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Conserved sequence

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(Redirected from Conserved gene) Similar DNA, RNA or protein sequences within genomes or among species Compare sequence motifs and protein domains.
A multiple sequence alignment of five mammalian histone H1 proteins
Sequences are the amino acids for residues 120-180 of the proteins. Residues that are conserved across all sequences are highlighted in grey. Below each site (i.e., position) of the protein sequence alignment is a key denoting conserved sites (*), sites with conservative replacements (:), sites with semi-conservative replacements (.), and sites with non-conservative replacements ( ).

In evolutionary biology, conserved sequences are identical or similar sequences in nucleic acids (DNA and RNA) or proteins across species (orthologous sequences), or within a genome (paralogous sequences), or between donor and receptor taxa (xenologous sequences). Conservation indicates that a sequence has been maintained by natural selection.

A highly conserved sequence is one that has remained relatively unchanged far back up the phylogenetic tree, and hence far back in geological time. Examples of highly conserved sequences include the RNA components of ribosomes present in all domains of life, the homeobox sequences widespread amongst eukaryotes, and the tmRNA in bacteria. The study of sequence conservation overlaps with the fields of genomics, proteomics, evolutionary biology, phylogenetics, bioinformatics and mathematics.

History

See also: History of molecular evolution

The discovery of the role of DNA in heredity, and observations by Frederick Sanger of variation between animal insulins in 1949, prompted early molecular biologists to study taxonomy from a molecular perspective. Studies in the 1960s used DNA hybridization and protein cross-reactivity techniques to measure similarity between known orthologous proteins, such as hemoglobin and cytochrome c. In 1965, Émile Zuckerkandl and Linus Pauling introduced the concept of the molecular clock, proposing that steady rates of amino acid replacement could be used to estimate the time since two organisms diverged. While initial phylogenies closely matched the fossil record, observations that some genes appeared to evolve at different rates led to the development of theories of molecular evolution. Margaret Dayhoff's 1966 comparison of ferredoxin sequences showed that natural selection would act to conserve and optimise protein sequences essential to life.

Mechanisms

See also: Natural selection and Neutral theory of molecular evolution

Over many generations, nucleic acid sequences in the genome of an evolutionary lineage can gradually change over time due to random mutations and deletions. Sequences may also recombine or be deleted due to chromosomal rearrangements. Conserved sequences are sequences which persist in the genome despite such forces, and have slower rates of mutation than the background mutation rate.

Conservation can occur in coding and non-coding nucleic acid sequences. Highly conserved DNA sequences are thought to have functional value, although the role for many highly conserved non-coding DNA sequences is poorly understood. The extent to which a sequence is conserved can be affected by varying selection pressures, its robustness to mutation, population size and genetic drift. Many functional sequences are also modular, containing regions which may be subject to independent selection pressures, such as protein domains.

Coding sequence

In coding sequences, the nucleic acid and amino acid sequence may be conserved to different extents, as the degeneracy of the genetic code means that synonymous mutations in a coding sequence do not affect the amino acid sequence of its protein product.

Amino acid sequences can be conserved to maintain the structure or function of a protein or domain. Conserved proteins undergo fewer amino acid replacements, or are more likely to substitute amino acids with similar biochemical properties. Within a sequence, amino acids that are important for folding, structural stability, or that form a binding site may be more highly conserved.

The nucleic acid sequence of a protein coding gene may also be conserved by other selective pressures. The codon usage bias in some organisms may restrict the types of synonymous mutations in a sequence. Nucleic acid sequences that cause secondary structure in the mRNA of a coding gene may be selected against, as some structures may negatively affect translation, or conserved where the mRNA also acts as a functional non-coding RNA.

Non-coding

See also: Conserved non-coding sequence

Non-coding sequences important for gene regulation, such as the binding or recognition sites of ribosomes and transcription factors, may be conserved within a genome. For example, the promoter of a conserved gene or operon may also be conserved. As with proteins, nucleic acids that are important for the structure and function of non-coding RNA (ncRNA) can also be conserved. However, sequence conservation in ncRNAs is generally poor compared to protein-coding sequences, and base pairs that contribute to structure or function are often conserved instead.

Identification

See also: Sequence alignment

Conserved sequences are typically identified by bioinformatics approaches based on sequence alignment. Advances in high-throughput DNA sequencing and protein mass spectrometry has substantially increased the availability of protein sequences and whole genomes for comparison since the early 2000s.

Homology search

Conserved sequences may be identified by homology search, using tools such as BLAST, HMMER, OrthologR, and Infernal. Homology search tools may take an individual nucleic acid or protein sequence as input, or use statistical models generated from multiple sequence alignments of known related sequences. Statistical models such as profile-HMMs, and RNA covariance models which also incorporate structural information, can be helpful when searching for more distantly related sequences. Input sequences are then aligned against a database of sequences from related individuals or other species. The resulting alignments are then scored based on the number of matching amino acids or bases, and the number of gaps or deletions generated by the alignment. Acceptable conservative substitutions may be identified using substitution matrices such as PAM and BLOSUM. Highly scoring alignments are assumed to be from homologous sequences. The conservation of a sequence may then be inferred by detection of highly similar homologs over a broad phylogenetic range.

