a catalog of biological databases
|Description:||The database is built to address some fundamental questions on the evolution of plastid genomes, especially on the gene order and variation events on the gene level. The first version of this database includes 470 plastid genomes.|
|University/Institution:||Beijing Institute of Genomics, Chinese Academy of Sciences|
|Address:||Beijing 100101, P. R. China|
|Contact name (PI/Team):||Dapeng Wang|
|Contact email (PI/Helpdesk):||email@example.com|
Plastid-LCGbase: a collection of evolutionarily conserved plastid-associated gene pairs. [PMID: 25378306]
Plastids carry their own genetic material that encodes a variable set of genes that are limited in number but functionally important. Aside from orthology, the lineage-specific order and orientation of these genes are also relevant. Here, we develop a database, Plastid-LCGbase (http://lcgbase.big.ac.cn/plastid-LCGbase/), which focuses on organizational variability of plastid genes and genomes from diverse taxonomic groups. The current Plastid-LCGbase contains information from 470 plastid genomes and exhibits several unique features. First, through a genome-overview page generated from OrganellarGenomeDRAW, it displays general arrangement of all plastid genes (circular or linear). Second, it shows patterns and modes of all paired plastid genes and their physical distances across user-defined lineages, which are facilitated by a step-wise stratification of taxonomic groups. Third, it divides the paired genes into three categories (co-directionally-paired genes or CDPGs, convergently-paired genes or CPGs and divergently-paired genes or DPGs) and three patterns (separation, overlap and inclusion) and provides basic statistics for each species. Fourth, the gene pairing scheme is expandable, where neighboring genes can also be included in species-/lineage-specific comparisons. We hope that Plastid-LCGbase facilitates gene variation (insertion-deletion, translocation and rearrangement) and transcription-level studies of plastid genomes. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.