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31:
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happened in the LCA of the organisms being compared. The example above is an example alloparalogy. Symparalogs are paralogs that evolved from gene duplication of paralogous genes in subsequent speciation events. From the example above, if the descendant with genes A1 and B underwent another speciation event where gene A1 duplicated, the new species would have genes B, A1a, and A1b. In this example, genes A1a and A1b are symparalogs.
521:: GudB is constitutively transcribed whereas RocG is tightly regulated. In their active, oligomeric states, both enzymes show similar enzymatic rates. However, swaps of enzymes and promoters cause severe fitness losses, thus indicating promoter–enzyme coevolution. Characterization of the proteins shows that, compared to RocG, GudB's enzymatic activity is highly dependent on glutamate and pH.
125:
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Then in a separate speciation event, one environment will favor a mutation in gene B (gene B1) giving rise to a new species with genes A and B1. The descendants' genes A1 and B1 are paralogous to each other because they are homologs that are related via a duplication event in the last common ancestor of the two species.
172:, is usually used to "quantify the homology." Based on the definition of homology specified above this terminology is incorrect since sequence similarity is the observation, homology is the conclusion. Sequences are either homologous or not. This involves that the term "percent homology" is a misnomer.
668:
by Ken Wolfe. Ohnologues are useful for evolutionary analysis because all ohnologues in a genome have been diverging for the same length of time (since their common origin in the whole genome duplication). Ohnologues are also known to show greater association with cancers, dominant genetic disorders,
292:
Orthologous sequences provide useful information in taxonomic classification and phylogenetic studies of organisms. The pattern of genetic divergence can be used to trace the relatedness of organisms. Two organisms that are very closely related are likely to display very similar DNA sequences between
415:
As an example, in the LCA, one gene (gene A) may get duplicated to make a separate similar gene (gene B), those two genes will continue to get passed to subsequent generations. During speciation, one environment will favor a mutation in gene A (gene A1), producing a new species with genes A1 and B.
317:
methods. Sequence comparison methods were first pioneered in the COGs database in 1997. These methods have been extended and automated in twelve different databases the most advanced being AYbRAH Analyzing Yeasts by
Reconstructing Ancestry of Homologs as well as these following databases right now.
992:
Where the homology is the result of gene duplication so that both copies have descended side by side during the history of an organism (for example, a and b hemoglobin) the genes should be called paralogous (para = in parallel). Where the homology is the result of speciation so that the history of
491:) are paralogs of each other. While each of these proteins serves the same basic function of oxygen transport, they have already diverged slightly in function: fetal hemoglobin (hemoglobin F) has a higher affinity for oxygen than adult hemoglobin. Function is not always conserved, however. Human
419:
Additional classifications of paralogs include alloparalogs (out-paralogs) and symparalogs (in-paralogs). Alloparalogs are paralogs that evolved from gene duplications that preceded the given speciation event. In other words, alloparalogs are paralogs that evolved from duplication events that
681:
between two organisms are termed xenologs. Xenologs can have different functions if the new environment is vastly different for the horizontally moving gene. In general, though, xenologs typically have similar function in both organisms. The term was coined by Walter Fitch.
234:
event: when a species diverges into two separate species, the copies of a single gene in the two resulting species are said to be orthologous. Orthologs, or orthologous genes, are genes in different species that originated by vertical descent from a single gene of the
412:(LCA) of the species being compared. They result from the mutation of duplicated genes during separate speciation events. When descendants from the LCA share mutated homologs of the original duplicated genes then those genes are considered paralogs.
288:
and genome rearrangement events, the strongest evidence that two similar genes are orthologous is usually found by carrying out phylogenetic analysis of the gene lineage. Orthologs often, but not always, have the same function.
