{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:45:15Z","timestamp":1740185115877,"version":"3.37.3"},"reference-count":54,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2017,9,28]],"date-time":"2017-09-28T00:00:00Z","timestamp":1506556800000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31571358, 21621004 and 31171238"],"award-info":[{"award-number":["31571358, 21621004 and 31171238"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>In the evolution of species, a kind of special sequences, termed ultraconserved sequences (UCSs), have been inherited without any change, which strongly suggests those sequences should be crucial for the species to survive or adapt to the environment. However, the UCSs are still regarded as mysterious genetic sequences so far. Here, we present a systematic study of ultraconserved genomic regions in the budding yeast based on the publicly available genome sequences, in order to reveal their relationship with the adaptability or fitness advantages of the budding yeast.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Our results indicate that, in addition to some fundamental biological functions, the UCSs play an important role in the adaptation of Saccharomyces cerevisiae to the acidic environment, which is backed up by the previous observation. Besides that, we also find the highly unchanged genes are enriched in some other pathways, such as the nutrient-sensitive signaling pathway. To facilitate the investigation of unique UCSs, the UCSC Genome Browser was utilized to visualize the chromosomal position and related annotations of UCSs in S.cerevisiae genome.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>For more details on UCSs, please refer to the Supplementary information online, and the custom code is available on request.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx619","type":"journal-article","created":{"date-parts":[[2017,9,26]],"date-time":"2017-09-26T11:09:36Z","timestamp":1506424176000},"page":"361-366","source":"Crossref","is-referenced-by-count":1,"title":["The systematic analysis of ultraconserved genomic regions in the budding yeast"],"prefix":"10.1093","volume":"34","author":[{"given":"Zhi-Kai","family":"Yang","sequence":"first","affiliation":[{"name":"Department of Physics, Tianjin University, Tianjin, China"},{"name":"SinoGenoMax Co., Ltd.\/Chinese National Human Genome Center, Beijing, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9563-3841","authenticated-orcid":false,"given":"Feng","family":"Gao","sequence":"additional","affiliation":[{"name":"Department of Physics, Tianjin University, Tianjin, China"},{"name":"Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China"},{"name":"SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, China"}]}],"member":"286","published-online":{"date-parts":[[2017,9,27]]},"reference":[{"key":"2023012712264345700_btx619-B1","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. Mol. Biol"},{"key":"2023012712264345700_btx619-B2","doi-asserted-by":"crossref","first-page":"1464","DOI":"10.1093\/bioinformatics\/bth088","article-title":"GOstat: find statistically overrepresented Gene Ontologies within a group of genes","volume":"20","author":"Beissbarth","year":"2004","journal-title":"Bioinformatics"},{"key":"2023012712264345700_btx619-B3","doi-asserted-by":"crossref","first-page":"1321","DOI":"10.1126\/science.1098119","article-title":"Ultraconserved elements in the human genome","volume":"304","author":"Bejerano","year":"2004","journal-title":"Science"},{"key":"2023012712264345700_btx619-B4","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1038\/348125a0","article-title":"The GTPase superfamily: a conserved switch for diverse cell functions","volume":"348","author":"Bourne","year":"1990","journal-title":"Nature"},{"key":"2023012712264345700_btx619-B5","doi-asserted-by":"crossref","DOI":"10.1128\/microbiolspec.FUNK-0048-2016","article-title":"Stress adaptation","volume":"5","author":"Brown","year":"2017","journal-title":"Microbiol. Spectrum"},{"key":"2023012712264345700_btx619-B6","doi-asserted-by":"crossref","first-page":"1256","DOI":"10.4161\/cc.8.8.8287","article-title":"A molecular mechanism of chronological aging in yeast","volume":"8","author":"Burtner","year":"2009","journal-title":"Cell Cycle"},{"key":"2023012712264345700_btx619-B7","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1016\/0025-5564(94)00093-F","article-title":"Comparative characterization of the fermentation pathway of Saccharomyces cerevisiae using biochemical systems theory and metabolic control analysis: steady-state analysis","volume":"130","author":"Cascante","year":"1995","journal-title":"Math. Biosci"},{"key":"2023012712264345700_btx619-B8","doi-asserted-by":"crossref","first-page":"692","DOI":"10.1086\/513149","article-title":"The