Automated identification of conserved synteny after whole-genome duplication

Abstract

An important objective for inferring the evolutionary history of gene families is the determination of orthologies and paralogies. Lineage-specific paralog loss following whole-genome duplication events can cause anciently related homologs to appear in some assays as orthologs. Conserved synteny—the tendency of neighboring genes to retain their relative positions and orders on chromosomes over evolutionary time—can help resolve such errors. Several previous studies examined genome-wide syntenic conservation to infer the contents of ancestral chromosomes and provided insights into the architecture of ancestral genomes, but did not provide methods or tools applicable to the study of the evolution of individual gene families. We developed an automated system to identify conserved syntenic regions in a primary genome using as outgroup a genome that diverged from the investigated lineage before a whole-genome duplication event. The product of this automated analysis, the Synteny Database, allows a user to examine fully or partially assembled genomes. The Synteny Database is optimized for the investigation of individual gene families in multiple lineages and can detect chromosomal inversions and translocations as well as ohnologs (paralogs derived by whole-genome duplication) gone missing. To demonstrate the utility of the system, we present a case study of gene family evolution, investigating the ARNTL gene family in the genomes of Ciona intestinalis, amphioxus, zebrafish, and human.

Subdivisions of the adult zebrafish pallium based on molecular marker analysis

“…We analyzed if there are two co-orthologous genes compared to the tetrapod gene using Ensembl73 gene trees ( http://www.ensembl.org) and synteny analysis with the Synteny Database ( http://syntenydb.uoregon.edu; 48 ). This is clearly the case, e.g., for human EOMES with two TGD co-orthologs in zebrafish, eomesa and eomesb ( Figure S1A,B).…”

A RAD-Tag Genetic Map for the Platyfish (Xiphophorus maculatus) Reveals Mechanisms of Karyotype Evolution Among Teleost Fish

“…The sequence for each of the initial set of 18,119 polymorphic RAD-tags was mapped onto sequenced genome contigs and annotated by the Synteny Database (Catchen et al 2009). In addition, the set of sequences surrounding microsatellites from a previous genetic map (Walter et al 2004) were identified in genomic contigs and each contig that contained both a mapped microsatellite and a mapped RAD-tag was associated to the RAD-tag map, thus providing anchor markers for numbering platyfish chromosomes in accord with previous assignments.…”

“…Orthologs of each transcriptome contig were called by algorithms of the Synteny Database as described (Catchen et al 2009). …”

Basidiomycetes Telomeres – A Bioinformatics Approach

“…This may involve relationships between genes within the syntenic regions involved, such as combinations of alleles that are advantegeous when inherited together, or shared regulatory mechanisms. The problem of identifying syntenic regions in different genomes has been addressed using different strategies including the use of FASTA (Lipman & Pearson, 1985) and Blast (Altschul et al, 1997), and different bioinformatics approaches (Catchen et al, 2009;Grabherr et al, 2010;Tang et al, 2011). We have used a method based on the identification of synteny regions at the chromosome ends by means of a BLASTP analysis of genes in the two genomes using a cut-off threshold of e-20.…”