534:. Sets of duplicated, triplicated and quadruplicated genes, with the related genes on different chromosomes, are deduced to be remnants from genome or chromosomal duplications. A set of paralogy regions is together called a
529:
Sometimes, large regions of chromosomes share gene content similar to other chromosomal regions within the same genome. They are well characterised in the human genome, where they have been used as evidence to support the
510:
Paralogs are often regulated differently, e.g. by having different tissue-specific expression patterns (see Hox genes). However, they can also be regulated differently on the protein level. For instance,
706:, leading to disomic inheritance; however in some allopolyploids, the homoeologous chromosomes of the parental genomes may be nearly as similar to one another as the homologous chromosomes, leading to
293:
two orthologs. Conversely, an organism that is further removed evolutionarily from another organism is likely to display a greater divergence in the sequence of the orthologs being studied.
269:
version is more complex: it crosses the membrane twice rather than once, contains additional domains and undergoes alternative splicing. However it can fully substitute the much simpler
702:, and whose relationship was completely homologous in an ancestral species. In allopolyploids, the homologous chromosomes within each parental sub-genome should pair faithfully during
881:
Reeck GR, de Haën C, Teller DC, Doolittle RF, Fitch WM, Dickerson RE, et al. (August 1987). ""Homology" in proteins and nucleic acids: a terminology muddle and a way out of it".
373:
approaches aim to distinguish speciation from gene duplication events by comparing gene trees with species trees, as implemented in databases and software tools such as:
926:"Protein Similarity Score: A Simplified Version of the Blast Score as a Superior Alternative to Percent Identity for Claiming Genuses of Related Protein Sequences"
309:
that provide tools to identify and analyze orthologous gene sequences. These resources employ approaches that can be generally classified into those that use
187:
sequences, where the amino acid at a specific position has been substituted with a different one that has functionally equivalent physicochemical properties.
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190:
Partial homology can occur where a segment of the compared sequences has a shared origin, while the rest does not. Such partial homology may result from a
112:
sequence similarity. Significant similarity is strong evidence that two sequences are related by evolutionary changes from a common ancestral sequence.
502:
It is often asserted that orthologs are more functionally similar than paralogs of similar divergence, but several papers have challenged this notion.
55:
1521:"Identification of Ohnolog Genes Originating from Whole Genome Duplication in Early Vertebrates, Based on Synteny Comparison across Multiple Genomes"
1604:"The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces"
284:
Orthology is strictly defined in terms of ancestry. Given that the exact ancestry of genes in different organisms is difficult to ascertain due to
1219:"eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations"
993:
the gene reflects the history of the species (for example a hemoglobin in man and mouse) the genes should be called orthologous (ortho = exact).
433:
are organized in sets of paralogs. Each Hox cluster (HoxA, HoxB, etc.) is on a different chromosome. For instance, the human HoxA cluster is on
347:
appreciates that the orthology concept is relative to different speciation points by providing a hierarchy of orthologs along the species tree.
1813:
389:
A third category of hybrid approaches uses both heuristic and phylogenetic methods to construct clusters and determine trees, for example:
499:, for example, and while the two paralogs remain similar in tertiary structure, their functions within the cell are now quite different.
2753:
Lundin LG (April 1993). "Evolution of the vertebrate genome as reflected in paralogous chromosomal regions in man and the house mouse".
457:. As a result, Hox genes in most vertebrates are clustered across multiple chromosomes with the HoxA-D clusters being the best studied.
277:. Significant sequence similarity and shared functional domains indicate that these two genes are orthologous genes, inherited from the
2064:
1653:"OrthoDB v9.1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs"
441:
Paralogous genes can shape the structure of whole genomes and thus explain genome evolution to a large extent. Examples include the
563:
550:
genes and other duplicated genes, regions of human chromosomes 4, 5, 8 and 10 containing neuropeptide receptor genes, NK class
2801:
179:, or, as with shorter sequences, by chance, meaning that they are not homologous. Homologous sequence regions are also called
50:). A speciation event produces orthologs in the two daughter species (human and chimpanzee). Bottom: in a separate species (
3552:
230:
Homologous sequences are orthologous if they are inferred to be descended from the same ancestral sequence separated by a
336:
is a repository of the genes retained from whole genome duplications in the vertebrate genomes including human and mouse.
