[1] |
Cui X, Lv Y, Chen M, Nikoloski Z, Twell D, et al. 2015. Young genes out of the male: an insight from evolutionary age analysis of the pollen transcriptome. Molecular Plant 8:935−45 doi: 10.1016/j.molp.2014.12.008 |
[2] |
Fischer D, Eisenberg D. 1999. Finding families for genomic ORFans. Bioinformatics 15:759−62 doi: 10.1093/bioinformatics/15.9.759 |
[3] |
Wissler L, Gadau J, Simola DF, Helmkampf M, Bornberg-Bauer E. 2013. Mechanisms and dynamics of orphan gene emergence in insect genomes. Genome Biology and Evolution 5:439−55 doi: 10.1093/gbe/evt009 |
[4] |
Goffeau A, Barrell BG, Bussey H, Davis RW, Dujon B, et al. 1996. Life with 6000 genes. Science 274:546−67 doi: 10.1126/science.274.5287.546 |
[5] |
Siew N, Fischer D. 2003. Analysis of singleton ORFans in fully sequenced microbial genomes. Proteins 53:241−51 doi: 10.1002/prot.10423 |
[6] |
Heather JM, Chain B. 2016. The sequence of sequencers: the history of sequencing DNA. Genomics 107:1−8 doi: 10.1016/j.ygeno.2015.11.003 |
[7] |
Sun W, Zhao XW, Zhang Z. 2015. Identification and evolution of the orphan genes in the domestic silkworm, Bombyx mori. FEBS Letters 589:2731−38 doi: 10.1016/j.febslet.2015.08.008 |
[8] |
Xu Y, Wu G, Hao B, Chen L, Deng X, et al. 2015. Identification, characterization and expression analysis of lineage-specific genes within sweet orange (Citrus sinensis). BMC Genomics 16:995 doi: 10.1186/s12864-015-2211-z |
[9] |
Zhao Z, Ma D. 2021. Genome-wide identification, characterization and function analysis of lineage-specific genes in the tea plant Camellia sinensis. Frontiers in Genetics 12:770570 doi: 10.3389/fgene.2021.770570 |
[10] |
Daubin V, Lerat E, Perrière G. 2003. The source of laterally transferred genes in bacterial genomes. Genome Biology 4:R57 doi: 10.1186/gb-2003-4-9-r57 |
[11] |
Long M, Betrán E, Thornton K, Wang W. 2003. The origin of new genes: glimpses from the young and old. Nature Reviews Genetics 4:865−75 doi: 10.1038/nrg1204 |
[12] |
Daubin V, Ochman H. 2004. Start-up entities in the origin of new genes. Current Opinion in Genetics and Development 14:616−19 doi: 10.1016/j.gde.2004.09.004 |
[13] |
Kaessmann H. 2010. Origins, evolution, and phenotypic impact of new genes. Genome Research 20:1313−26 doi: 10.1101/gr.101386.109 |
[14] |
Wu DD, Irwin DM, Zhang YP. 2011. De novo origin of human protein-coding genes. Plos Genetics 7:e1002379 doi: 10.1371/journal.pgen.1002379 |
[15] |
Lin H, Moghe G, Ouyang S, Iezzoni A, Shiu SH, et al. 2010. Comparative analyses reveal distinct sets of lineage-specific genes within Arabidopsis thaliana. BMC Evolutionary Biology 10:41 doi: 10.1186/1471-2148-10-41 |
[16] |
Domazet-Loso T, Tautz D. 2003. An evolutionary analysis of orphan genes in Drosophila. Genome Research 13:2213−19 doi: 10.1101/gr.1311003 |
[17] |
Campbell MA, Zhu W, Jiang N, Lin H, Ouyang S, et al. 2007. Identification and characterization of lineage-specific genes within the Poaceae. Plant Physiology 145:1311−22 doi: 10.1104/pp.107.104513 |
[18] |
Yang L, Zou M, Fu B, He S. 2013. Genome-wide identification, characterization, and expression analysis of lineage-specific genes within zebrafish. BMC Genomics 14:65 doi: 10.1186/1471-2164-14-65 |
[19] |
