Background

Human genome is littered with paralogy blocks consisting large syntenic regions with duplicated/triplicated/quadruplicated distribution in multiple distinct locations. For instance the popular paralogy blocks such as the HOX-cluster bearing homo sapiens autosomes (Hsa) 2/7/12/17, human FGFR-bearing paralogon (Hsa 4/5/8/10), MHC paralogon (Hsa 1/6/9/19) and  Hsa 1/2/8/20 are investigated intensively over the past couple of decades to understand mechanisms that have shaped the current architecture of human genome. Some argued that such triplicated/quadruplicated human paralogy blocks are evidence of ancient polyploidy events in vertebrate history, whereas others have taken them as a consequence of small scale segmental/independant gene duplications and translocation events. 


The current database focuses upon the history of subset of paralogy blocks residing on Hsa 2/7/12/17, Hsa 4/5/8/10, Hsa 1/2/8/20 and Hsa 1/6/9/19. Phylogenomic analysis of our data will provide the user to hunt knowledge about history of evolution of multigene families residing these paralogy blocks. Following features of database make it an interactive and comprehensive platform for phylogenomic understanding of human paralogy blocks.



  1. The current database incorporates thorough and robust phylogenetic history of human multigene families residing on each of the relevant paralogy blocks.

  2. Based on these phylogenetic histories, the database provides relative timings of duplications for each of these families by employing topology comparison approach.

  3. Furthermore, the database employs topology comparison approach that combines the map positioning information with phylogenetic history of relevant gene families to reveal mechanisms of ancient genome shaping events. 

  4. Above mentioned all information is summed up in summary tables provided for each paralogon. The location and function tables enclosed in "Browse" tab provide the bird's eye view of human multigene families and their corresponding members.

  5. The vertebrate and invertebrate sequences in Fasta format can be obtained and downloaded by searching respective family using "Search via Family". The "Search via sequence" allows rapid searching of similar sequences present in database.

  6. Information stored in this database is also linked to its sources in Ensembl, NCBI and UniProt. Database also navigates users to other widely used databases and tools for genome analysis like (GeneCards, HGNC, MEGA, UCSC, JGI and SOURCE).


Evolutionary Biologists, Geneticists, Biochemists, Biotechnologists, Bioinformaticians and researchers from versatile biological communities can utilize distinct features of this database to obtain evolutionary histories of human genes of their interest/human multigene families/human paralogy blocks in an interactive graphical manner. 


Useful references:


Abbasi, A. A., (2008) Are we degenerate tetraploids? More genomes, new facts. Biol Direct, 3, 50.

Abbasi, A. A., (2010a) Piecemeal or big bangs: correlating the vertebrate evolution with proposed models of gene expansion events. Nat Rev Genet, 11, 166.

Abbasi, A. A., (2010b) Unraveling ancient segmental duplication events in human genome by phylogenetic analysis of multigene families residing on HOX-cluster paralogons. Mol Phylogenet Evol, 57, 836-48.

Abbasi, A. A., Grzeschik, K. H., (2007) An insight into the phylogenetic history of HOX linked gene families in vertebrates. BMC Evol Biol, 7, 239.

Abbasi, A. A., Hanif, H., (2012) Phylogenetic history of paralogous gene quartets on human chromosomes 1, 2, 8 and 20 provides no evidence in favor of the vertebrate octoploidy hypothesis. Mol Phylogenet Evol, 63, 922-7.

Asrar, Z., Haq, F., & Abbasi, A. A. (2013) Fourfold paralogy regions on human HOX-bearing chromosomes: role of ancient segmental duplications in the evolution of vertebrate genome. Molecular phylogenetics and evolution, 66(3), 737-747.

Furlong, R. F., Holland, P. W., (2002) Were vertebrates octoploid? Philos Trans R Soc Lond B Biol Sci, 357, 531-44.

Gibson, T. J., Spring, J., (2000) Evidence in favour of ancient octaploidy in the vertebrate genome. Biochem Soc Trans, 28, 259-64.

Hokamp, K., McLysaght, A., Wolfe, K. H., (2003) The 2R hypothesis and the human genome sequence. J Struct Funct Genomics, 3, 95-110.

Hughes, A. L., (1998) Phylogenetic tests of the hypothesis of block duplication of homologous genes on human chromosomes 6, 9, and 1. Mol Biol Evol, 15, 854-70.

Hughes, A. L., da Silva, J., Friedman, R., (2001) Ancient genome duplications did not structure the human Hox-bearing chromosomes. Genome Res, 11, 771-80.