Insights Into Vertebrate Evolution From The Chicken Genome Sequence

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Evolution of Matrix and Bone γ-Carboxyglutamic Acid Proteins

provide key insights into vertebrate evolution. Specific goals of this work were: (i) to identify new MGP and BGP homologues using standard cloning methods or comparative genomics and data mining of available genomic and EST (expressed sequence tag) libraries, (ii) to provide insight into MGP and BGP com-

Elephant Shark Sequence Reveals Unique Insights into the

of the phylogenetic tree. Here, we show how the genome sequence from the oldest living phylogenetic group of jawed vertebrates, the cartilaginous fishes, can dramatically change our inferences of the state of the ancestral vertebrate genome. The protocadherin gene cluster is one of the most evolution arily dynamic loci in vertebrates.

Evolutionarily conserved non-protein-coding regions in the

Mar 27, 2020 the chicken genome has been conserved across more than 280 million years of vertebrate evolution. The vast majority of the conserved elements are in non-protein-coding regions, which display SNP densities and allele frequency distributions characteristic of genomic regions constrained by purifying selection. By

Multi-Platform Next-Generation Sequencing of the Domestic

second domestic avian genome to be sequenced, and this permits a genome-level comparison of the two most economically important poultry species. When added to the recently published zebra finch genome [7], analysis of the three avian genomes reveals new insights into the evolutionary relationships among avian species and their relationships to

Evolution of the vertebrate gene regulatory network

Evolution of the vertebrate gene regulatory network controlled by the transcriptional repressor REST. Research Article Rory Johnson1*, John Samuel2, Calista Keow Leng Ng3, Ralf Jauch3, Lawrence W. Stanton1 and Ian C. Wood2*. 1. Stem Cell and Developmental Biology Group, Genome Institute of Singapore, Singapore 138672. 2.

BMC Evolutionary Biology BioMed Central

new insights into breakage and fusion events during mammalian karyotype evolution Claus Kemkemer 1,4 , Matthias Kohn 1 , David N Cooper 2 , Lutz Froenicke 3 ,

9 chordate species 1. Reptile 1 2. Reptile 2: 3. 4. 5.

coverage of all major nodes of chordate evolution with at least two sequenced species. These include; 1. Reptile 1: Alligator mississipiensis (2.5 Gb genome), the American alligator, for high quality draft genomic sequence (approx. 6x) plus ESTs. 2. Reptile 2: Chrysemys picta (2.6 Gb genome), the painted turtle, for high quality

OPEN LETTER Sequencing three crocodilian genomes to

genome drafts from crocodilians would provide insights into ancestral reptilian and amniote genomes. These genome assemblies will also enable more detailed inferences on the evolution of three additional lineages of substantial interest to vertebrate biologists: dinosaurs, pterosaurs and birds. Crocodilians and birds are the only

RESEARCH ARTICLE ityofbirdsandtoinvestigatelinksbetweentheir

ments (TEs) may drive vertebrate genome size evolution (29 31). Consistent with the zebra finch and galliformes genomes (11 13, 32), almost all avian genomes contained lower levels of repeat elements (~4 to 10% of each genome) (table S4) than in other tetrapod vertebrates (for example, 34 to52%inmammals)(33).Thesoleoutlierwas

BMC Evolutionary Biology BioMed Central

atively recent WGD shared by a large vertebrate group, i.e., teleosts. Therefore, we can expect that teleost genomes contain many more WGD-derived duplicate genes and their 'traces' of evolution than tetrapod genomes. In addi-tion, in teleosts, whole-genome sequence data from mul-tiple species [16,20,27], reliable phylogenetic

A Linkage Map of the Zebra Finch Taeniopygia guttata Provides

addition to providing new insight into avian genome evolution. Unlike other vertebrate genome sequencing projects there was no linkage or physical map already available when the zebra finch genome sequencing commenced. Therefore, the zebra finch genome link-age map will aid genome assembly, acting as an inde-

BMC Evolutionary Biology BioMed Central

give important insights into the evolutionary history of a genomic region, both in terms of gene loss events as well as for the evolution of the regulatory sequences surround-ing it. The most prominent examples for this type of approach are the Hox gene clusters [24-28], a family of transcription factors that are not only arranged in uninter-