Heinen TJAJ, Staubach F, Häming D, Tautz D. 2009. Emergence of a new gene from an intergenic region. Current Biology 19:1527−31 doi: 10.1016/j.cub.2009.07.049 |
[20] |
Joppich C, Scholz S, Korge G, Schwendemann A. 2009. Umbrea, a chromo shadow domain protein in Drosophila melanogaster heterochromatin, interacts with Hip, HP1 and HOAP. Chromosome Research 17:19−36 doi: 10.1007/s10577-008-9002-1 |
[21] |
Chen S, Zhang YE, Long M. 2010. New genes in Drosophila quickly become essential. Science 330:1682−85 doi: 10.1126/science.1196380 |
[22] |
Li L, Zheng W, Zhu Y, Ye H, Tang B, et al. 2015. QQS orphan gene regulates carbon and nitrogen partitioning across species via NF-YC interactions. Proceedings of the National Academy of Sciences of the United States of America 112:14734−39 doi: 10.1073/pnas.1514670112 |
[23] |
Yeh SD, Do T, Chan C, Cordova A, Carranza F, et al. 2012. Functional evidence that a recently evolved Drosophila sperm-specific gene boosts sperm competition. Proceedings of the National Academy of Sciences of the United States of America 109:2043−48 doi: 10.1073/pnas.1121327109 |
[24] |
Ni F, Qi J, Hao Q, Lyu B, Luo M, et al. 2017. Wheat Ms2 encodes for an orphan protein that confers male sterility in grass species. Nature Communications 8:15121 doi: 10.1038/ncomms15121 |
[25] |
Li G, Wu X, Hu Y, Muñoz-Amatriaín M, Luo J, et al. 2019. Orphan genes are involved in drought adaptations and ecoclimatic-oriented selections in domesticated cowpea. Journal of Experimental Botany 70:3101−10 doi: 10.1093/jxb/erz145 |
[26] |
Colbourne JK, Pfrender ME, Gilbert D, Thomas WK, Tucker A, et al. 2011. The ecoresponsive genome of Daphnia pulex. Science 331:555−61 doi: 10.1126/science.1197761 |
[27] |
Donoghue MT, Keshavaiah C, Swamidatta SH, Spillane C. 2011. Evolutionary origins of Brassicaceae specific genes in Arabidopsis thaliana. BMC Evolutionary Biology 11:47 doi: 10.1186/1471-2148-11-47 |
[28] |
Guo WJ, Li P, Ling J, Ye SP. 2007. Significant comparative characteristics between orphan and nonorphan genes in the rice (Oryza sativa L.) genome. Comparative and Functional Genomics 2007:21676 doi: 10.1155/2007/21676 |
[29] |
Dong X, Jiang X, Kuang G, Wang Q, Zhong M, et al. 2017. Genetic control of flowering time in woody plants: roses as an emerging model. Plant Diversity 39:104−10 doi: 10.1016/j.pld.2017.01.004 |
[30] |
Martin M, Piola F, Chessel D, Jay M, Heizmann P. 2001. The domestication process of the Modern Rose: genetic structure and allelic composition of the rose complex. Theoretical and Applied Genetics 102:398−404 doi: 10.1007/s001220051660 |
[31] |
Raymond O, Gouzy J, Just J, Badouin H, Verdenaud M, et al. 2018. The Rosa genome provides new insights into the domestication of modern roses. Nature Genetics 50:772−77 doi: 10.1038/s41588-018-0110-3 |
[32] |
Zhang G, Wang H, Shi J, Wang X, Zheng H, et al. 2007. Identification and characterization of insect-specific proteins by genome data analysis. BMC Genomics 8:93 doi: 10.1186/1471-2164-8-93 |
[33] |
Xia X. 2018. DAMBE7: New and improved tools for data analysis in molecular biology and evolution. Molecular Biology and Evolution 35:1550−52 doi: 10.1093/molbev/msy073 |
[34] |