218:
in the two daughter species. Bottom: in a separate species, an unrelated gene has a similar function (Gene C) but has a
86:
1943:"OrthoMaM v10: Scaling-Up Orthologous Coding Sequence and Exon Alignments with More than One Hundred Mammalian Genomes"
1007:"The FLP proteins act as regulators of chlorophyll synthesis in response to light and plastid signals in Chlamydomonas"
156:
The term "percent homology" is often used to mean "sequence similarity”, that is the percentage of identical residues (
1796:
Egan M, Lee EK, Chiu JC, Coruzzi G, Desalle R (2009). "Gene orthology assessment with
OrthologID". In Posada D (ed.).
2860:"Ancient large-scale genome duplications: phylogenetic and linkage analyses shed light on chordate genome evolution"
3508:"Rooting a phylogeny with homologous genes on opposite sex chromosomes (gametologs): a case study using avian CHD"
690:
Homoeologous (also spelled homeologous) chromosomes or parts of chromosomes are those brought together following
140:
of the proteins. Residues that are conserved across all sequences are highlighted in grey. The key below denotes
82:
2690:
727:
678:
616:
98:
3107:
McLysaght A, Hokamp K, Wolfe KH (June 2002). "Extensive genomic duplication during early chordate evolution".
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Ruddle FH, Bentley KL, Murtha MT, Risch N (1994). "Gene loss and gain in the evolution of the vertebrates".
726:. The term was coined by GarcĂa-Moreno and Mindell. 2000. Gametologs result from the origination of genetic
699:
518:
3557:
2406:"GeneSeqToFamily: a Galaxy workflow to find gene families based on the Ensembl Compara GeneTrees pipeline"
2045:"Using OrthoMCL to assign proteins to OrthoMCL-DB groups or to cluster proteomes into new ortholog groups"
465:
1651:
Zdobnov EM, Tegenfeldt F, Kuznetsov D, Waterhouse RM, SimĂŁo FA, Ioannidis P, et al. (January 2017).
2901:"Early vertebrate chromosome duplications and the evolution of the neuropeptide Y receptor gene regions"
711:
145:
1902:"OrthoMaM v8: a database of orthologous exons and coding sequences for comparative genomics in mammals"
538:. Well-studied sets of paralogy regions include regions of human chromosome 2, 7, 12 and 17 containing
202:
1602:
Altenhoff AM, Glover NM, Train CM, Kaleb K, Warwick
Vesztrocy A, Dylus D, et al. (January 2018).
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3195:"On the expansion of "dangerous" gene repertoires by whole-genome duplications in early vertebrates"
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Powell S, Forslund K, Szklarczyk D, Trachana K, Roth A, Huerta-Cepas J, et al. (January 2014).
30:
778:
274:
240:
2706:"Bacilli glutamate dehydrogenases diverged via coevolution of transcription and enzyme regulation"
1166:"AYbRAH: a curated ortholog database for yeasts and fungi spanning 600 million years of evolution"
1005:
Falciatore A, Merendino L, Barneche F, Ceol M, Meskauskiene R, Apel K, Rochaix JD (January 2005).
3332:
McLysaght A, Makino T, Grayton HM, Tropeano M, Mitchell KJ, Vassos E, Collier DA (January 2014).
3275:"Human dominant disease genes are enriched in paralogs originating from whole genome duplication"
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113:
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Larsson TA, Olsson F, Sundstrom G, Lundin LG, Brenner S, Venkatesh B, Larhammar D (June 2008).
2691:"Special Guest Post & Discussion Invitation from Matthew Hahn on Ortholog Conjecture Paper"
2556:
Zakany J, Duboule D (August 2007). "The role of Hox genes during vertebrate limb development".
1421:
Ostlund G, Schmitt T, Forslund K, Köstler T, Messina DN, Roopra S, et al. (January 2010).
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Douzery EJ, Scornavacca C, Romiguier J, Belkhir K, Galtier N, Delsuc F, Ranwez V (July 2014).