RESEARCH ARTICLE On the Origin and Evolution of Vertebrate

investigate the origin and evolution of vertebrate OR genes, I attempted to determine near-complete OR gene repertoires by searching whole-genome sequences of 14 nonmammalian chordates, including

University of Nebraska - Lincoln [email protected] of

vertebrate globins combined with a comparative analysis of genome sequences from three sauropsid taxa: anole liz-ard, zebra finch, and chicken. Comparative genomic analy-ses of the three sauropsid taxa can be expected to yield im-portant insights into globin gene family evolution because lepidosaur reptiles (represented by anole lizard) diverged

Elephant shark sequence reveals unique insights into the

evolution of vertebrate genomes. ancestral jawed vertebrate clustered protocadherins cartilaginous fish Callorhinchus milii gene conversion R econstructing the evolutionary history of vertebrate ge-nomes, and in particular the human genome, is a major goal of vertebrate comparative genomics. Efforts are underway to

Lineage-Specific Patterns of Functional Diversification in the

Until recently, investigations into this possibility have been hindered by the dearth of genomic sequence data from nonmammalian vertebrates. Here, we report new insights into globin gene family evolution that were provided by a phylogenetic analysis of vertebrate globins combined with a comparative genomic analysis of three key sauropsid taxa:

Elephant shark genome provides unique insights into

Gnathostomes subsequently diverged into two groups, the cartilaginous fishes and the bony vertebrates. Here we report the whole-genome analysis of a cartilaginous fish, the elephant shark (Callorhinchus milii). We find that the C.milii genome is the slowest evolving of all known vertebrates, including the living fossil coelacanth, and

Communication No. 30, THE OF 1989 B~ology, Inc. in U.S.A.

of copies (2) per haploid genome (similar to that of chicken). The reported quail protamine cDNA se- quence is the second avian protamine for which the amino acid sequence is available so far and provides new insights into vertebrate protamine function and evolution. Protamines are small highly basic proteins which act by

Shark genomes provide insights into elasmobranch evolution

Shark genomes provide insights into elasmobranch evolution and the origin of vertebrates Yuichiro Hara 1,2,14 , Kazuaki Yamaguchi 1,2,14 , Koh Onimaru 1,2 , Mitsutaka Kadota 1,2 ,


International Chicken Genome Sequencing Consortium; Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution ; Nature; 2004; 432:695-716. Lindblad-Toh K, et al.; Genome sequence, comparative analysis and haplotype structure of the domestic dog ; Nature; 2005; 438:803-819.

2008Ordoñezet al.Volume 9, Issue 5, Article R81Research Open

Genome Biology 2008, 9:R81 2008Ordoñezet al.Volume 9, Issue 5, Article R81Research Open Access Loss of genes implicated in gastric function during platypus evolution Gonzalo R Ordoñez*, LaDeana

The western painted turtle genome, a model for the evolution

an extraordinarily slow rate of sequence evolution in the painted turtle. The ability of the painted turtle to withstand complete anoxia and partial freezing appears to be associated with common vertebrate gene networks, and we identify candidate genes for future functional analyses. Tooth loss shares a common pattern of

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However, insights into the evolution of these expression differences have been limited by the lack of information from non-avian reptiles. We analyzed the segmentation clock of the first Lepidosaurian reptile sequenced, the green anole lizard, Anolis carolinensis, for comparison with avian and mammalian models. Using genomic sequence,

articles Sequence and comparative analysis of the chicken

synteny, provide additional insights into vertebrate chromosome architecture. Genome sequence comparison is a modern extension of the long-standing use of other species as models to illuminate aspects of human biology and medicine. Large-scale genome analyses also highlight the evolutionary dynamics of selective and mutational

Insights into Cyclostome Phylogenomics: Pre-2R or Post-2R?

Insights into Cyclostome Phylogenomics 961 (Fitch, 2000). In discussing early vertebrate evolution, the closest attention should be paid to this, because two rounds

The transposable element profile of the Anolis genome

insights into the repetitive landscape of the Anolis genome, and discuss how they may impact our knowledge of vertebrate genome evolution. The Transposable Element Profile of the Green Anole. The Anolis genome (and possibly squamate genomes in gen-eral, as we will discuss later) is characterized by an extraordi-

Early Evolution of Vertebrate Mybs: An Integrative Gene

were linked to the two rounds of whole-genome duplication early in vertebrate evolution. to gain insights into the origin and evolution of the frog, chicken

Sequencing of the Sea Lamprey (Petromyzon marinus) Genome

Sequencing of the Sea Lamprey (Petromyzon marinus) Genome Provides Insights into Vertebrate Evolution Notes/Citation Information Published inNature Genetics, v. 45, no. 4, p. 415-421. This work is licensed under a Creative Commons Attribution-NonCommercial-Share Alike 3.0 Unported License.

