Coding exon-structure aware realigner (CESAR) utilizes genome alignments for accurate comparative gene annotation

Abstract

Identifying coding genes is an essential step in genome annotation. Here, we utilize existing whole genome alignments to detect conserved coding exons and then map gene annotations from one genome to many aligned genomes. We show that genome alignments contain thousands of spurious frameshifts and splice site mutations in exons that are truly conserved. To overcome these limitations, we have developed CESAR (Coding Exon-Structure Aware Realigner) that realigns coding exons, while considering reading frame and splice sites of each exon. CESAR effectively avoids spurious frameshifts in conserved genes and detects 91% of shifted splice sites. This results in the identification of thousands of additional conserved exons and 99% of the exons that lack inactivating mutations match real exons. Finally, to demonstrate the potential of using CESAR for comparative gene annotation, we applied it to 188 788 exons of 19 865 human genes to annotate human genes in 99 other vertebrates. These comparative gene annotations are available as a resource (http://bds.mpi-cbg.de/hillerlab/CESAR/). CESAR (https://github.com/hillerlab/CESAR/) can readily be applied to other alignments to accurately annotate coding genes in many other vertebrate and invertebrate genomes.

Convergent vomeronasal system reduction in mammals coincides with convergent losses of calcium signalling and odorant‐degrading genes

“…In the red deer ( Cervus elaphus ), which possesses a functional VNS, we found a confirmed frameshifting mutation in the last exon (Table ); however, this mutation is far downstream of the last transmembrane domain therefore just leads to a different C‐terminal protein sequence (Figure ). Such C‐terminal alterations are a common evolutionary change in conserved genes (Sharma et al, ). Further supporting that Trpc2 is a functional gene in Cervus elaphus , we estimated Trpc2 to evolve under purifying selection in this species without any evidence for significantly relaxed selection rates ( p ‐value > .1; Table ).…”

Genes lost during the transition from land to water in cetaceans highlight genomic changes involved in aquatic adaptations

“…The approach performs a series of filter steps to remove artifacts related to genome assembly or alignment and evolutionary exonintron structure changes in conserved genes. These steps comprise excluding those deletions that overlap assembly gaps in a query genome (131), re-aligning all coding exons with CESAR to detect evolutionary splice site shifts and to avoid spurious frameshifts due to alignment ambiguities (132,133), and excluding alignments to paralogs or processed pseudogenes. Finally, the approach considers all principal or alternative APPRIS isoforms of a gene (134) and outputs data for the isoform with the smallest number of inactivating mutations.…”

Interspecies transcriptome analyses identify genes that control the development and evolution of limb skeletal proportion

“…All specimens were blinded for measurements as described above. Using the Coding Exon-Structure Aware Realigner (CESAR) 9 we aligned exons from jerboa (JacJac1.0, NCBI) and mouse (mm10, NCBI) genomes to generate a custom 1:1 orthologous transcript annotation set with no paralogs. Briefly, we first generated a whole genome alignment between the mouse and jerboa genome assemblies 81 .…”