On the origin of new genes in <i>Drosophila</i>

Zhou, Qi; Zhang, Guojie; Zhang, Yue; Xu, Shiyu; Zhao, Ruoping; Zhan, Zubing; Li, Xin; Ding, Yun; Yang, Shuang; Wang, Wen

doi:10.1101/gr.076588.108

Cited by 238 publications

(289 citation statements)

References 88 publications

(124 reference statements)

Supporting

Mentioning

257

Contrasting

Unclassified

Order By: Relevance

“…Prior to this study, there were few reports of novel gene origination by this mechanism and none identified human-specific genes (Levine et al 2006;Begun et al 2007;Cai et al 2008;Zhou et al 2008;Toll-Riera et al 2009). The novel proteins identified in this study are all short, encoded by an uninterrupted ORF, are supported by expression data, and the corresponding regions of chromosome where the ortholog is expected to be found in chimp and macaque harbor disabling mutations, which mean that the protein cannot be produced.…”

Section: Discussionmentioning

confidence: 99%

“…There are many examples in the literature of new genes with functionality in brain and testis (Burki and Kaessmann 2004;Emerson et al 2004;Begun et al 2007;Potrzebowski et al 2008;Rosso et al 2008;Zhou et al 2008). One of the novel genes is expressed in male reproductive tissue and one was identified in brain tissues, but they were also identified in many other tissues (Table 1) and there is no statistical trend.…”

Section: Sequence Characteristics and Expression Evidencementioning

confidence: 99%

“…New genes frequently arise through duplication of existing genes, or through fusion, fission, or exon shuffling between genes (Long et al 2003). Origination of genes from noncoding DNA is extremely rare: A few eukaryotic examples are known in yeast and Drosophila (Levine et al 2006;Begun et al 2007;Cai et al 2008;Zhou et al 2008) and a very recent paper reported initial evidence for this process in a primate ancestor (Toll-Riera et al 2009). No cases have been previously reported in human.…”

mentioning

confidence: 99%

See 2 more Smart Citations

Recent de novo origin of human protein-coding genes

Knowles¹,

McLysaght²

2009

Genome Res.

266

299

View full text Add to dashboard Cite

The origin of new genes is extremely important to evolutionary innovation. Most new genes arise from existing genes through duplication or recombination. The origin of new genes from noncoding DNA is extremely rare, and very few eukaryotic examples are known. We present evidence for the de novo origin of at least three human protein-coding genes since the divergence with chimp. Each of these genes has no protein-coding homologs in any other genome, but is supported by evidence from expression and, importantly, proteomics data. The absence of these genes in chimp and macaque cannot be explained by sequencing gaps or annotation error. High-quality sequence data indicate that these loci are noncoding DNA in other primates. Furthermore, chimp, gorilla, gibbon, and macaque share the same disabling sequence difference, supporting the inference that the ancestral sequence was noncoding over the alternative possibility of parallel gene inactivation in multiple primate lineages. The genes are not well characterized, but interestingly, one of them was first identified as an upregulated gene in chronic lymphocytic leukemia. This is the first evidence for entirely novel human-specific protein-coding genes originating from ancestrally noncoding sequences. We estimate that 0.075% of human genes may have originated through this mechanism leading to a total expectation of 18 such cases in a genome of 24,000 protein-coding genes.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Sequence Characteristics and Expression Evidencementioning

confidence: 99%

mentioning

confidence: 99%

See 1 more Smart Citation

Recent de novo origin of human protein-coding genes

Knowles¹,

McLysaght²

2009

Genome Res.