strength of selection on ultraconserved elements in the human genome","volume":"80","author":"Chen","year":"2007","journal-title":"Am. J. Hum. Genet"},{"key":"2023012712264345700_btx619-B9","doi-asserted-by":"crossref","first-page":"1216","DOI":"10.1038\/ng1888","article-title":"Mammalian ultraconserved elements are strongly depleted among segmental duplications and copy number variants","volume":"38","author":"Derti","year":"2006","journal-title":"Nat. Genet"},{"key":"2023012712264345700_btx619-B10","doi-asserted-by":"crossref","first-page":"D101","DOI":"10.1093\/nar\/gks1092","article-title":"UCNEbase\u2014a database of ultraconserved non-coding elements and genomic regulatory blocks","volume":"41","author":"Dimitrieva","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"2023012712264345700_btx619-B11","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1038\/ng1710","article-title":"Conserved noncoding sequences are selectively constrained and not mutation cold spots","volume":"38","author":"Drake","year":"2006","journal-title":"Nat. Genet"},{"key":"2023012712264345700_btx619-B12","doi-asserted-by":"crossref","first-page":"219","DOI":"10.1007\/978-1-4939-2398-4_14","article-title":"Gene essentiality analysis based on DEG 10, an updated database of essential genes","volume":"1279","author":"Gao","year":"2015","journal-title":"Methods Mol. Biol"},{"key":"2023012712264345700_btx619-B13","doi-asserted-by":"crossref","first-page":"172","DOI":"10.1016\/j.gene.2007.07.017","article-title":"Analysis of invariant sequences in 266 complete genomes","volume":"401","author":"Goto","year":"2007","journal-title":"Gene"},{"key":"2023012712264345700_btx619-B14","doi-asserted-by":"crossref","first-page":"D121","DOI":"10.1093\/nar\/gki081","article-title":"Rfam: annotating non-coding RNAs in complete genomes","volume":"33","author":"Griffiths-Jones","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"2023012712264345700_btx619-B15","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/nar\/gkn923","article-title":"Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists","volume":"37","author":"Huang","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"2023012712264345700_btx619-B16","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1038\/nrm1018","article-title":"TOR signaling in bugs, brain and brawn","volume":"4","author":"Jacinto","year":"2003","journal-title":"Nat. Rev. Mol. Cell Biol"},{"key":"2023012712264345700_btx619-B17","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1042\/BJ20071518","article-title":"TOR regulation of AGC kinases in yeast and mammals","volume":"410","author":"Jacinto","year":"2008","journal-title":"Biochem. J"},{"key":"2023012712264345700_btx619-B18","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1007\/PL00006280","article-title":"Relics from the RNA world","volume":"46","author":"Jeffares","year":"1998","journal-title":"J. Mol. Evol"},{"key":"2023012712264345700_btx619-B19","doi-asserted-by":"crossref","first-page":"e01867-14","DOI":"10.1128\/mBio.01867-14","article-title":"Flexibility and symmetry of prokaryotic genome rearrangement reveal lineage-associated core-gene-defined genome organizational frameworks","volume":"5","author":"Kang","year":"2014","journal-title":"MBio"},{"key":"2023012712264345700_btx619-B20","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1093\/molbev\/mst010","article-title":"MAFFT multiple sequence alignment software version 7: improvements in performance and usability","volume":"30","author":"Katoh","year":"2013","journal-title":"Mol. Biol. Evol"},{"key":"2023012712264345700_btx619-B21","doi-asserted-by":"crossref","first-page":"915.","DOI":"10.1126\/science.1142430","article-title":"Human genome ultraconserved elements are ultraselected","volume":"317","author":"Katzman","year":"2007","journal-title":"Science"},{"key":"2023012712264345700_btx619-B22","doi-asserted-by":"crossref","first-page":"371","DOI":"10.1038\/s41598-017-00414-2","article-title":"Complete genome sequence and comparative genomics of the probiotic yeast Saccharomyces boulardii","volume":"7","author":"Khatri","year":"2017","journal-title":"Sci. Rep"},{"key":"2023012712264345700_btx619-B23","doi-asserted-by":"crossref","first-page":"e1000223","DOI":"10.1371\/journal.pgen.1000223","article-title":"Variations in stress sensitivity and genomic expression in diverse S. cerevisiae isolates","volume":"4","author":"Kvitek","year":"2008","journal-title":"PLoS Genet"},{"key":"2023012712264345700_btx619-B24","doi-asserted-by":"crossref","first-page":"860","DOI":"10.1038\/35057062","article-title":"Initial sequencing and analysis of the human