Multiple sequence alignment

A sequence logo for the LexA-binding motif of gram-positive bacteria. As the adenosine at position 5 is highly conserved, it appears larger than other characters.

Multiple sequence alignments can be used to visualise conserved sequences. The CLUSTAL format includes a plain-text key to annotate conserved columns of the alignment, denoting conserved sequence (*), conservative mutations (:), semi-conservative mutations (.), and non-conservative mutations ( ) Sequence logos can also show conserved sequence by representing the proportions of characters at each point in the alignment by height.

Genome alignment

This image from the ECR browser shows the result of aligning different vertebrate genomes to the human genome at the conserved OTX2 gene. Top: Gene annotations of exons and introns of the OTX2 gene. For each genome, sequence similarity (%) compared to the human genome is plotted. Tracks show the zebrafish, dog, chicken, western clawed frog, opossum, mouse, rhesus macaque and chimpanzee genomes. The peaks show regions of high sequence similarity across all genomes, showing that this sequence is highly conserved.

Whole genome alignments (WGAs) may also be used to identify highly conserved regions across species. Currently the accuracy and scalability of WGA tools remains limited due to the computational complexity of dealing with rearrangements, repeat regions and the large size of many eukaryotic genomes. However, WGAs of 30 or more closely related bacteria (prokaryotes) are now increasingly feasible.

Scoring systems

Other approaches use measurements of conservation based on statistical tests that attempt to identify sequences which mutate differently to an expected background (neutral) mutation rate.

The GERP (Genomic Evolutionary Rate Profiling) framework scores conservation of genetic sequences across species. This approach estimates the rate of neutral mutation in a set of species from a multiple sequence alignment, and then identifies regions of the sequence that exhibit fewer mutations than expected. These regions are then assigned scores based on the difference between the observed mutation rate and expected background mutation rate. A high GERP score then indicates a highly conserved sequence.

LIST (Local Identity and Shared Taxa) is based on the assumption that variations observed in species closely related to human are more significant when assessing conservation compared to those in distantly related species. Thus, LIST utilizes the local alignment identity around each position to identify relevant sequences in the multiple sequence alignment (MSA) and then it estimates conservation based on the taxonomy distances of these sequences to human. Unlike other tools, LIST ignores the count/frequency of variations in the MSA.

Aminode combines multiple alignments with phylogenetic analysis to analyze changes in homologous proteins and produce a plot that indicates the local rates of evolutionary changes. This approach identifies the Evolutionarily Constrained Regions in a protein, which are segments that are subject to purifying selection and are typically critical for normal protein function.

Other approaches such as PhyloP and PhyloHMM incorporate statistical phylogenetics methods to compare probability distributions of substitution rates, which allows the detection of both conservation and accelerated mutation. First, a background probability distribution is generated of the number of substitutions expected to occur for a column in a multiple sequence alignment, based on a phylogenetic tree. The estimated evolutionary relationships between the species of interest are used to calculate the significance of any substitutions (i.e. a substitution between two closely related species may be less likely to occur than distantly related ones, and therefore more significant). To detect conservation, a probability distribution is calculated for a subset of the multiple sequence alignment, and compared to the background distribution using a statistical test such as a likelihood-ratio test or score test. P-values generated from comparing the two distributions are then used to identify conserved regions. PhyloHMM uses hidden Markov models to generate probability distributions. The PhyloP software package compares probability distributions using a likelihood-ratio test or score test, as well as using a GERP-like scoring system.

Extreme conservation

Ultra-conserved elements

Ultra-conserved elements or UCEs are sequences that are highly similar or identical across multiple taxonomic groupings. These were first discovered in vertebrates, and have subsequently been identified within widely-differing taxa. While the origin and function of UCEs are poorly understood, they have been used to investigate deep-time divergences in amniotes, insects, and between animals and plants.

Universally conserved genes

The most highly conserved genes are those that can be found in all organisms. These consist mainly of the ncRNAs and proteins required for transcription and translation, which are assumed to have been conserved from the last universal common ancestor of all life.

Genes or gene families that have been found to be universally conserved include GTP-binding elongation factors, Methionine aminopeptidase 2, Serine hydroxymethyltransferase, and ATP transporters. Components of the transcription machinery, such as RNA polymerase and helicases, and of the translation machinery, such as ribosomal RNAs, tRNAs and ribosomal proteins are also universally conserved.