Savojardo C, Martelli PL, Fariselli P, Profiti G, Casadio R. 2018. BUSCA: an integrative web server to predict subcellular localization of proteins. Nucleic Acids Research 46:W459−W466 doi: 10.1093/nar/gky320 |
[35] |
Zhang J. 2003. Evolution by gene duplication: an update. Trends in Ecology and Evolution 18:292−98 doi: 10.1016/s0169-5347(03)00033-8 |
[36] |
Wang Y, Tang H, DeBarry JD, Tan X, Li J, et al. 2022. MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Research e49 |
[37] |
Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114−20 doi: 10.1093/bioinformatics/btu170 |
[38] |
Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, et al. 2011. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature Biotechnology 29:644−52 doi: 10.1038/nbt.1883 |
[39] |
Ma S, Yuan Y, Tao Y, Jia H, Ma Z. 2020. Identification, characterization and expression analysis of lineage-specific genes within Triticeae. Genomics 112:1343−50 doi: 10.1016/j.ygeno.2019.08.003 |
[40] |
Pan JB, Hu SC, Wang H, Zou Q, Ji ZL. 2012. PaGeFinder: quantitative identification of spatiotemporal pattern genes. Bioinformatics 28:1544−45 doi: 10.1093/bioinformatics/bts169 |
[41] |
Langfelder P, Horvath S. 2008. WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics 9:559 doi: 10.1186/1471-2105-9-559 |
[42] |
Toll-Riera M, Bosch N, Bellora N, Castelo R, Armengol L, et al. 2009. Origin of primate orphan genes: a comparative genomics approach. Molecular Biology and Evolution 26:603−12 doi: 10.1093/molbev/msn281 |
[43] |
Yang X, Jawdy S, Tschaplinski TJ, Tuskan GA. 2009. Genome-wide identification of lineage-specific genes in Arabidopsis, Oryza and Populus. Genomics 93:473−80 doi: 10.1016/j.ygeno.2009.01.002 |
[44] |
Kapas S, Clark AJL. 1995. Identification of an orphan receptor gene as a type 1 calcitonin gene-related peptide receptor. Biochemical and Biophysical Research Communications 217:832−38 doi: 10.1006/bbrc.1995.2847 |
[45] |
Prabh N, Rödelsperger C. 2019. De novo divergence, and mixed origin contribute to the emergence of orphan genes in Pristionchus nematodes. G3 Genes|Genomes|Genetics 9:2277−86 doi: 10.1534/g3.119.400326 |
[46] |
Zhang W, Gao Y, Long M, Shen B. 2019. Origination and evolution of orphan genes and de novo genes in the genome of Caenorhabditis elegans. Science China Life Sciences 62:579−93 doi: 10.1007/s11427-019-9482-0 |
[47] |
Arendsee ZW, Li L, Wurtele ES. 2014. Coming of age: orphan genes in plants. Trends in Plant Science 19:698−708 doi: 10.1016/j.tplants.2014.07.003 |
[48] |
Neme R, Tautz D. 2013. Phylogenetic patterns of emergence of new genes support a model of frequent de novo evolution. BMC Genomics 14:117 doi: 10.1186/1471-2164-14-117 |
[49] |
Ma D, Ding Q, Guo Z, Zhao Z, Wei L, et al. 2021. Identification, characterization and expression analysis of lineage-specific genes within mangrove species Aegiceras corniculatum. Molecular Genetics and Genomics 296:1235−47 doi: 10.1007/s00438-021-01810-0 |
[50] |
Galtier N, Piganeau G, Mouchiroud D, Duret L. 2001. GC-content evolution in mammalian genomes: the biased gene conversion hypothesis. Genetics 159:907−11 doi: 10.1093/genetics/159.2.907 |
[51] |
Lassalle F, Périan S, Bataillon T, Nesme X, Duret L, et al. 2015. GC-content evolution in bacterial genomes: the biased gene conversion hypothesis expands. Plos Genetics 11:e1004941 doi: 10.1371/journal.pgen.1004941 |