1882:
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59:
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1757:"OrthologID: automation of genome-scale ortholog identification within a parsimony framework"
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and are considered to be ancient paralogs. Similarly, the four known classes of hemoglobins (
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3068:"Comparative genomics of the MHC: glimpses into the evolution of the adaptive immune system"
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Sayers EW, Barrett T, Benson DA, Bolton E, Bryant SH, Canese K, et al. (January 2011).
2425:
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As with morphological and anatomical structures, sequence similarity might occur because of
149:
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1941:
Scornavacca C, Belkhir K, Lopez J, Dernat R, Delsuc F, Douzery EJ, Ranwez V (April 2019).
1700:
Nevers Y, Kress A, Defosset A, Ripp R, Linard B, Thompson JD, et al. (January 2019).
735:
731:
723:
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Gametology denotes the relationship between homologous genes on non-recombining, opposite
661:
590:
353:
is a repository of orthologous genes for 4753 organisms covering the three domains of life
243:
116:
of multiple sequences are used to indicate which regions of each sequence are homologous.
3393:"Ohnologs in the human genome are dosage balanced and frequently associated with disease"
2357:"EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates"
1217:
Muller J, Szklarczyk D, Julien P, Letunic I, Roth A, Kuhn M, et al. (January 2010).
566:(MHC) on human chromosome 6 has paralogy regions on chromosomes 1, 9 and 19. Much of the
3408:
3349:
3290:
3024:
2916:
2647:
2592:
1858:
1843:"OrthoMaM: a database of orthologous genomic markers for placental mammal phylogenetics"
1536:
1368:
Rouard M, Guignon V, Aluome C, Laporte MA, Droc G, Walde C, et al. (January 2011).
1134:
1071:
925:
637:
A speciation event produces orthologs of a gene in the two daughter species. Subsequent
3480:
3451:
3427:
3392:
3368:
3333:
3309:
3274:
3043:
3008:
2935:
2900:
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2705:
2666:
2632:"Testing the ortholog conjecture with comparative functional genomic data from mammals"
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2479:
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302:
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2959:
2788:
Coulier F, Popovici C, Villet R, Birnbaum D (December 2000). "MetaHox gene clusters".
2043:
Fischer S, Brunk BP, Chen F, Gao X, Harb OS, Iodice JB, et al. (September 2011).
1031:
1006:
730:
and barriers to recombination between sex chromosomes. Examples of gametologs include
3546:
894:
747:
642:
555:
531:
480:
261:
3193:
Singh PP, Affeldt S, Cascone I, Selimoglu R, Camonis J, Isambert H (November 2012).
3179:
2993:
2836:
2120:
2103:
1773:
1756:
910:
160:), or the percentage of residues conserved with similar physicochemical properties (
89:. Two segments of DNA can have shared ancestry because of three phenomena: either a
3136:
1996:"OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups"
567:
496:
484:
476:
434:
370:
314:
78:
74:
47:
43:
3471:
2704:
Noda-Garcia L, Romero Romero ML, Longo LM, Kolodkin-Gal I, Tawfik DS (July 2017).
2355:
Vilella AJ, Severin J, Ureta-Vidal A, Heng L, Durbin R, Birney E (February 2009).
3299:
3211:
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383:
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Proceedings of the
National Academy of Sciences of the United States of America
3338:
Proceedings of the
National Academy of Sciences of the United States of America
3013:
Proceedings of the
National Academy of Sciences of the United States of America
2102:
Deluca TF, Wu IH, Pu J, Monaghan T, Peshkin L, Singh S, Wall DP (August 2006).
1841:
Ranwez V, Delsuc F, Ranwez S, Belkhir K, Tilak MK, Douzery EJ (November 2007).
3463:
3251:
2608:
2569:
2322:
1181:
492:
472:
450:
427:
231:
184:
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137:
109:
105:
90:
3236:"On the retention of gene duplicates prone to dominant deleterious mutations"
2202:
Ruan J, Li H, Chen Z, Coghlan A, Coin LJ, Guo Y, et al. (January 2008).