Applications

Phylogenetics and taxonomy

Sets of conserved sequences are often used for generating phylogenetic trees, as it can be assumed that organisms with similar sequences are closely related. The choice of sequences may vary depending on the taxonomic scope of the study. For example, the most highly conserved genes such as the 16S RNA and other ribosomal sequences are useful for reconstructing deep phylogenetic relationships and identifying bacterial phyla in metagenomics studies. Sequences that are conserved within a clade but undergo some mutations, such as housekeeping genes, can be used to study species relationships. The internal transcribed spacer (ITS) region, which is required for spacing conserved rRNA genes but undergoes rapid evolution, is commonly used to classify fungi and strains of rapidly evolving bacteria.

Medical research

As highly conserved sequences often have important biological functions, they can be useful a starting point for identifying the cause of genetic diseases. Many congenital metabolic disorders and Lysosomal storage diseases are the result of changes to individual conserved genes, resulting in missing or faulty enzymes that are the underlying cause of the symptoms of the disease. Genetic diseases may be predicted by identifying sequences that are conserved between humans and lab organisms such as mice or fruit flies, and studying the effects of knock-outs of these genes. Genome-wide association studies can also be used to identify variation in conserved sequences associated with disease or health outcomes. More than two dozen novel potential susceptibility loci have been discovered for Alzehimer's disease.

Functional annotation

Identifying conserved sequences can be used to discover and predict functional sequences such as genes. Conserved sequences with a known function, such as protein domains, can also be used to predict the function of a sequence. Databases of conserved protein domains such as Pfam and the Conserved Domain Database can be used to annotate functional domains in predicted protein coding genes.