[52] |
Kiraga J, Mackiewicz P, Mackiewicz D, Kowalczuk M, Biecek P, et al. 2007. The relationships between the isoelectric point and: length of proteins, taxonomy and ecology of organisms. BMC Genomics 8:163 doi: 10.1186/1471-2164-8-163 |
[53] |
Alendé N, Nielsen JE, Shields DC, Khaldi N. 2011. Evolution of the isoelectric point of mammalian proteins as a consequence of indels and adaptive evolution. Proteins 79:1635−48 doi: 10.1002/prot.22990 |
[54] |
Nandi S, Mehra N, Lynn AM, Bhattacharya A. 2005. Comparison of theoretical proteomes: Identification of COGs with conserved and variable pI within the multimodal pI distribution. BMC Genomics 6:116 doi: 10.1186/1471-2164-6-116 |
[55] |
Chen S, Krinsky BH, Long M. 2013. New genes as drivers of phenotypic evolution. Nature Reviews Genetics 14:645−60 doi: 10.1038/nrg3521 |
[56] |
Wang Z, Gerstein M, Snyder M. 2009. RNA-Seq: a revolutionary tool for transcriptomics. Nature Reviews Genetics 10:57−63 doi: 10.1038/nrg2484 |
[57] |
Begun DJ, Lindfors HA, Kern AD, Jones CD. 2007. Evidence for de novo evolution of testis-expressed genes in the Drosophila yakuba/Drosophila erecta clade. Genetics 176:1131−37 doi: 10.1534/genetics.106.069245 |
[58] |
Wu DD, Wang X, Li Y, Zeng L, Irwin DM, et al. 2014. "Out of pollen" hypothesis for origin of new genes in flowering plants: study from Arabidopsis thaliana. Genome Biology and Evolution 6:2822−29 doi: 10.1093/gbe/evu206 |
[59] |
Obayashi T, Kinoshita K. 2009. Rank of correlation coefficient as a comparable measure for biological significance of gene coexpression. DNA Research 16:249−60 doi: 10.1093/dnares/dsp016 |
[60] |
Jeong HJ, Kang JH, Zhao M, Kwon JK, Choi HS, et al. 2014. Tomato Male sterile 10 35 is essential for pollen development and meiosis in anthers. Journal of Experimental Botany 65:6693−709 doi: 10.1093/jxb/eru389 |
[61] |
Geng X, Ye J, Yang X, Li S, Zhang L, et al. 2018. Identification of proteins involved in carbohydrate metabolism and energy metabolism pathways and their regulation of cytoplasmic male sterility in wheat. International Journal of Molecular Sciences 19:324 doi: 10.3390/ijms19020324 |
[62] |
Yue J, Ren Y, Wu S, Zhang X, Wang H, et al. 2014. Differential proteomic studies of the genic male-sterile line and fertile line anthers of upland cotton (Gossypium hirsutum L.). Genes and Genomics 36:415−26 doi: 10.1007/s13258-014-0176-y |
[63] |
Liu H, Wang J, Li C, Qiao L, Wang X, et al. 2018. Phenotype characterisation and analysis of expression patterns of genes related mainly to carbohydrate metabolism and sporopollenin in male-sterile anthers induced by high temperature in wheat (Triticum aestivum). Crop and Pasture Science 69:469−78 doi: 10.1071/CP18034 |
[64] |
Kunz S, Pesquet E, Kleczkowski LA. 2014. Functional dissection of sugar signals affecting gene expression in Arabidopsis thaliana. PLoS ONE 9:e100312 doi: 10.1371/journal.pone.0100312 |
[65] |
Hirsche J, García Fernández JM, Stabentheiner E, Großkinsky DK, Roitsch T. 2017. Differential effects of carbohydrates on Arabidopsis pollen germination. Plant and Cell Physiology 58:691−701 doi: 10.1093/pcp/pcx020 |
[66] |