genome","volume":"409","author":"Lander","year":"2001","journal-title":"Nature"},{"key":"2023012712264345700_btx619-B25","doi-asserted-by":"crossref","first-page":"926","DOI":"10.1038\/nature05676","article-title":"Unproductive splicing of SR genes associated with highly conserved and ultraconserved DNA elements","volume":"446","author":"Lareau","year":"2007","journal-title":"Nature"},{"key":"2023012712264345700_btx619-B26","doi-asserted-by":"crossref","first-page":"5896","DOI":"10.1073\/pnas.0730857100","article-title":"Natural variation in human membrane transporter genes reveals evolutionary and functional constraints","volume":"100","author":"Leabman","year":"2003","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023012712264345700_btx619-B27","doi-asserted-by":"crossref","first-page":"2178","DOI":"10.1101\/gr.1224503","article-title":"OrthoMCL: identification of ortholog groups for eukaryotic genomes","volume":"13","author":"Li","year":"2003","journal-title":"Genome Res"},{"key":"2023012712264345700_btx619-B28","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1038\/nature07743","article-title":"Population genomics of domestic and wild yeasts","volume":"458","author":"Liti","year":"2009","journal-title":"Nature"},{"key":"2023012712264345700_btx619-B29","doi-asserted-by":"crossref","first-page":"D574","DOI":"10.1093\/nar\/gkt1131","article-title":"DEG 10, an update of the database of essential genes that includes both protein-coding genes and noncoding genomic elements","volume":"42","author":"Luo","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"2023012712264345700_btx619-B30","doi-asserted-by":"crossref","first-page":"13210.","DOI":"10.1038\/srep13210","article-title":"Evolutionary conservation analysis between the essential and nonessential genes in bacterial genomes","volume":"5","author":"Luo","year":"2015","journal-title":"Sci. Rep"},{"key":"2023012712264345700_btx619-B31","doi-asserted-by":"crossref","first-page":"501","DOI":"10.1002\/yea.1601","article-title":"Relatedness of medically important strains of Saccharomyces cerevisiae as revealed by phylogenetics and metabolomics","volume":"25","author":"MacKenzie","year":"2008","journal-title":"Yeast"},{"key":"2023012712264345700_btx619-B32","doi-asserted-by":"crossref","first-page":"e1004646.","DOI":"10.1371\/journal.pgen.1004646","article-title":"Abnormal dosage of ultraconserved elements is highly disfavored in healthy cells but not cancer cells","volume":"10","author":"McCole","year":"2014","journal-title":"PLoS Genet"},{"key":"2023012712264345700_btx619-B33","doi-asserted-by":"crossref","first-page":"142","DOI":"10.1016\/S1473-3099(10)70218-8","article-title":"Emerging opportunistic yeast infections","volume":"11","author":"Miceli","year":"2011","journal-title":"Lancet Infect. Dis"},{"key":"2023012712264345700_btx619-B34","doi-asserted-by":"crossref","first-page":"W182","DOI":"10.1093\/nar\/gkm321","article-title":"KAAS: an automatic genome annotation and pathway reconstruction server","volume":"35","author":"Moriya","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"2023012712264345700_btx619-B35","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1101\/gr.10.4.403","article-title":"Evolution and variation of the yeast (Saccharomyces) genome","volume":"10","author":"Mortimer","year":"2000","journal-title":"Genome Res"},{"key":"2023012712264345700_btx619-B36","doi-asserted-by":"crossref","first-page":"2933","DOI":"10.1093\/bioinformatics\/btt509","article-title":"Infernal 1.1: 100-fold faster RNA homology searches","volume":"29","author":"Nawrocki","year":"2013","journal-title":"Bioinformatics"},{"key":"2023012712264345700_btx619-B37","doi-asserted-by":"crossref","first-page":"829","DOI":"10.18388\/abp.2001_3850","article-title":"Structure of small G proteins and their regulators","volume":"48","author":"Paduch","year":"2001","journal-title":"Acta Biochim. Polonica"},{"key":"2023012712264345700_btx619-B38","doi-asserted-by":"crossref","first-page":"499","DOI":"10.1038\/nature05295","article-title":"In vivo enhancer analysis of human conserved non-coding sequences","volume":"444","author":"Pennacchio","year":"2006","journal-title":"Nature"},{"key":"2023012712264345700_btx619-B39","doi-asserted-by":"crossref","first-page":"892.","DOI":"10.1126\/science.356.6341.892","article-title":"Mysterious unchanging DNA finds a purpose in life","volume":"356","author":"Pennisi","year":"2017","journal-title":"Science"},{"key":"2023012712264345700_btx619-B40","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1016\/j.tig.2006.02.002","article-title":"How did Saccharomyces evolve to become a good brewer?","volume":"22","author":"Pi\u0161kur","year":"2006","journal-title":"Trends Genet"},{"key":"2023012712264345700_btx619-B41","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1016\/S0168-1605(03)00244-7","article-title":"Adaptive