See also

References

  1. "Clustal FAQ #Symbols". Clustal. Archived from the original on 24 October 2016. Retrieved 8 December 2014.
  2. Sanger, F. (24 September 1949). "Species Differences in Insulins". Nature. 164 (4169): 529. Bibcode:1949Natur.164..529S. doi:10.1038/164529a0. PMID 18141620. S2CID 4067991.
  3. ^ Marmur, J; Falkow, S; Mandel, M (October 1963). "New Approaches to Bacterial Taxonomy". Annual Review of Microbiology. 17 (1): 329–372. doi:10.1146/annurev.mi.17.100163.001553. PMID 14147455.
  4. ^ Pace, N. R.; Sapp, J.; Goldenfeld, N. (17 January 2012). "Phylogeny and beyond: Scientific, historical, and conceptual significance of the first tree of life". Proceedings of the National Academy of Sciences. 109 (4): 1011–1018. Bibcode:2012PNAS..109.1011P. doi:10.1073/pnas.1109716109. PMC 3268332. PMID 22308526.
  5. Zuckerlandl, Emile; Pauling, Linus B. (1962). "Molecular disease, evolution, and genetic heterogeneity". Horizons in Biochemistry: 189–225.
  6. Margoliash, E (October 1963). "Primary Structure and Evolution of Cytochrome C". Proceedings of the National Academy of Sciences. 50 (4): 672–679. Bibcode:1963PNAS...50..672M. doi:10.1073/pnas.50.4.672. PMC 221244. PMID 14077496.
  7. Zuckerkandl, E; Pauling, LB (1965). "Evolutionary Divergence and Convergence in Proteins". Evolving Genes and And Proteins: 96–166. doi:10.1016/B978-1-4832-2734-4.50017-6. ISBN 9781483227344.
  8. Eck, R. V.; Dayhoff, M. O. (15 April 1966). "Evolution of the Structure of Ferredoxin Based on Living Relics of Primitive Amino Acid Sequences". Science. 152 (3720): 363–366. Bibcode:1966Sci...152..363E. doi:10.1126/science.152.3720.363. PMID 17775169. S2CID 23208558.
  9. Kimura, M (17 February 1968). "Evolutionary Rate at the Molecular Level". Nature. 217 (5129): 624–626. Bibcode:1968Natur.217..624K. doi:10.1038/217624a0. PMID 5637732. S2CID 4161261.
  10. King, J. L.; Jukes, T. H. (16 May 1969). "Non-Darwinian Evolution". Science. 164 (3881): 788–798. Bibcode:1969Sci...164..788L. doi:10.1126/science.164.3881.788. PMID 5767777.
  11. Kimura, M; Ohta, T (1974). "On Some Principles Governing Molecular Evolution". Proc Natl Acad Sci USA. 71 (7): 2848–2852. Bibcode:1974PNAS...71.2848K. doi:10.1073/pnas.71.7.2848. PMC 388569. PMID 4527913.
  12. Asthana, Saurabh; Roytberg, Mikhail; Stamatoyannopoulos, John; Sunyaev, Shamil (28 December 2007). Brudno, Michael (ed.). "Analysis of Sequence Conservation at Nucleotide Resolution". PLOS Computational Biology. 3 (12): e254. Bibcode:2007PLSCB...3..254A. doi:10.1371/journal.pcbi.0030254. ISSN 1553-7358. PMC 2230682. PMID 18166073.
  13. Cooper, G. M.; Brown, C. D. (1 February 2008). "Qualifying the relationship between sequence conservation and molecular function". Genome Research. 18 (2): 201–205. doi:10.1101/gr.7205808. ISSN 1088-9051. PMID 18245453.
  14. Gilson, Amy I.; Marshall-Christensen, Ahmee; Choi, Jeong-Mo; Shakhnovich, Eugene I. (2017). "The Role of Evolutionary Selection in the Dynamics of Protein Structure Evolution". Biophysical Journal. 112 (7): 1350–1365. arXiv:1606.05802. Bibcode:2017BpJ...112.1350G. doi:10.1016/j.bpj.2017.02.029. PMC 5390048. PMID 28402878.
  15. Hunt, Ryan C.; Simhadri, Vijaya L.; Iandoli, Matthew; Sauna, Zuben E.; Kimchi-Sarfaty, Chava (2014). "Exposing synonymous mutations". Trends in Genetics. 30 (7): 308–321. doi:10.1016/j.tig.2014.04.006. PMID 24954581.
  16. Zhang, Jianzhi (2000). "Rates of Conservative and Radical Nonsynonymous Nucleotide Substitutions in Mammalian Nuclear Genes". Journal of Molecular Evolution. 50 (1): 56–68. Bibcode:2000JMolE..50...56Z. doi:10.1007/s002399910007. ISSN 0022-2844. PMID 10654260. S2CID 15248867.
  17. Sousounis, Konstantinos; Haney, Carl E; Cao, Jin; Sunchu, Bharath; Tsonis, Panagiotis A (2012). "Conservation of the three-dimensional structure in non-homologous or unrelated proteins". Human Genomics. 6 (1): 10. doi:10.1186/1479-7364-6-10. ISSN 1479-7364. PMC 3500211. PMID 23244440.
  18. Kairys, Visvaldas; Fernandes, Miguel X. (2007). "SitCon: Binding site residue conservation visualization and protein sequence-to-function tool". International Journal of Quantum Chemistry. 107 (11): 2100–2110. Bibcode:2007IJQC..107.2100K. doi:10.1002/qua.21396. hdl:10400.13/5004. ISSN 0020-7608.