Sudan C, Prakash S, Bhomkar P, Jain S, Bhalla-Sarin N. 2006. Ubiquitous presence of beta-glucuronidase (GUS) in plants and its regulation in some model plants. Planta 224:853−64 doi: 10.1007/s00425-006-0276-2 |
[67] |
Witcher DR, Hood EE, Peterson D, Bailey M, Bond D, et al. 1998. Commercial production of β-glucuronidase (GUS): a model system for the production of proteins in plants. Molecular Breeding 4:301−12 doi: 10.1023/A:1009622429758 |
[68] |
Tian A, Zhang E, Cui Z. 2021. Full-length transcriptome analysis reveals the differences between floral buds of recessive genic male-sterile line (RMS3185A) and fertile line (RMS3185B) of cabbage. Planta 253:21 doi: 10.1007/s00425-020-03542-8 |
[69] |
Zhang Y, Chen J, Liu J, Xia M, Wang W, et al. 2015. Transcriptome analysis of early anther development of cotton revealed male sterility genes for major metabolic pathways. Journal of Plant Growth Regulation 34:223−32 doi: 10.1007/s00344-014-9458-5 |
[70] |
Li Y, Qin T, Wei C, Sun J, Dong T, et al. 2019. Using transcriptome analysis to screen for key genes and pathways related to cytoplasmic male sterility in cotton (Gossypium hirsutum L.). International Journal of Molecular Sciences 20:5120 doi: 10.3390/ijms20205120 |
[71] |
Han Y, Yong X, Yu J, Cheng T, Wang J, et al. 2019. Identification of candidate adaxial-abaxial-related genes regulating petal expansion during flower opening in Rosa chinensis "old blush". Frontiers in Plant Science 10:1098 doi: 10.3389/fpls.2019.01098 |
[72] |
Tholl D, Gershenzon J. 2015. The flowering of a new scent pathway in rose. Science 349:28−29 doi: 10.1126/science.aac6509 |
[73] |
Hemmerlin A, Harwood JL, Bach TJ. 2012. A raison d’être for two distinct pathways in the early steps of plant isoprenoid biosynthesis? Progress in Lipid Research 51:95−148 doi: 10.1016/j.plipres.2011.12.001 |
[74] |
Caissard JC, Bergougnoux V, Martin M, Mauriat M, Baudino S. 2006. Chemical and histochemical analysis of 'Quatre Saisons Blanc Mousseux', a moss rose of the Rosa × damascena group. Annals of Botany 97:231−38 doi: 10.1093/aob/mcj034 |
[75] |
Dudareva N, Pichersky E, Gershenzon J. 2004. Biochemistry of plant volatiles. Plant Physiology 135:1893−902 doi: 10.1104/pp.104.049981 |
[76] |
Glick A, Philosoph-Hadas S, Vainstein A, Meir A, Tadmor Y, et al. 2007. Methyl jasmonate enhances color and carotenoid content of yellow-pigmented cut rose flowers. Acta Horticulturae 755:243−50 doi: 10.17660/actahortic.2007.755.31 |
[77] |
Carvunis AR, Rolland T, Wapinski I, Calderwood MA, Yildirim MA, et al. 2012. Proto-genes and de novo gene birth. Nature 487:370−74 doi: 10.1038/nature11184 |
[78] |
Al-Yasi H, Attia H, Alamer K, Hassan F, Ali E, et al. 2020. Impact of drought on growth, photosynthesis, osmotic adjustment, and cell wall elasticity in Damask rose. Plant Physiology and Biochemistry 150:133−39 doi: 10.1016/j.plaphy.2020.02.038 |
[79] |
Schachtman DP, Goodger JQD. 2008. Chemical root to shoot signaling under drought. Trends in Plant Science 13:281−87 doi: 10.1016/j.tplants.2008.04.003 |
[80] |
Lü P, Kang M, Jiang X, Dai F, Gao J, et al. 2013. RhEXPA4, a rose expansin gene, modulates leaf growth and confers drought and salt tolerance to Arabidopsis. Planta 237:1547−59 doi: 10.1007/s00425-013-1867-3 |