谱系特有基因(Lineage-specific genes,LSGs)是指在一个谱系中特有并与其他物种谱系所有基因没有明显序列相似性的基因,约为物种基因组全部基因数量的10%~20%,于1996年首次在完成全基因组测序的酵母基因组中大量发现。大规模测序技术的发展使谱系特有基因研究成为比较基因组学的研究热点,已在微生物、海洋低等生物、植物(如拟南芥、水稻、杨树)、昆虫及高等灵长类动物等多个物种或类群中展开,其生物功能对于阐明物种进化历程和生物适应性具有重要意义。文章介绍了谱系特有基因的研究背景和现状,从谱系特有基因获取、基因结构分析、进化起源、生物功能、表达特性分析等方面阐述谱系特有基因的研究进展,分析了存在的问题和后续研究方向,以期为相关研究提供参考。
Lineage-specific genes (LSGs) are defined as genes found in one particular taxonomic group but have no significant sequence similarity with genes from other lineages, which compose about 10%?20% of the total genes in the genome of a focal organism. LSGs were first uncovered in the yeast genome in 1996. The development of the whole genome sequencing leads to the emergence of studies on LSGs as a hot topic in comparative genomics. LSGs have been extensively studied on microbial species, lower marine organisms, plant (such as Arabidopsis thaliana, Oryza sativa, Populus), insects, primate, etc; the biological functions of LSGs are important to clarify the evolution and adaptability of a species. In this review, we summarize the progress of LSGs studies, including LSGs identification, gene characterization, origin and evolution of LSGs, biological function, and expression analysis of LSGs. In addition, we discuss the existing problems and future directions for studies in this area. Our purpose is to provide some unique insights into the researches of LSGs.
[1] Tautz D, Domazet-Lošo T. The evolutionary origin of orphan genes. Nat Rev Genet , 2011, 12(10): 692-702.
[2] Fischer D. Eisenberg D. Finding families for genomic ORFans. Bioinformatics , 1999, 15(9): 759-762.
[3] Dujon B. The yeast genome project: what did we learn? Trends Genet , 1996, 12(7): 263-270.
[4] Khalturin K, Hemmrich G, Fraune S, Augustin R, Bosch TCG. More than just orphans: are taxonomically-restricted genes important in evolution? Trends Genet , 2009, 25(9): 404-413.
[5] Chen SD, Krinsky BH, Long MY. New genes as drivers of phenotypic evolution. Nat Rev Genet , 2013, 14(9): 645-660.
[6] Zhang YE, Landback P, Vibranovski MD, Long MY. Accelerated recruitment of new brain development genes into the human genome. PLoS Biol , 2011, 9(10): e1001179.
[7] Neme R, Tautz D. Phylogenetic patterns of emergence of new genes support a model of frequent de novo evolution. BMC Genomics , 2013, 14: 117.
[8] Magadum S, Banerjee U, Murugan P, Gangapur D, Ravikesavan R. Gene duplication as a major force in evolution. J Genet , 2013, 92(1): 155-161.
[9] Yang LD, Zou M, Fu BD, He SP. Genome-wide identification, characterization, and expression analysis of lineage-specific genes within zebrafish. BMC Genomics , 2013, 14: 65.
[10] Yin YB, Fischer D. Identification and investigation of ORFans in the viral world. BMC Genomics , 2008, 9: 24.
[11] Yin YB, Fischer D. On the origin of microbial ORFans: Quantifying the strength of the evidence for viral lateral transfer. BMC Evol Biol , 2006, 6: 63.
[12] Wilson GA, Bertrand N, Patel Y, Hughes JB, Feil EJ, Field D. Orphans as taxonomically restricted and ecologically important genes. Microbiology , 2005, 151(8): 2499-2501.
[13] Tay SK, Blythe J, Lipovich L. Global discovery of primate-specific genes in the human genome. Proc Natl Acad Sci USA , 2009, 106(29): 12019-12024.
[14] Toll-Riera M, Bosch N, Bellora N, Castelo R, Armengol L, Estivill X, Albà MM. Origin of primate orphan genes: a comparative genomics approach. Mol Biol Evol , 2009, 26(3): 603-612.
[15] Lindskog C, Kuhlwilm M, Davierwala A, Fu N, Hegde G, Uhlén M, Navani S, Pääbo S, Pontén F. Analysis of candidate genes for lineage-specific expression changes in humans and primates. J Proteome Res , 2014, 13(8): 3596-3606.
[16] Zhang Q. Using pseudogene database to identify lineage-specific genes and pseudogenes in humans and chimpanzees. J Hered , 2014, 105(3): 436-443.
[17] Johnson BR, Tsutsui ND. Taxonomically restricted genes are associated with the evolution of sociality in the honey bee. BMC Genomics , 2011, 12: 164.
[18] Zhang GJ, Wang HS, Shi JJ, Wang XL, Zheng HK, Wong GKS, Clark T, Wang W, Wang J, Kang L. Identification and characterization of insect-specific proteins by genome data analysis. BMC Genomics , 2007, 8: 93.
[19] Palmieri N, Kosiol C, Schlötterer C. The life cycle of Drosophila orphan genes. Elife , 2014, 3: e01311.
[20] Rogers RL, Shao L, Sanjak JS, Andolfatto P, Thornton KR. Revised annotations, sex-biased expression, and lineage-specific genes in the Drosophila melanogaster group. G3 (Bethesda) , 2014, 4(12):2345-2351.
[21] Lin HN, Moghe G, Ouyang S, Iezzoni A, Shiu SH, Gu X, Buell CR. Comparative analyses reveal distinct sets of lineage-specific genes within Arabidopsis thaliana . BMC Evol Biol , 2010, 10: 41.
[22] Donoghue MT, Keshavaiah C, Swamidatta SH, Spillane C. Evolutionary origins of Brassicaceae specific genes in Arabidopsis thaliana . BMC Evol Biol , 2011, 11: 47.
[23] Campbell MA, Zhu W, Jiang N, Lin HN, Ouyang S, Childs KL, Haas BJ, Hamilton JP, Buell CR. Identification and characterization of lineage-specific genes within the poaceae. Plant Physiol , 2007, 145(4): 1311-1322.
[24] Lin WL, Cai B, Cheng ZM. Identification and characterization of lineage-specific genes in Populus trichocarpa . Plant Cell Tiss Org , 2014, 116(2)
