CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes

By Genís Parra, Keith R Bradnam, Ian Korf. Bioinform., 2007

2,171 citations recorded by the source corpus.

MOTIVATION The numbers of finished and ongoing genome projects are increasing at a rapid rate, and providing the catalog of genes for these new genomes is a key challenge. Obtaining a set of well-characterized genes is a basic requirement in the initial steps of any genome annotation process. An accurate set of genes is needed in order to learn about species-specific properties, to train gene-finding programs, and to validate automatic predictions. Unfortunately, many new genome projects lack comprehensive experimental data to derive a reliable initial set of genes. RESULTS In this study, we report a computational method, CEGMA (Core Eukaryotic Genes Mapping Approach), for building a highly reliable set of gene annotations in the absence of experimental data. We define a set of conserved protein families that occur in a wide range of eukaryotes, and present a mapping procedure that accurately identifies their exon-intron structures in a novel genomic sequence. CEGMA includes the use of profile-hidden Markov models to ensure the reliability of the gene structures. Our procedure allows one to build an initial set of reliable gene annotations in potentially any eukaryotic genome, even those in draft stages. AVAILABILITY Software and data sets are available online at http://korflab.ucdavis.edu/Datasets.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/7c914e1f0ff137d64cd7d2d8acb568f1a0ea6e5e

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Citations in the corpus

Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers (2011, methodology): “To further validate the gene predictions, we used the predicted pigeonpea gene set to search KOGs, the core genes from the core eukaryotic gene mapping approach (CEGMA) pipelin”
Genome of an arbuscular mycorrhizal fungus provides insight into the oldest plant symbiosis (2013, background): “irregularis assembly encompasses 98% of conserved core eukaryotic single-copy genes (17).”
BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes (2021, background): “2018), the now discontinued CEGMA (Parra et al. 2007), CheckM (Parks et al.”
MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects (2011, neutral): “CEGMA gene models were converted to SNAP ’ s required ZFF format using the cegma2zff script that comes bundled with MAKER2.”
Genome Annotation and Curation Using MAKER and MAKER-P (2014, background): “Programs such as CEGMA (Parra et al., 2007) can be used to estimate what fraction of gene content will be recoverable from your genome assembly.”
Tardigrades use intrinsically disordered proteins to survive desiccation (2018, neutral): “…al. (2013) https://github.com/trinityrnaseq/trinityrnaseq/wiki RSEM Li and Dewey (2011) http://deweylab.github.io/RSEM/ edgeR Robinson et al. (2010) https://bioconductor.org/packages/release/bioc/ html/edgeR.html CEGMA Parra et al. (2007) https://github.com/KorfLab/CEGMA_v2/ Excel 2008 for Mac V12.”
Integration of mapped RNA-Seq reads into automatic training of eukaryotic gene finding algorithm (2014, background): “A supervised gene collection naturally starts from more readily validated genes and is thus likely to be biased towards highly expressed genes, genes with rather long exons, evolutionary conserved ‘core’ genes (9), etc.”
Assessing genome assembly quality using the LTR Assembly Index (LAI) (2018, background): “Currently, the Benchmarking Universal Single-Copy Orthologs (BUSCO) and Core Eukaryotic Genes Mapping Approach (CEGMA) programs represent the ‘state-of-the-art’ methods for evaluation of gene space quality through the evaluation of presence or absence of numerous highly conserved orthologous genes (”
Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement (2013, neutral): “Analysis of the draft genome assembly for core eukaryotic genes 11 reveals homologs for >98% of conserved genes in the assembly ( Supplementary Table 11 ).”
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species (2013, methodology): “Key metrics are CEGMA (number of 458 core eukaryotic genes present); COVERAGE and VALIDITY (of validated Fosmid regions, calculated using COMPASS); OPTICAL MAP 1 and OPTICAL MAP 1–3 (coverage of optical maps at level 1 or at all levels); VFRT SCORE (summary score of validated Fosmid region tag analy”
A tissue-mapped axolotl de novo transcriptome enables identification of limb regeneration factors (2017, positive): “We finally applied the Core Eukaryotic Genes Mapping Approach (CEGMA) (Parra et al., 2007), which further indicated that our transcriptome is more than 98% complete (Table S1).”
GeneMark-EP+: eukaryotic gene prediction with self-training in the space of genes and proteins (2020, neutral): “On the other hand, giving too much weights to protein hints may generate parameters dictated by a narrow set of conserved genes and proteins (22).”