266

299

View full text Add to dashboard Cite

show abstract

“…An important source of genetic variation for adapting to environmental stresses is that of gene duplication, a process by which most new genes are gained (Ohno 1970;Zhou et al 2008;Zhang et al 2009). Despite the fact that the rate of gene duplication is of the same order of magnitude as or higher than the rate of nucleotide mutation, duplicate genes are more likely to be lost than preserved (Li 1999;Sebat et al 2004;Lupski 2007;Emerson et al 2008).…”

Section: Introductionmentioning

confidence: 99%

Evolutionary Toxicogenomics: Diversification of the Cyp12d1 and Cyp12d3 Genes in Drosophila Species

et al. 2012

View full text Add to dashboard Cite

“…One class of structural variant, termed copy number variation (CNV), includes deletions, duplications, insertions, and genomic rearrangements which affect the number of occurrences of a specific DNA sequence present in the genome . CNV is known to occur extensively in the Drosophila genome with functionally significant consequences (Bridges 1936;Dopman and Hartl 2007;Tibshirani and Wang 2008;Zhou et al 2008). In one study of 15 Drosophila strains, as many as 10% of genes were observed to harbor CNVs (Emerson et al 2008).…”

Section: Introductionmentioning

confidence: 99%

High-Throughput Multiplex Sequencing to Discover Copy Number Variants in Drosophila

Daines¹,

Wang²,

et al. 2009

Genetics

View full text Add to dashboard Cite

Copy number variation (CNV) contributes in phenotypically relevant ways to the genetic variability of many organisms. Cost-effective genomewide methods for identifying copy number variation are necessary to elucidate the contribution that these structural variants make to the genomes of model organisms. We have developed a novel approach for the identification of copy number variation by next generation sequencing. As a proof of concept our method has been applied to map the deletions of three Drosophila deficiency strains. We demonstrate that low sequence coverage is sufficient for identifying and mapping large deletions at kilobase resolution, suggesting that data generated from high-throughput sequencing experiments are sufficient for simultaneously analyzing many strains. Genomic DNA from two Drosophila deficiency stocks was barcoded and sequenced in multiplex, and the breakpoints associated with each deletion were successfully identified. The approach we describe is immediately applicable to the systematic exploration of copy number variation in model organisms and humans. S TRUCTURAL variation is known to contribute extensively to the genetic variability of humans, mammals, and many model organisms. One class of structural variant, termed copy number variation (CNV), includes deletions, duplications, insertions, and genomic rearrangements which affect the number of occurrences of a specific DNA sequence present in the genome . CNV is known to occur extensively in the Drosophila genome with functionally significant consequences (Bridges 1936;Dopman and Hartl 2007;Tibshirani and Wang 2008;Zhou et al. 2008). In one study of 15 Drosophila strains, as many as 10% of genes were observed to harbor CNVs (Emerson et al. 2008). Cryptic CNVs that affect the phenotype observed in a model organism have the potential to confound research on multiple levels. For example, a recent report indicates that terminal deletions on chromosome (chr) 2L are frequent among deficiency kit stocks with mutations on the second chromosome and that the associated deletion of lgl has distorted the results of several previous studies (Roegiers et al. 2009). Despite widespread existence of CNV, the biological consequences of this phenomenon remain largely unexplored due to the lack of efficient tools for detection and characterization.Until recently, comparative genomic hybridization with whole-genome tiling arrays (array-CGH) was the primary method for characterizing CNVs (Carter 2007); however, several limitations for this platform reduce its efficacy and efficiency. First, cross-hybridization and reliance on intensity scores lead to data that are difficult to interpret. Second, custom array design and optimization is labor intensive and costly. Third, array-CGH methods can only detect CNV, not other complex rearrangements such as balanced translocations and inversions. Finally, the overall cost of array-CGH methods is relatively high, particularly when high-resolution, whole-genome tiling arrays are employed.Direct sequencing usin...

show abstract

On the origin of new genes in Drosophila

Cited by 238 publications

References 88 publications

Recent de novo origin of human protein-coding genes

Recent de novo origin of human protein-coding genes

Evolutionary Toxicogenomics: Diversification of the Cyp12d1 and Cyp12d3 Genes in Drosophila Species

High-Throughput Multiplex Sequencing to Discover Copy Number Variants in Drosophila

Contact Info

Product

Resources

About