GenTree Edit

Citations: 0

z-index: 0

Basic information
Short name GenTree
Full name the time tree of genes along the evolution history
Description GenTree is a central portal to catalog lineage-specific genes in various species. As a first step, they present the age information for protein-coding genes in human together with the inferred origination mechanism.
Year founded 2019
Last update & version v1.0
Accessibility Accessible
Contact information

The contact information is provided to facilitate update of database information, and it is curated based on the contact details in the database or the related publications. To ensure effective contact with database constructors, we give priority to the contact details in the database.

University/Institution Institute of Zoology, Chinese Academy of Sciences
Address 1 Beichen West Road, Chaoyang District, Beijing 100101, P.R.China
City Beijing
Country/Region China
Contact name (PI/Team) Yong E. Zhang
Contact email (PI/Helpdesk)
Data information
Data object
Data type
Database category
Major organism
  • GenTree, an integrated resource for analyzing the evolution and function of primate-specific coding genes. [PMID: 30862647]
    Shao Y, Chen C, Shen H, He BZ, Yu D, Jiang S, Zhao S, Gao Z, Zhu Z, Chen X, Fu Y, Chen H, Gao G, Long M, Zhang YE.

    The origination of new genes contributes to phenotypic evolution in humans. Two major challenges in the study of new genes are the inference of gene ages and annotation of their protein-coding potential. To tackle these challenges, we created GenTree, an integrated online database that compiles age inferences from three major methods together with functional genomic data for new genes. Genome-wide comparison of the age inference methods revealed that the synteny-based pipeline (SBP) is most suited for recently duplicated genes, whereas the protein-family-based methods are useful for ancient genes. For SBP-dated primate-specific protein-coding genes (PSGs), we performed manual evaluation based on published PSG lists and showed that SBP generated a conservative data set of PSGs by masking less reliable syntenic regions. After assessing the coding potential based on evolutionary constraint and peptide evidence from proteomic data, we curated a list of 254 PSGs with different levels of protein evidence. This list also includes 41 candidate misannotated pseudogenes that encode primate-specific short proteins. Coexpression analysis showed that PSGs are preferentially recruited into organs with rapidly evolving pathways such as spermatogenesis, immune response, mother-fetus interaction, and brain development. For brain development, primate-specific KRAB zinc-finger proteins (KZNFs) are specifically up-regulated in the mid-fetal stage, which may have contributed to the evolution of this critical stage. Altogether, hundreds of PSGs are either recruited to processes under strong selection pressure or to processes supporting an evolving novel organ.

    Genome Res 2019:()

    0 Citations (from Europe PMC, 2019-06-08)


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The box plots depict Z-index distribution for all databases in Database Commons and for specific database category/categories. The red line indicates log2(Z-index) of GenTree.

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  • Created on: 2019-03-21
    • ***ina@*** [2019-03-21]
    • ***d@*** [2019-03-21]

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