evolution of wine yeast","volume":"86","author":"Querol","year":"2003","journal-title":"Int. J. Food Microbiol"},{"key":"2023012712264345700_btx619-B42","doi-asserted-by":"crossref","first-page":"W116","DOI":"10.1093\/nar\/gki442","article-title":"InterProScan: protein domains identifier","volume":"33","author":"Quevillon","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"2023012712264345700_btx619-B43","doi-asserted-by":"crossref","first-page":"89","DOI":"10.2174\/1389203043486874","article-title":"Mechanisms of ATPases-A multi-disciplinary approach","volume":"5","author":"Rappas","year":"2004","journal-title":"Curr. Protein Peptide Sci"},{"key":"2023012712264345700_btx619-B44","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1016\/0005-2736(81)90354-0","article-title":"Processes involved in the creation of buffering capacity and in substrate-induced proton extrusion in the yeast Saccharomyces cerevisiae","volume":"643","author":"Sigler","year":"1981","journal-title":"Biochim. Biophys. Acta (BBA)-Biomembranes"},{"key":"2023012712264345700_btx619-B45","doi-asserted-by":"crossref","first-page":"1312","DOI":"10.1093\/bioinformatics\/btu033","article-title":"RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies","volume":"30","author":"Stamatakis","year":"2014","journal-title":"Bioinformatics"},{"key":"2023012712264345700_btx619-B46","doi-asserted-by":"crossref","first-page":"762","DOI":"10.1101\/gr.185538.114","article-title":"The 100-genomes strains, an S. cerevisiae resource that illuminates its natural phenotypic and genotypic variation and emergence as an opportunistic pathogen","volume":"25","author":"Strope","year":"2015","journal-title":"Genome Res"},{"key":"2023012712264345700_btx619-B47","doi-asserted-by":"crossref","first-page":"2725","DOI":"10.1093\/molbev\/mst197","article-title":"MEGA6: molecular evolutionary genetics analysis version 6.0","volume":"30","author":"Tamura","year":"2013","journal-title":"Mol. Biol. Evol"},{"key":"2023012712264345700_btx619-B48","doi-asserted-by":"crossref","first-page":"41.","DOI":"10.1186\/1471-2105-4-41","article-title":"The COG database: an updated version includes eukaryotes","volume":"4","author":"Tatusov","year":"2003","journal-title":"BMC Bioinformatics"},{"key":"2023012712264345700_btx619-B49","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1007\/BF01206331","article-title":"On-line construction of suffix trees","volume":"14","author":"Ukkonen","year":"1995","journal-title":"Algorithmica"},{"key":"2023012712264345700_btx619-B50","doi-asserted-by":"crossref","first-page":"4637","DOI":"10.1021\/bi00233a001","article-title":"The ras protein family: evolutionary tree and role of conserved amino acids","volume":"30","author":"Valencia","year":"1991","journal-title":"Biochemistry"},{"key":"2023012712264345700_btx619-B51","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1007\/s00424-009-0657-z","article-title":"Regulated acid-base transport in the collecting duct","volume":"458","author":"Wagner","year":"2009","journal-title":"Pfl\u00fcgers Arch. Eur. J. Physiol"},{"key":"2023012712264345700_btx619-B52","doi-asserted-by":"crossref","first-page":"276","DOI":"10.1038\/nrg1315","article-title":"Applied bioinformatics for the identification of regulatory elements","volume":"5","author":"Wasserman","year":"2004","journal-title":"Nat. Rev. Genet"},{"key":"2023012712264345700_btx619-B53","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1016\/j.hepres.2004.08.011","article-title":"mTOR signaling pathway","volume":"30","author":"Yonezawa","year":"2004","journal-title":"Hepatology Research"},{"key":"2023012712264345700_btx619-B54","first-page":"75","article-title":"Predicting essential genes and proteins based on machine learning and network topological features: a comprehensive review","volume":"7","author":"Zhang","year":"2016","journal-title":"Front. Physiol"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/3\/361\/48912925\/bioinformatics_34_3_361.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/3\/361\/48912925\/bioinformatics_34_3_361.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T13:13:49Z","timestamp":1674825229000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/34\/3\/361\/4259192"}},"subtitle":[],"editor":[{"given":"John","family":"Hancock","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2017,9,27]]},"references-count":54,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2018,2,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btx619","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"type":"print","value":"1367-4803"},{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2018,2,1]]},"published":{"date-parts":[[2017,9,27]]}}}