1800:. Methods in Molecular Biology. Vol. 537. Humana Press. pp. 23–38.
941:
3417:
3358:
3033:
2925:
2721:
2520:
2251:
Schreiber F, Patricio M, Muffato M, Pignatelli M, Bateman A (January 2014).
2104:"Roundup: a multi-genome repository of orthologs and evolutionary distances"
1958:
1918:
1901:
1867:
707:
468:
449:) genes in animals. These genes not only underwent gene duplications within
437:. The mouse HoxA cluster shown here has 11 paralogous genes (2 are missing).
310:
3533:
3489:
3436:
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3318:
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3093:
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2616:
2577:
2539:
2488:
2439:
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2341:
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2149:"Orthology prediction at scalable resolution by phylogenetic tree analysis"
2129:
2084:
2029:
1976:
1927:
1886:
1823:
1782:
1737:
1686:
1637:
1564:
1505:
1472:"InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic"
1456:
1403:
1354:
1301:
1252:
1199:
1099:
1040:
958:
Fitch WM (June 1970). "Distinguishing homologous from analogous proteins".
839:
423:
2885:
2844:
2774:
2593:"How confident can we be that orthologs are similar, but paralogs differ?"
2502:
Fulton DL, Li YY, Laird MR, Horsman BG, Roche FM, Brinkman FS (May 2006).
2470:
2372:
2268:
2219:
1718:
1668:
1619:
1487:
1423:"InParanoid 7: new algorithms and tools for eukaryotic orthology analysis"
1283:
1213:
eggNOG: evolutionary genealogy of genes: Non-supervised
Orthologous Groups
1150:
987:
902:
408:
Paralogous genes are genes that are related via duplication events in the
38:
as red and blue branches within grey species phylogeny. Top: An ancestral
17:
2455:"Database resources of the National Center for Biotechnology Information"
2011:
1755:
Chiu JC, Lee EK, Egan MG, Sarkar IN, Coruzzi GM, DeSalle R (March 2006).
1438:
1385:
1336:
1234:
788:
612:
543:
539:
446:
442:
430:
2306:"OrthoFinder: phylogenetic orthology inference for comparative genomics"
1022:
979:
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757:
703:
631:
559:
547:
344:
165:
133:
51:
1750:
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Homology among DNA, RNA, or proteins is typically inferred from their
2802:
10.1002/1097-010X(20001215)288:4<345::AID-JEZ7>3.0.CO;2-Y
1836:
768:
461:
3009:"Breakup of a homeobox cluster after genome duplication in teleosts"
1118:
1112:
971:
815:
605:
583:
3235:
2858:
PĂ©busque MJ, Coulier F, Birnbaum D, Pontarotti P (September 1998).
350:
3334:"Ohnologs are overrepresented in pathogenic copy number mutations"
3163:
3150:
Wolfe K (May 2000). "Robustness--it's not where you think it is".
3120:
2504:"Improving the specificity of high-throughput ortholog prediction"
2253:"TreeFam v9: a new website, more species and orthology-on-the-fly"
2097:
1990:
OrthoMCL: Identification of
Ortholog Groups for Eukaryotic Genomes
313:
analysis of all pairwise sequence comparisons, and those that use
278:
2960:"Evidence for 14 homeobox gene clusters in human genome ancestry"
2147:
van der
Heijden RT, Snel B, van Noort V, Huynen MA (March 2007).
1370:"GreenPhylDB v2.0: comparative and functional genomics in plants"
1319:
Conte MG, Gaillard S, Lanau N, Rouard M, PĂ©rin C (January 2008).
657:
2299:
1268:"eggNOG v4.0: nested orthology inference across 3686 organisms"
558:, and parts of human chromosomes 13, 4, 5 and X containing the
305:, orthologous genes have been organized in several specialized
273:
protein, if transferred from algae to plant genome by means of
1578:
333:
1314:
1056:"Getting started in gene orthology and functional analysis"
1054:
Fang G, Bhardwaj N, Robilotto R, Gerstein MB (March 2010).