  19. Chamary, JV; Hurst, Laurence D (2005). "Evidence for selection on synonymous mutations affecting stability of mRNA secondary structure in mammals". Genome Biology. 6 (9): R75. doi:10.1186/gb-2005-6-9-r75. PMC 1242210. PMID 16168082.
  20. Wadler, C. S.; Vanderpool, C. K. (27 November 2007). "A dual function for a bacterial small RNA: SgrS performs base pairing-dependent regulation and encodes a functional polypeptide". Proceedings of the National Academy of Sciences. 104 (51): 20454–20459. Bibcode:2007PNAS..10420454W. doi:10.1073/pnas.0708102104. PMC 2154452. PMID 18042713.
  21. Johnsson, Per; Lipovich, Leonard; Grandér, Dan; Morris, Kevin V. (March 2014). "Evolutionary conservation of long non-coding RNAs; sequence, structure, function". Biochimica et Biophysica Acta (BBA) - General Subjects. 1840 (3): 1063–1071. doi:10.1016/j.bbagen.2013.10.035. PMC 3909678. PMID 24184936.
  22. Freyhult, E. K.; Bollback, J. P.; Gardner, P. P. (6 December 2006). "Exploring genomic dark matter: A critical assessment of the performance of homology search methods on noncoding RNA". Genome Research. 17 (1): 117–125. doi:10.1101/gr.5890907. PMC 1716261. PMID 17151342.
  23. Margulies, E. H. (1 December 2003). "Identification and Characterization of Multi-Species Conserved Sequences". Genome Research. 13 (12): 2507–2518. doi:10.1101/gr.1602203. ISSN 1088-9051. PMC 403793. PMID 14656959.
  24. Edwards, John R.; Ruparel, Hameer; Ju, Jingyue (2005). "Mass-spectrometry DNA sequencing". Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis. 573 (1–2): 3–12. Bibcode:2005MRFMM.573....3E. doi:10.1016/j.mrfmmm.2004.07.021. PMID 15829234.
  25. Drost, Hajk-Georg; Gabel, Alexander; Grosse, Ivo; Quint, Marcel (1 May 2015). "Evidence for Active Maintenance of Phylotranscriptomic Hourglass Patterns in Animal and Plant Embryogenesis". Molecular Biology and Evolution. 32 (5): 1221–1231. doi:10.1093/molbev/msv012. ISSN 0737-4038. PMC 4408408. PMID 25631928.
  26. Nawrocki, E. P.; Eddy, S. R. (4 September 2013). "Infernal 1.1: 100-fold faster RNA homology searches". Bioinformatics. 29 (22): 2933–2935. doi:10.1093/bioinformatics/btt509. PMC 3810854. PMID 24008419.
  27. Eddy, SR; Durbin, R (11 June 1994). "RNA sequence analysis using covariance models". Nucleic Acids Research. 22 (11): 2079–88. doi:10.1093/nar/22.11.2079. PMC 308124. PMID 8029015.
  28. Trivedi, Rakesh; Nagarajaram, Hampapathalu Adimurthy (2020). "Substitution scoring matrices for proteins - An overview". Protein Science. 29 (11): 2150–2163. doi:10.1002/pro.3954. ISSN 0961-8368. PMC 7586916. PMID 32954566.
  29. ^ "Weblogo". UC Berkeley. Retrieved 30 December 2017.
  30. "Clustal FAQ #Symbols". Clustal. Archived from the original on 24 October 2016. Retrieved 8 December 2014.
  31. "ECR Browser". ECR Browser. Retrieved 9 January 2018.
  32. Earl, Dent; Nguyen, Ngan; Hickey, Glenn; Harris, Robert S.; Fitzgerald, Stephen; Beal, Kathryn; Seledtsov, Igor; Molodtsov, Vladimir; Raney, Brian J.; Clawson, Hiram; Kim, Jaebum; Kemena, Carsten; Chang, Jia-Ming; Erb, Ionas; Poliakov, Alexander; Hou, Minmei; Herrero, Javier; Kent, William James; Solovyev, Victor; Darling, Aaron E.; Ma, Jian; Notredame, Cedric; Brudno, Michael; Dubchak, Inna; Haussler, David; Paten, Benedict (December 2014). "Alignathon: a competitive assessment of whole-genome alignment methods". Genome Research. 24 (12): 2077–2089. doi:10.1101/gr.174920.114. PMC 4248324. PMID 25273068.
  33. Rouli, L.; Merhej, V.; Fournier, P.-E.; Raoult, D. (September 2015). "The bacterial pangenome as a new tool for analysing pathogenic bacteria". New Microbes and New Infections. 7: 72–85. doi:10.1016/j.nmni.2015.06.005. PMC 4552756. PMID 26442149.
  34. Méric, Guillaume; Yahara, Koji; Mageiros, Leonardos; Pascoe, Ben; Maiden, Martin C. J.; Jolley, Keith A.; Sheppard, Samuel K.; Bereswill, Stefan (27 March 2014). "A Reference Pan-Genome Approach to Comparative Bacterial Genomics: Identification of Novel Epidemiological Markers in Pathogenic Campylobacter". PLOS ONE. 9 (3): e92798. Bibcode:2014PLoSO...992798M. doi:10.1371/journal.pone.0092798. PMC 3968026. PMID 24676150.
