CEG: a database of essential gene clusters

Ye, Yuan-Nong; Hua, Zhi-Gang; Huang, Jian; Rao, Nini; Guo, Feng‐Biao

doi:10.1186/1471-2164-14-769

Cited by 52 publications

(34 citation statements)

References 32 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…6). We BLASTaligned 458 core eukaryotic genes (Cluster of Essential Genes (CEG) database) 25 to the genome assembly with core eukaryotic genes mapping approach (CEGMA) pipeline 26 , which showed high-confidence hits of 453 (98.8%) and 458 (100%) CEG proteins for all 458 essential genes in CEG with full length (>70% alignment) in the genome of B. juncea and B. nigra, respectively (Supplementary Table 14a). We validated the assembled genomes by matching expressed sequence tags (ESTs) downloaded from the US National Center for Biotechnology Information (NCBI) database, which indicated that 98.9% and 98.2% ESTs were supported by the assembled genomes of B. juncea and B. nigra (>50% alignments), respectively (Supplementary Table 14b).…”

Section: Genome Assembly Scaffold Anchoring and Annotationmentioning

confidence: 99%

The genome sequence of allopolyploid Brassica juncea and analysis of differential homoeolog gene expression influencing selection

et al. 2016

View full text Add to dashboard Cite

2 2 5The Brassica genus contains a diverse range of oilseed and vegetable crops important for human nutrition 1 . Crops of particular agricultural importance include three diploid species, Brassica rapa (AA), Brassica nigra (BB) and Brassica oleracea (CC), and three allopolyploid species, B. napus (AACC), B. juncea (AABB) and Brassica carinata (BBCC). The evolutionary relationships among these Brassica species are described by what is called the 'triangle of U' model 2 , which proposes how the genomes of the three ancestral Brassica species, B. rapa, B. nigra and Brassica oleracae, combined to give rise to the allopolyploid species of this genus. B. juncea formed by hybridization between the diploid ancestors of B. rapa and B. nigra, followed by spontaneous chromosome doubling. Subsequent diversifying selection then gave rise to the vegetable-and oil-use subvarieties of B. juncea. These subvarieties include vegetable and oilseed mustard in China, oilseed crops in India, canola crops in Canada and Australia, and condiment crops in Europe and other regions 3 . Cultivation of B. juncea began in China about 6,000 to 7,000 years ago 4 , and flourished in India from 2,300 BC onward 5 .The genomes of B. rapa, B. oleracea and their allopolyploid offspring B. napus have been published recently [6][7][8] , and are often used to explain genome evolution in angiosperms [6][7][8] . The genomes of all Brassica species underwent a lineage-specific whole-genome triplication 6,7,9 , followed by diploidization that involved substantial genome reshuffling and gene losses 6,10-13 . In general, plant genomes are typically repetitive, polyploid and heterozygous, which complicates genome assembly 14 . The short read lengths of next-generation sequencing hinder assembly through complex regions, and fragmented draft and reference genomes usually lack skewed (G+C)-content sequences and repetitive intergenic sequences. Furthermore, in allopolyploid species, homoeolog expression dominance or bias, and specifically differential homoelog gene expression, has often been detected, for instance in Gossypium [15][16][17] Triticum 18,19 and Arabidopsis 20,21 , but the role of this phenomenon in selection for phenotypic traits remains mechanistically mysterious 22 .We reported here the draft genomes of an allopolyploid, B. juncea var. tumida, constructed by de novo assembly using shotgun reads, single-molecule long reads (PacBio sequencing), genomic (optical) mapping (BioNano sequencing) and genetic mapping, serving to resolve complicated allopolyploid genomes. The multiuse allopolyploid B. juncea genome offers a distinctive model to study the underlying genomic basis for selection in breeding improvement. These findings place this work into the broader context of plant breeding, highlighting The Brassica genus encompasses three diploid and three allopolyploid genomes, but a clear understanding of the evolution of agriculturally important traits via polyploidy is lacking. We assembled an allopolyploid Brassica juncea genome by shotgun and single-m...

show abstract

Section: Genome Assembly Scaffold Anchoring and Annotationmentioning

confidence: 99%

The genome sequence of allopolyploid Brassica juncea and analysis of differential homoeolog gene expression influencing selection

et al. 2016

View full text Add to dashboard Cite

show abstract

“…In addition, we curated different lists of genes and other genomic elements that were expected to be under negative selection against CNV (see Supplementary information (Tables S2-S5)). These lists included Mendelian disease implication, essentiality 53 , the International Standards for Cytogenomic Arrays (ISCA) dosage sensitivity map 28 , Database of Chromosomal Imbalance and Phenotype in Humans using Ensembl Resources (DECIPHER) 27 , and genomic indices of selective pressure and conservation (see Supplementary information (Table S4)). Significantly higher variability for constrained elements in one study than others was interpreted as a sign of lower specificity (see Supplementary information (Figures S7-S15; Table S6)).…”

Section: Segmental Duplicationsmentioning

confidence: 99%

A copy number variation map of the human genome

et al. 2015

View full text Add to dashboard Cite

A major contribution to the genome variability among individuals comes from deletions and duplications - collectively termed copy number variations (CNVs) - which alter the diploid status of DNA. These alterations may have no phenotypic effect, account for adaptive traits or can underlie disease. We have compiled published high-quality data on healthy individuals of various ethnicities to construct an updated CNV map of the human genome. Depending on the level of stringency of the map, we estimated that 4.8-9.5% of the genome contributes to CNV and found approximately 100 genes that can be completely deleted without producing apparent phenotypic consequences. This map will aid the interpretation of new CNV findings for both clinical and research applications.

show abstract

“…We used all 296 single-copy essential genes of E. coli , which are used as a reference set in Geptop, to test the impact of duplication events on gene essentiality. Similar to the Cluster of Essential Genes database (CEG) ( 29 ), in IFIM, only the gene name is used to identify multiple copy genes. By searching the annotations of Salmonella enterica , we found that the E. coli essential genes ssb , ftsl and trpS had multiple copies in S. enterica serovar Typhi Ty2, and trpS had multiple copies in S. enterica serovar Typhimurium 14028S.…”

Section: Construction and Content Of The Ifim Databasementioning

confidence: 99%

IFIM: a database of integrated fitness information for microbial genes

Wang

Luo

et al. 2014

Database

View full text Add to dashboard Cite

Knowledge of an organism’s fitness for survival is important for a complete understanding of microbial genetics and effective drug design. Current essential gene databases provide only binary essentiality data from genome-wide experiments. We therefore developed a new database that Integrates quantitative Fitness Information for Microbial genes (IFIM). The IFIM database currently contains data from 16 experiments and 2186 theoretical predictions. The highly significant correlation between the experiment-derived fitness data and our computational simulations demonstrated that the computer-generated predictions were often as reliable as the experimental data. The data in IFIM can be accessed easily, and the interface allows users to browse through the gene fitness information that it contains. IFIM is the first resource that allows easy access to fitness data of microbial genes. We believe this database will contribute to a better understanding of microbial genetics and will be useful in designing drugs to resist microbial pathogens, especially when experimental data are unavailable.Database URL: http://cefg.uestc.edu.cn/ifim/ or http://cefg.cn/ifim/

show abstract

CEG: a database of essential gene clusters

Cited by 52 publications

References 32 publications

The genome sequence of allopolyploid Brassica juncea and analysis of differential homoeolog gene expression influencing selection

The genome sequence of allopolyploid Brassica juncea and analysis of differential homoeolog gene expression influencing selection

A copy number variation map of the human genome

IFIM: a database of integrated fitness information for microbial genes

Contact Info

Product

Resources

About