The syntenic relationship of zebrafish and human genomes

the syntenic relationship of zebrafish and human genomes

1Fugu Genomics, United Kingdom Human Genome Mapping Project Resource Centre, . served synteny groups between the zebrafish and human ge-. In this report the zebrafish genetic linkage groups are assigned to SL: The syntenic relationship of the zebrafish and human genomes. Identifying and utilizing synteny blocks, which are genomic regions conserved pig, rat, rhesus, chicken and zebra fish, from the UCSC genome browser represent syntenic relationships between human chromosome 1 and.

Here, we present Synteny Portal, a versatile web-based application portal for constructing, visualizing and browsing synteny blocks.

The syntenic relationship of the zebrafish and human genomes. - Semantic Scholar

With Synteny Portal, users can easily i construct synteny blocks among multiple species by using prebuilt alignments in the UCSC genome browser database, ii visualize and download syntenic relationships as high-quality images, iii browse synteny blocks with genetic information and iv download the details of synteny blocks to be used as input for downstream synteny-based analyses, all in an intuitive and easy-to-use web-based interface. We believe that Synteny Portal will serve as a highly valuable tool that will enable biologists to easily perform comparative genomics studies by compensating limitations of existing tools.

Synteny Portal is freely available at http: These genome sequences are usually stored in public databases, such as the NCBI Reference Sequence database 4the Genome OnLine Database 5the UCSC genome browser database 6 and Ensembl Genomes 7 ; they have been used to uncover genomic similarities and differences between different species and the functional consequences of such similarities and differences.

Comparative genomics studies have contributed to a better understanding of the molecular-level mechanisms of species diversity and genome evolution 8— Synteny blocks, which are genomic regions that are conserved among multiple species, play a pivotal role in comparative genomics. Therefore, the construction of synteny blocks using such tools requires computer resources, and advanced bioinformatics skills to properly prepare input data and running command-line programs.

Zebrafish Syntenic Relationship to Human/Mouse Genomes Revealed by Radiation Hybrid Mapping

To alleviate these difficulties, more user-friendly tools for utilizing and visualizing synteny blocks have been developed. For example, GenomeMatcher 19Mauve 20MizBee 21 and SyMap 22 are stand-alone synteny browsers that support graphical user interface. GSV 25 and mGSV 26 are web-based synteny viewers that help to visualize user-provided synteny information. Cinteny 27 is a web server for identifying synteny blocks and analyzing genome rearrangements. Genomicus 31 is a web browser that displays the homologous genomic contexts of different species.

C-Sibelia 32 is a web server for comparing assemblies to a reference genome together with the annotation of variants in genes. GRIMM-Synteny 33 is a web server for analyzing genome rearrangements by using the list of genomic markers represented by numbers with the annotation of variants in genes. However, different tools still have different weaknesses, such as only supporting pairwise comparison, requiring the generation of synteny information by users, limited features for visualization and not supporting the saving or downloading of high-quality images Supplementary Data for tool comparison.

Here, we present Synteny Portal, a versatile web-based application portal that allows for construction, visualization and browsing of synteny blocks by compensating limitations of existing tools. With Synteny Portal, users can easily i construct synteny blocks among multiple species by using prebuilt alignments in the UCSC genome browser database 6ii visualize and download syntenic relationships as high-quality images, iii browse synteny blocks together with genetic information and iv download the details of synteny blocks that can be used as input for downstream synteny-based analyses, all in an intuitive and easy-to-use web interface.

MATERIALS AND METHODS Data preparation Data collection We collected genomic information on well-studied reference species, including human, mouse, cow, dog, horse, pig, rat, rhesus, chicken and zebra fish, from the UCSC genome browser database 6which includes genome assembly sequences, gene annotation, whole-genome pairwise alignments of the reference species in the chain and net format 34cytobands and assembly sizes of the reference species.

In total, whole-genome pairwise alignments for 67 different species, including different assembly versions and 33 assembly sequences for the ten reference species with different assembly versions are available on our web server.

The mapping information using different identifiers was obtained from the Uniprot website http: Synteny block construction and visualization Synteny blocks were built using the inferCars program package 16 with four different resolutions, and Kbp. Specifically, pairwise collinear genome segments PCGSs of two species i.

The syntenic relationship of the zebrafish and human genomes.

This merging process repeats until the PCGSs of all species are merged, and the final MCGSs, which are larger than the given resolution, are reported as synteny blocks.

If outgroup species are provided, which is optional, genomic regions of the outgroup species matched to each of the calculated synteny blocks are added.

Natural History of the Major Histocompatibility Complex.

the syntenic relationship of zebrafish and human genomes

Composite origin of major histocompatibility complex genes. Current Opinion in Genetics and Development 3: Birth of the major histocompatibility complex. Scandinavian J Immunol Characterization of whole genome radiation hybrid mapping resources for non-mammalian vertebrates. Nucleic Acids Research 26 Check list - fresh water fishes of India. The Tetra encyclopedia of freshwater tropical aquarium fishes.

the syntenic relationship of zebrafish and human genomes

Freshwater fishes of Bangladesh. Zoological Society of Bangladesh. Department of Zoology, University of Dhaka. A new method for reconstructing phylogenetic trees, Molecular Biology and Evolution 4 4: A genome-wide survey of major histocompatibility complex MHC genes and their paralogues in zebrafish.

Molecular Dialogues with the Microbiota: Insights from the Zebrafish Intestine

Implications for the Evolution of the Complement and Mhc Systems. Scandinavian J Immunol 56 4: Non-linkage of the major histocompatibility complex of class I and class II loci in bony fishes.

Resource ecology of the Himalayan waters. Curriculum Development Centre, Tribhuvan University. Conservation of major histocompatibility complex class III region synteny between zebrafish and human as determined by radiation hybrid mapping.