  35. Cooper, G. M. (17 June 2005). "Distribution and intensity of constraint in mammalian genomic sequence". Genome Research. 15 (7): 901–913. doi:10.1101/gr.3577405. PMC 1172034. PMID 15965027.
  36. "Sidow Lab - GERP". Archived from the original on 14 January 2017. Retrieved 23 April 2016.
  37. Nawar Malhis; Steven J. M. Jones; Jörg Gsponer (2019). "Improved measures for evolutionary conservation that exploit taxonomy distances". Nature Communications. 10 (1): 1556. Bibcode:2019NatCo..10.1556M. doi:10.1038/s41467-019-09583-2. PMC 6450959. PMID 30952844.
  38. Nawar Malhis; Matthew Jacobson; Steven J. M. Jones; Jörg Gsponer (2020). "LIST-S2: Taxonomy Based Sorting of Deleterious Missense Mutations Across Species". Nucleic Acids Research. 48 (W1): W154–W161. doi:10.1093/nar/gkaa288. PMC 7319545. PMID 32352516.
  39. Chang KT, Guo J, di Ronza A, Sardiello M (January 2018). "Aminode: Identification of Evolutionary Constraints in the Human Proteome". Sci. Rep. 8 (1): 1357. Bibcode:2018NatSR...8.1357C. doi:10.1038/s41598-018-19744-w. PMC 5778061. PMID 29358731.
  40. Pollard, K. S.; Hubisz, M. J.; Rosenbloom, K. R.; Siepel, A. (26 October 2009). "Detection of nonneutral substitution rates on mammalian phylogenies". Genome Research. 20 (1): 110–121. doi:10.1101/gr.097857.109. PMC 2798823. PMID 19858363.
  41. "PHAST: Home".
  42. Fan, Xiaodan; Zhu, Jun; Schadt, Eric E; Liu, Jun S (2007). "Statistical power of phylo-HMM for evolutionarily conserved element detection". BMC Bioinformatics. 8 (1): 374. doi:10.1186/1471-2105-8-374. PMC 2194792. PMID 17919331.
  43. Bejerano, G. (28 May 2004). "Ultraconserved Elements in the Human Genome". Science. 304 (5675): 1321–1325. Bibcode:2004Sci...304.1321B. CiteSeerX 10.1.1.380.9305. doi:10.1126/science.1098119. PMID 15131266. S2CID 2790337.
  44. Siepel, A. (1 August 2005). "Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes". Genome Research. 15 (8): 1034–1050. doi:10.1101/gr.3715005. PMC 1182216. PMID 16024819.
  45. Harmston, N.; Baresic, A.; Lenhard, B. (11 November 2013). "The mystery of extreme non-coding conservation". Philosophical Transactions of the Royal Society B: Biological Sciences. 368 (1632): 20130021. doi:10.1098/rstb.2013.0021. PMC 3826495. PMID 24218634.
  46. Faircloth, B. C.; McCormack, J. E.; Crawford, N. G.; Harvey, M. G.; Brumfield, R. T.; Glenn, T. C. (9 January 2012). "Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales". Systematic Biology. 61 (5): 717–726. doi:10.1093/sysbio/sys004. PMID 22232343.
  47. Faircloth, Brant C.; Branstetter, Michael G.; White, Noor D.; Brady, Seán G. (May 2015). "Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among Hymenoptera". Molecular Ecology Resources. 15 (3): 489–501. doi:10.1111/1755-0998.12328. PMC 4407909. PMID 25207863.
  48. Reneker, J.; Lyons, E.; Conant, G. C.; Pires, J. C.; Freeling, M.; Shyu, C.-R.; Korkin, D. (10 April 2012). "Long identical multispecies elements in plant and animal genomes". Proceedings of the National Academy of Sciences. 109 (19): E1183–E1191. doi:10.1073/pnas.1121356109. PMC 3358895. PMID 22496592.
  49. Isenbarger, Thomas A.; Carr, Christopher E.; Johnson, Sarah Stewart; Finney, Michael; Church, George M.; Gilbert, Walter; Zuber, Maria T.; Ruvkun, Gary (14 October 2008). "The Most Conserved Genome Segments for Life Detection on Earth and Other Planets". Origins of Life and Evolution of Biospheres. 38 (6): 517–533. Bibcode:2008OLEB...38..517I. doi:10.1007/s11084-008-9148-z. PMID 18853276. S2CID 15707806.
  50. Harris, J. K. (12 February 2003). "The Genetic Core of the Universal Ancestor". Genome Research. 13 (3): 407–412. doi:10.1101/gr.652803. PMC 430263. PMID 12618371.
  51. Ban, Nenad; Beckmann, Roland; Cate, Jamie HD; Dinman, Jonathan D; Dragon, François; Ellis, Steven R; Lafontaine, Denis LJ; Lindahl, Lasse; Liljas, Anders; Lipton, Jeffrey M; McAlear, Michael A; Moore, Peter B; Noller, Harry F; Ortega, Joaquin; Panse, Vikram Govind; Ramakrishnan, V; Spahn, Christian MT; Steitz, Thomas A; Tchorzewski, Marek; Tollervey, David; Warren, Alan J; Williamson, James R; Wilson, Daniel; Yonath, Ada; Yusupov, Marat (February 2014). "A new system for naming ribosomal proteins". Current Opinion in Structural Biology. 24: 165–169. doi:10.1016/j.sbi.2014.01.002. PMC 4358319. PMID 24524803.