2197:
2142:
1989:
1702:"OrthoInspector 3.0: open portal for comparative genomics"
3273:
Singh PP, Affeldt S, Malaguti G, Isambert H (July 2014).
1994:
Chen F, Mackey AJ, Stoeckert CJ, Roos DS (January 2006).
1212:
1321:"GreenPhylDB: a database for plant comparative genomics"
2404:
Thanki AS, Soranzo N, Haerty W, Davey RP (March 2018).
2630:
Nehrt NL, Clark WT, Radivojac P, Hahn MW (June 2011).
58:) but has a separate evolutionary origin and so is an
3452:"Homoeologs: What Are They and How Do We Infer Them?"
330:
InParanoid focuses on pairwise ortholog relationships
27:
Shared ancestry between DNA, RNA or protein sequences
710:(four chromosomes pairing at meiosis), intergenomic
3501:
3499:
301:Given their tremendous importance for biology and
183:. This is not to be confused with conservation in
1117:Tatusov RL, Koonin EV, Lipman DJ (October 1997).
953:
951:
1113:COGs: Clusters of Orthologous Groups of proteins
816:"Orthologs, paralogs, and evolutionary genomics"
239:. The term "ortholog" was coined in 1970 by the
3450:Glover NM, Redestig H, Dessimoz C (July 2016).
1164:Correia K, Yu SM, Mahadevan R (January 2019).
3506:GarcĂa-Moreno J, Mindell DP (December 2000).
3234:Malaguti G, Singh PP, Isambert H (May 2014).
2558:Current Opinion in Genetics & Development
214:(Genes A and B). A speciation event produces
85:, defined in terms of shared ancestry in the
8:
3007:Mulley JF, Chiu CH, Holland PW (July 2006).
809:
807:
805:
803:
570:seems to be assignable to paralogy regions.
1519:Singh PP, Arora J, Isambert H (July 2015).
1119:"A genomic perspective on protein families"
876:
874:
136:proteins. Sequences are the middle 120-180
2591:Studer RA, Robinson-Rechavi M (May 2009).
148:(:), semi-conservative mutations (.), and
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3426:
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3210:
3083:
3066:Flajnik MF, Kasahara M (September 2001).
3042:
3032:
2975:
2958:Pollard SL, Holland PW (September 2000).
2934:
2924:
2875:
2729:
2665:
2655:
2551:
2549:
2529:
2519:
2478:
2429:
2380:
2331:
2321:
2276:
2227:
2174:
2164:
2119:
2074:
2019:
1966:
1917:
1876:
1866:
1772:
1727:
1717:
1676:
1627:
1554:
1544:
1495:
1470:Sonnhammer EL, Ă–stlund G (January 2015).
1446:
1393:
1344:
1291:
1242:
1189:
1089:
1079:
1030:
619:event from one species to another adds a
615:of a gene in the two daughter species. A
56:histone-like nucleoid-structuring protein
1798:Bioinformatics for DNA Sequence Analysis
664:. The name was first given in honour of
422:
201:
123:
29:
930:Santa Clara High Technology Law Journal
799:
669:and pathogenic copy number variations.
2300:OrthoFinder: Orthologs from gene trees
1417:Inparanoid: Eukaryotic Ortholog Groups
832:10.1146/annurev.genet.39.073003.114725
120:Identity, similarity, and conservation
3525:10.1093/oxfordjournals.molbev.a026283
2877:10.1093/oxfordjournals.molbev.a026022
660:that have originated by a process of
99:horizontal (or lateral) gene transfer
7:
649:copy of each gene from both species.
2790:The Journal of Experimental Zoology
2049:Current Protocols in Bioinformatics
3563:Evolutionary developmental biology
3391:Makino T, McLysaght A (May 2010).
2304:Emms DM, Kelly S (November 2019).
54:), a gene has a similar function (
25:
2051:. Chapter 6 (1): Unit 6.12.1–19.