Visual and nonvisual opsin genes of sharks and other

genome-wide sequence information had long been limited to one species, the elephantfish Callorhinchus milii (Venkatesh et al., 2014), in the species-poor lineage Holocephali (Rizzari & Finucci, 2019). Later, in the other subclass Elasmobranchii, genome sequence infor - mation of two orectolobiform shark species (brownbanded bamboo

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Dec 07, 2007 insights into the evolution of vertebrate sex chromosomes. Polymorphisms between two inbred strains of medaka, Hd-rR and HNI As mentioned above, we identified 16.4 million SNP, 1.40 million insertions and 1.45 million deletions by aligning the HNI contigs with the Hd-rR genome (Fig. 3a). The genome-wide SNP rate between the two

Insights into the evolution of Darwin s finches from

Results: 13,291 protein-coding genes were predicted from a 991.0 MbG. magnirostris genome assembly. We then defined gene orthology relationships and constructed whole genome alignments between the G. magnirostris and other vertebrate genomes. We estimate that 15% of genomic sequence is functionally constrained between G. magnirostris and zebra

Draft Battle Plans for the ENCODE Multi-species Sequence

[8] Rat Genome Sequencing Project Consortium. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature, 428(6982):493 521, Apr 2004. [9] International Chicken Genome Sequencing Consortium. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution.

Step-by-Step Evolution of Vertebrate Blood Coagulation

SEARCHING WHOLE-GENOME SEQUENCE DATABASES The whole-genome sequence (WGS) databases of sea squirt, amphioxus (lancelet), lamprey, puffer fish, frog, green anole lizard, chicken, platypus, and opossum were examined in search of ~20 genes known to be associated with blood clotting in mammals (Table 1). The general strategy for identifying

The Genome of Austrofundulus Limnaeus Offers Insights into

This genome will be a valuable resource for comparative genomics to determine the genetic and evolutionary mechanisms that support the unique biology of annual killifishes. In a broader context, this genome will be a valuable tool for exploring genome-environment interactions and their impacts on vertebrate physiology and evolution.

The draft genome of the grass carp (Ctenopharyngodon idellus

idellus) provides insights into its evolution and vegetarian adaptation Yaping Wang 1 ,11 , Ying Lu 2 , Yong Zhang 3 ,4 11 , Zemin Ning 5 , Yan Li 2 , Qiang Zhao , Hengyun Lu ,

Expression of an Msx homeobox gene in ascidians: Insights

amino acid sequence with the corresponding regions of other Msx proteins (Fig. 1B) confirmed its identifica- tion as an ascidian Msx gene. Based on specific differences in the conserved homeodomain and adjacent regions, the Msx gene family is divided into msh-like, Msxl -like, and Msx2-like subclasses (Bell et al., 1993). The Mocu-

EHM Current Topics 2005 - National Human Genome Research

Insights from vertebrate genome sequence comparisons Takes the phylogeny into account Additional Chicken Fugu Tetraodon Zebrafish Genome-Wide Sequences

A proposal to sequence the genome of a garter snake

the only genome sequence available for a non-avian reptile. Thus, the garter snake at this time would be the first available snake genome sequence and as such would provide much needed comparative representation of non-avian reptilian genomes, and would also allow critical new isights for vertebrate comparative genomic studies.

Insights into the evolution of mammalian telomerase: Platypus

maintaining telomere length. Vertebrate telomerase has been studied in eutherian mammals, fish, and the chicken, but less attention has been paid to other vertebrates. The platypus occupies an important evolutionary position, providing unique insight into the evolution of mammalian genes. We report the cloning of a platypus TERT

SCIENCE & SCILFELI AB PRIZE Evolution of Vertebrate

and chicken were reported. The tremen-dous effort put into sequencing and assem-bling these genome sequences is a prereq-uisite to furthering our understanding of genetic information and its role in devel-opment, disease, and evolution. One of the first insights from comparative genomics was unexpected, namely, that the majority of