  52. Gadagkar, Sudhindra R.; Rosenberg, Michael S.; Kumar, Sudhir (15 January 2005). "Inferring species phylogenies from multiple genes: Concatenated sequence tree versus consensus gene tree". Journal of Experimental Zoology Part B: Molecular and Developmental Evolution. 304B (1): 64–74. Bibcode:2005JEZB..304...64G. doi:10.1002/jez.b.21026. PMID 15593277.
  53. Ludwig, W; Schleifer, KH (October 1994). "Bacterial phylogeny based on 16S and 23S rRNA sequence analysis". FEMS Microbiology Reviews. 15 (2–3): 155–73. doi:10.1111/j.1574-6976.1994.tb00132.x. PMID 7524576.
  54. Hug, Laura A.; Baker, Brett J.; Anantharaman, Karthik; Brown, Christopher T.; Probst, Alexander J.; Castelle, Cindy J.; Butterfield, Cristina N.; Hernsdorf, Alex W.; Amano, Yuki; Ise, Kotaro; Suzuki, Yohey; Dudek, Natasha; Relman, David A.; Finstad, Kari M.; Amundson, Ronald; Thomas, Brian C.; Banfield, Jillian F. (11 April 2016). "A new view of the tree of life". Nature Microbiology. 1 (5): 16048. doi:10.1038/nmicrobiol.2016.48. PMID 27572647.
  55. Zhang, Liqing; Li, Wen-Hsiung (February 2004). "Mammalian Housekeeping Genes Evolve More Slowly than Tissue-Specific Genes". Molecular Biology and Evolution. 21 (2): 236–239. doi:10.1093/molbev/msh010. PMID 14595094.
  56. Clermont, O.; Bonacorsi, S.; Bingen, E. (1 October 2000). "Rapid and Simple Determination of the Escherichia coli Phylogenetic Group". Applied and Environmental Microbiology. 66 (10): 4555–4558. Bibcode:2000ApEnM..66.4555C. doi:10.1128/AEM.66.10.4555-4558.2000. PMC 92342. PMID 11010916.
  57. Kullberg, Morgan; Nilsson, Maria A.; Arnason, Ulfur; Harley, Eric H.; Janke, Axel (August 2006). "Housekeeping Genes for Phylogenetic Analysis of Eutherian Relationships". Molecular Biology and Evolution. 23 (8): 1493–1503. doi:10.1093/molbev/msl027. PMID 16751257.
  58. Schoch, C. L.; Seifert, K. A.; Huhndorf, S.; Robert, V.; Spouge, J. L.; Levesque, C. A.; Chen, W.; Bolchacova, E.; Voigt, K.; Crous, P. W.; Miller, A. N.; Wingfield, M. J.; Aime, M. C.; An, K.-D.; Bai, F.-Y.; Barreto, R. W.; Begerow, D.; Bergeron, M.-J.; Blackwell, M.; Boekhout, T.; Bogale, M.; Boonyuen, N.; Burgaz, A. R.; Buyck, B.; Cai, L.; Cai, Q.; Cardinali, G.; Chaverri, P.; Coppins, B. J.; Crespo, A.; Cubas, P.; Cummings, C.; Damm, U.; de Beer, Z. W.; de Hoog, G. S.; Del-Prado, R.; Dentinger, B.; Dieguez-Uribeondo, J.; Divakar, P. K.; Douglas, B.; Duenas, M.; Duong, T. A.; Eberhardt, U.; Edwards, J. E.; Elshahed, M. S.; Fliegerova, K.; Furtado, M.; Garcia, M. A.; Ge, Z.-W.; Griffith, G. W.; Griffiths, K.; Groenewald, J. Z.; Groenewald, M.; Grube, M.; Gryzenhout, M.; Guo, L.-D.; Hagen, F.; Hambleton, S.; Hamelin, R. C.; Hansen, K.; Harrold, P.; Heller, G.; Herrera, C.; Hirayama, K.; Hirooka, Y.; Ho, H.-M.; Hoffmann, K.; Hofstetter, V.; Hognabba, F.; Hollingsworth, P. M.; Hong, S.-B.; Hosaka, K.; Houbraken, J.; Hughes, K.; Huhtinen, S.; Hyde, K. D.; James, T.; Johnson, E. M.; Johnson, J. E.; Johnston, P. R.; Jones, E. B. G.; Kelly, L. J.; Kirk, P. M.; Knapp, D. G.; Koljalg, U.; Kovacs, G. M.; Kurtzman, C. P.; Landvik, S.; Leavitt, S. D.; Liggenstoffer, A. S.; Liimatainen, K.; Lombard, L.; Luangsa-ard, J. J.; Lumbsch, H. T.; Maganti, H.; Maharachchikumbura, S. S. N.; Martin, M. P.; May, T. W.; McTaggart, A. R.; Methven, A. S.; Meyer, W.; Moncalvo, J.-M.; Mongkolsamrit, S.; Nagy, L. G.; Nilsson, R. H.; Niskanen, T.; Nyilasi, I.; Okada, G.; Okane, I.; Olariaga, I.; Otte, J.; Papp, T.; Park, D.; Petkovits, T.; Pino-Bodas, R.; Quaedvlieg, W.; Raja, H. A.; Redecker, D.; Rintoul, T. L.; Ruibal, C.; Sarmiento-Ramirez, J. M.; Schmitt, I.; Schussler, A.; Shearer, C.; Sotome, K.; Stefani, F. O. P.; Stenroos, S.; Stielow, B.; Stockinger, H.; Suetrong, S.; Suh, S.-O.; Sung, G.-H.; Suzuki, M.; Tanaka, K.; Tedersoo, L.; Telleria, M. T.; Tretter, E.; Untereiner, W. A.; Urbina, H.; Vagvolgyi, C.; Vialle, A.; Vu, T. D.; Walther, G.; Wang, Q.-M.; Wang, Y.; Weir, B. S.; Weiss, M.; White, M. M.; Xu, J.; Yahr, R.; Yang, Z. L.; Yurkov, A.; Zamora, J.-C.; Zhang, N.; Zhuang, W.-Y.; Schindel, D. (27 March 2012). "Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi". Proceedings of the National Academy of Sciences. 109 (16): 6241–6246. doi:10.1073/pnas.1117018109. PMC 3341068. PMID 22454494.