593:event produces a genome with two
259:(multicellular higher plant) and
656:Ohnologous genes are paralogous
630:
604:
582:
564:Major histocompatibility complex
3512:Molecular Biology and Evolution
2864:Molecular Biology and Evolution
2837:10.1242/dev.1994.Supplement.155
2198:TreeFam: Tree families database
2143:TreeFam: Tree families database
1947:Molecular Biology and Evolution
1906:Molecular Biology and Evolution
562:genes and their neighbors. The
265:(single cell green algae). The
3240:Theoretical Population Biology
525:Paralogous chromosomal regions
297:Databases of orthologous genes
1:
3472:10.1016/j.tplants.2016.02.005
3085:10.1016/S1074-7613(01)00198-4
2977:10.1016/S0960-9822(00)00676-X
2689:Eisen J (20 September 2011).
2121:10.1093/bioinformatics/btl286
1774:10.1093/bioinformatics/btk040
1380:(Database issue): D1095-102.
641:of those species generates a
3300:10.1371/journal.pcbi.1003754
3212:10.1016/j.celrep.2012.09.034
2657:10.1371/journal.pcbi.1002073
2057:10.1002/0471250953.bi0612s35
1546:10.1371/journal.pcbi.1004394
1433:(Database issue): D196-203.
1143:10.1126/science.278.5338.631
1081:10.1371/journal.pcbi.1000703
895:10.1016/0092-8674(87)90322-9
611:A speciation event produces
220:separate evolutionary origin
87:evolutionary history of life
2214:(Database issue): D735-40.
1806:10.1007/978-1-59745-251-9_2
692:inter-species hybridization
3579:
3279:PLOS Computational Biology
2636:PLOS Computational Biology
2465:(Database issue): D38-51.
2422:10.1093/gigascience/giy005
2263:(Database issue): D922-5.
2006:(Database issue): D363-8.
1525:PLOS Computational Biology
1482:(Database issue): D234-9.
1331:(Database issue): D991-8.
1278:(Database issue): D231-9.
1229:(Database issue): D190-5.
1060:PLOS Computational Biology
623:of the gene to its genome.
517:encodes two paralogues of
150:non-conservative mutations
3252:10.1016/j.tpb.2014.01.004
2609:10.1016/j.tig.2009.03.004
2570:10.1016/j.gde.2007.05.011
2323:10.1186/s13059-019-1832-y
924:Holman C (January 2004).
820:Annual Review of Genetics
714:, and reduced fertility.
455:whole genome duplications
2905:BMC Evolutionary Biology
1847:BMC Evolutionary Biology
679:horizontal gene transfer
677:Homologs resulting from
662:whole-genome duplication
617:horizontal gene transfer
591:whole genome duplication
460:Another example are the
393:EnsemblCompara GeneTrees
249:For instance, the plant
93:event (orthologs), or a
3456:Trends in Plant Science
3418:10.1073/pnas.0914697107
3359:10.1073/pnas.1309324111
3034:10.1073/pnas.0600341103
2926:10.1186/1471-2148-8-184
2722:10.15252/embr.201743990
2521:10.1186/1471-2105-7-270
1868:10.1186/1471-2148-7-241
1182:10.1093/database/baz022
1011:Genes & Development
519:glutamate dehydrogenase
206:Top: An ancestral gene
42:produces two paralogs (
2767:10.1006/geno.1993.1133
2459:Nucleic Acids Research
2257:Nucleic Acids Research
2208:Nucleic Acids Research
2204:"TreeFam: 2008 Update"
2166:10.1186/1471-2105-8-83
2000:Nucleic Acids Research
1706:Nucleic Acids Research
1657:Nucleic Acids Research
1608:Nucleic Acids Research
1476:Nucleic Acids Research
1427:Nucleic Acids Research
1374:Nucleic Acids Research
1325:Nucleic Acids Research
1272:Nucleic Acids Research
1223:Nucleic Acids Research
854:"Clustal FAQ #Symbols"
708:tetrasomic inheritance
438:
327:GreenPhylDB for plants
251:Flu regulatory protein
241:molecular evolutionist
227:
153:
146:conservative mutations
97:(paralogs), or else a
63:
2373:10.1101/gr.073585.107
1959:10.1093/molbev/msz015
1919:10.1093/molbev/msu132
1579:"Vertebrate Ohnologs"
426:
205:
127:
33:
3553:Evolutionary biology
696:allopolyploidization
597:copies of each gene.
