract：:OAS (2'-5'-oligoadenylate synthases) proteins and cyclic GMP-AMP synthase (cGAS, gene symbol: MB21D1) patrol the cytoplasm for the presence of foreign nucleic acids. Upon binding to double-stranded RNA or double-stranded DNA, OAS proteins and cGAS produce nucleotide second messengers to activate RNase L and STING (sti...

    journal_title：Genome biology and evolution

    pub_type： 杂志文章

    doi：10.1093/gbe/evv046

    authors： Mozzi A,Pontremoli C,Forni D,Clerici M,Pozzoli U,Bresolin N,Cagliani R,Sironi M

    更新日期：2015-03-09 00:00:00

  • Getting a full dose? Reconsidering sex chromosome dosage compensation in the silkworm, Bombyx mori.

    abstract：:Dosage compensation--equalizing gene expression levels in response to differences in gene dose or copy number--is classically considered to play a critical role in the evolution of heteromorphic sex chromosomes. As the X and Y diverge through degradation and gene loss on the Y (or the W in female-heterogametic ZW taxa...

    journal_title：Genome biology and evolution

    pub_type： 杂志文章

    doi：10.1093/gbe/evr036

    authors： Walters JR,Hardcastle TJ

    更新日期：2011-01-01 00:00:00