  59. Man, S. M.; Kaakoush, N. O.; Octavia, S.; Mitchell, H. (26 March 2010). "The Internal Transcribed Spacer Region, a New Tool for Use in Species Differentiation and Delineation of Systematic Relationships within the Campylobacter Genus". Applied and Environmental Microbiology. 76 (10): 3071–3081. Bibcode:2010ApEnM..76.3071M. doi:10.1128/AEM.02551-09. PMC 2869123. PMID 20348308.
  60. Ranjard, L.; Poly, F.; Lata, J.-C.; Mougel, C.; Thioulouse, J.; Nazaret, S. (1 October 2001). "Characterization of Bacterial and Fungal Soil Communities by Automated Ribosomal Intergenic Spacer Analysis Fingerprints: Biological and Methodological Variability". Applied and Environmental Microbiology. 67 (10): 4479–4487. Bibcode:2001ApEnM..67.4479R. doi:10.1128/AEM.67.10.4479-4487.2001. PMC 93193. PMID 11571146.
  61. Bidet, Philippe; Barbut, Frédéric; Lalande, Valérie; Burghoffer, Béatrice; Petit, Jean-Claude (June 1999). "Development of a new PCR-ribotyping method for based on ribosomal RNA gene sequencing". FEMS Microbiology Letters. 175 (2): 261–266. doi:10.1111/j.1574-6968.1999.tb13629.x. PMID 10386377.
  62. Ala, Ugo; Piro, Rosario Michael; Grassi, Elena; Damasco, Christian; Silengo, Lorenzo; Oti, Martin; Provero, Paolo; Di Cunto, Ferdinando; Tucker-Kellogg, Greg (28 March 2008). "Prediction of Human Disease Genes by Human-Mouse Conserved Coexpression Analysis". PLOS Computational Biology. 4 (3): e1000043. Bibcode:2008PLSCB...4E0043A. doi:10.1371/journal.pcbi.1000043. PMC 2268251. PMID 18369433.
  63. Pandey, U. B.; Nichols, C. D. (17 March 2011). "Human Disease Models in Drosophila melanogaster and the Role of the Fly in Therapeutic Drug Discovery". Pharmacological Reviews. 63 (2): 411–436. doi:10.1124/pr.110.003293. PMC 3082451. PMID 21415126.
  64. Huang, Hui; Winter, Eitan E; Wang, Huajun; Weinstock, Keith G; Xing, Heming; Goodstadt, Leo; Stenson, Peter D; Cooper, David N; Smith, Douglas; Albà, M Mar; Ponting, Chris P; Fechtel, Kim (2004). "Evolutionary conservation and selection of human disease gene orthologs in the rat and mouse genomes". Genome Biology. 5 (7): R47. doi:10.1186/gb-2004-5-7-r47. PMC 463309. PMID 15239832.
  65. Ge, Dongliang; Fellay, Jacques; Thompson, Alexander J.; Simon, Jason S.; Shianna, Kevin V.; Urban, Thomas J.; Heinzen, Erin L.; Qiu, Ping; Bertelsen, Arthur H.; Muir, Andrew J.; Sulkowski, Mark; McHutchison, John G.; Goldstein, David B. (16 August 2009). "Genetic variation in IL28B predicts hepatitis C treatment-induced viral clearance". Nature. 461 (7262): 399–401. Bibcode:2009Natur.461..399G. doi:10.1038/nature08309. PMID 19684573. S2CID 1707096.
  66. Bertram, L. (2009). "Genome-wide association studies in Alzheimer's disease". Human Molecular Genetics. 18 (R2): R137–R145. doi:10.1093/hmg/ddp406. PMC 2758713. PMID 19808789.
  67. Kellis, Manolis; Patterson, Nick; Endrizzi, Matthew; Birren, Bruce; Lander, Eric S. (15 May 2003). "Sequencing and comparison of yeast species to identify genes and regulatory elements". Nature. 423 (6937): 241–254. Bibcode:2003Natur.423..241K. doi:10.1038/nature01644. PMID 12748633. S2CID 1530261.
  68. Marchler-Bauer, A.; Lu, S.; Anderson, J. B.; Chitsaz, F.; Derbyshire, M. K.; DeWeese-Scott, C.; Fong, J. H.; Geer, L. Y.; Geer, R. C.; Gonzales, N. R.; Gwadz, M.; Hurwitz, D. I.; Jackson, J. D.; Ke, Z.; Lanczycki, C. J.; Lu, F.; Marchler, G. H.; Mullokandov, M.; Omelchenko, M. V.; Robertson, C. L.; Song, J. S.; Thanki, N.; Yamashita, R. A.; Zhang, D.; Zhang, N.; Zheng, C.; Bryant, S. H. (24 November 2010). "CDD: a Conserved Domain Database for the functional annotation of proteins". Nucleic Acids Research. 39 (Database): D225–D229. doi:10.1093/nar/gkq1189. PMC 3013737. PMID 21109532.

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