The origin of new genes: glimpses from the young and old

Long, Manyuan; Betrán, Esther; Thornton, Kevin R.; Wang, Wen

doi:10.1038/nrg1204

Cited by 832 publications

(755 citation statements)

References 116 publications

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“…The K a /K s ratio should be 1 for pseudogenes, <1 for genes subject to functional constraint and >1 for genes subject to strong positive darwinian selection 13 . But because new genes have rapid changes in protein sequences 4,8 , they may have more similar values of K a and K s than their parental genes, bringing the K a /K s ratio closer to 1. Therefore, the K a /K s ratio of a new gene may not be a powerful measure of functionality.…”

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confidence: 99%

“…Although gene fission is a common process in prokaryotes 2 and has been reported in eukaryotes 4,21 , the mechanism involved was unknown. The process by which mkg originated identified the first such mechanism: duplication followed by complementary partial degeneration.…”

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confidence: 99%

“…The molecular origins of the mkg family are reminiscent of the multifunctional gene model 23 that proposes specification of protein functions in duplicate copies and the later subfunctionalization model 24 in which gene duplicates are maintained by a complementary expression pattern. But the mkg family shows that two or more distinct genes can be derived from different domains of an ancestral protein through a fission process whose mechanism differs entirely from that of its inverse, gene fusion [3][4][5]25 . (Fig.…”

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Duplication-degeneration as a mechanism of gene fission and the origin of new genes in Drosophila species

2004

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Gene fission and fusion, the processes by which a single gene is split into two separate genes and two adjacent genes are fused into a single gene, respectively, are among the primary processes that generate new genes 1-4 . Despite their seeming reversibility 4,5 , nothing is known about the mechanism of gene fission. Because the nucleotide sequences of fission genes record little about their origination process, conventional analysis of duplicate genes may not be powerful enough to unravel the underlying mechanism. In a survey for young genes in species of the Drosophila melanogaster subgroup using fluorescence in situ hybridization, we identified a young gene family, monkey king, whose genesis sheds light on the evolutionary process of gene fission. Its members originated 1-2 million years ago as retroposed duplicates and evolved into fission genes that separately encode protein domains from a multidomain ancestor. The mechanism underlying this process is gene duplication with subsequent partial degeneration.To identify young genes in closely related Drosophila species (Fig. 1a), we used fluorescence in situ hybridization FISH analysis of polytene chromosomes with D. melanogaster cDNA probes. We selected the cDNAs that generated additional hybridization signals as candidates for further analysis. In this screening, we identified a gene family with up to three new members in the clade of D. simulans, D. sechellia and D. mauritiana, which have diverged in less than 1 million years 6 . We named this gene family monkey-king (mkg) after a mythical monkey king in ancient China who could transform his hair into many offspring.

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Duplication-degeneration as a mechanism of gene fission and the origin of new genes in Drosophila species

2004

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“…We observed that gene duplication and exaptation from TEs are the main mechanisms to generate GSGs, however, it is likely that there are other origin mechanisms forming the majority of SSGs, such as exon shuffling, lateral gene transfer, gene fusion/fission, and de novo origination [22], which remain poorly understood for LSGs.…”

Section: Discussionmentioning

confidence: 86%

“…Gene duplication is generally thought to be an important means for many genes to evolve new functions and helps the evolution of developmental programs in a variety of organisms [22,23]. The integration of Transposable Elements (TEs) into the genome to form new functions is also a general phenomenon, which has been shown in the analyses of Procedure for identifying lineage-specific genes within C. elegans.…”

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Genome-wide identification of lineage-specific genes within Caenorhabditis elegans

et al. 2015

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With the rapid growth of sequencing technology, a number of genomes and transcriptomes of various species have been sequenced, contributing to the study of lineage-specific genes (LSGs). We identified two sets of LSGs using BLAST: one included Caenorhabditis elegans species-specific genes (1423, SSGs), and the other consisted of Caenorhabditis genus-specific genes (4539, GSGs). The subsequent characterization and analysis of the SSGs and GSGs showed that they have significant differences in evolution and that most LSGs were generated by gene duplication and integration of transposable elements (TEs). We then performed temporal expression profiling and protein function prediction and observed that many SSGs and GSGs are expressed and that genes involved with sex determination, specific stress, immune response, and morphogenesis are over-represented, suggesting that these specific genes may be related to the Caenorhabditis nematodes' special ability to survive in severe and extreme environments.

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Genome‐wide comparative identification and analysis of membrane‐FADS‐like superfamily genes in freshwater economic fishes

Zhang

Gao

et al. 2023

FEBS Open Bio

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Membrane fatty acid desaturase (FADS)‐like superfamily proteins (FADSs) are essential for the synthesis of unsaturated fatty acids (UFAs). Recently, studies on FADS in fishes have mostly focused on marine species, and a comprehensive analysis of the FADS superfamily, including the FADS, stearoyl‐CoA desaturase (SCD), and sphingolipid delta 4‐desaturase (DEGS) families, in freshwater economic fishes is urgently required. To this end, we conducted a thorough analysis of the number, gene/protein structure, chromosomal location, gene linkage map, phylogeny, and expression of the FADS superfamily. We identified 156 FADSs genes in the genome of 27 representative species. Notably, FADS1 and SCD5 were lost in most freshwater fish and other teleosts. All FADSs proteins contain 4 transmembrane helices and 2–3 amphipathic α‐helices. FADSs in the same family are often linked on the same chromosome; moreover, FADS and SCD or DEGS are frequently collocated on the same chromosome. In addition, FADS, SCD, and DEGS family proteins share similar evolutionary patterns. Interestingly, FADS6, as a member of the FADS family, exhibits a similar gene structure and chromosome location to that of SCD family members, which may be the transitional form of FADS and SCD. This study shed light on the type, structure, and phylogenetic relationship of FADSs in freshwater fishes, offering a new perspective into the functional mechanism analysis of FADSs.

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The origin of new genes: glimpses from the young and old

Cited by 832 publications

References 116 publications

Duplication-degeneration as a mechanism of gene fission and the origin of new genes in Drosophila species

Duplication-degeneration as a mechanism of gene fission and the origin of new genes in Drosophila species

Genome-wide identification of lineage-specific genes within Caenorhabditis elegans

Genome‐wide comparative identification and analysis of membrane‐FADS‐like superfamily genes in freshwater economic fishes

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