410:last common ancestor
359:OrthoMaM for mammals
237:last common ancestor
177:convergent evolution
3409:2010PNAS..107.9270M
3350:2014PNAS..111..361M
3291:2014PLSCB..10E3754S
3025:2006PNAS..10310369M
3019:(27): 10369–10372.
2917:2008BMCEE...8..184L
2648:2011PLSCB...7E2073N
2471:10.1093/nar/gkq1172
2269:10.1093/nar/gkt1055
2220:10.1093/nar/gkm1005
1859:2007BMCEE...7..241R
1719:10.1093/nar/gky1068
1669:10.1093/nar/gkw1119
1620:10.1093/nar/gkx1019
1537:2015PLSCB..11E4394S
1488:10.1093/nar/gku1203
1284:10.1093/nar/gkt1253
1135:1997Sci...278..631T
1072:2010PLSCB...6E0703F
779:Protein superfamily
275:genetic engineering
253:is present both in
138:amino acid residues
71:biological homology
2597:Trends in Genetics
2508:BMC Bioinformatics
2153:BMC Bioinformatics
2012:10.1093/nar/gkj123
1439:10.1093/nar/gkp931
1386:10.1093/nar/gkq811
1337:10.1093/nar/gkm934
1235:10.1093/nar/gkp951
1023:10.1101/gad.321305
960:Systematic Zoology
814:Koonin EV (2005).
763:Orthologous MAtrix
439:
228:
162:percent similarity
154:
142:conserved sequence
130:sequence alignment
101:event (xenologs).
64:
1815:978-1-59745-251-9
1712:(D1): D411–D418.
1663:(D1): D744–D749.
1614:(D1): D477–D485.
1583:ohnologs.curie.fr
753:EggNOG (database)
728:sex determination
514:Bacillus subtilis
95:duplication event
83:protein sequences
67:Sequence homology
16:(Redirected from
3570:
3538:
3537:
3527:
3503:
3494:
3493:
3483:
3447:
3441:
3440:
3430:
3420:
3388:
3382:
3381:
3371:
3361:
3329:
3323:
3322:
3312:
3302:
3270:
3264:
3263:
3231:
3225:
3224:
3214:
3190:
3184:
3183:
3147:
3141:
3140:
3104:
3098:
3097:
3087:
3063:
3057:
3056:
3046:
3036:
3004:
2998:
2997:
2979:
2955:
2949:
2948:
2938:
2928:
2896:
2890:
2889:
2879:
2855:
2849:
2848:
2820:
2814:
2813:
2785:
2779:
2778:
2750:
2744:
2743:
2733:
2716:(7): 1139–1149.
2701:
2695:
2694:
2686:
2680:
2679:
2669:
2659:
2627:
2621:
2620:
2588:
2582:
2581:
2553:
2544:
2543:
2533:
2523:
2499:
2493:
2492:
2482:
2450:
2444:
2443:
2433:
2401:
2395:
2394:
2384:
2352:
2346:
2345:
2335:
2325:
2297:
2291:
2290:
2280:
2248:
2242:
2241:
2231:
2195:
2189:
2188:
2178:
2168:
2140:
2134:
2133:
2123:
2095:
2089:
2088:
2078:
2040:
2034:
2033:
2023:
1987:
1981:
1980:
1970:
1938:
1932:
1931:
1921:
1897:
1891:
1890:
1880:
1870:
1834:
1828:
1827:
1793:
1787:
1786:
1776:
1748:
1742:
1741:
1731:
1721:
1697:
1691:
1690:
1680:
1648:
1642:
1641:
1631:
1599:
1593:
1592:
1590:
1589:
1575:
1569:
1568:
1558:
1548:
1516:
1510:
1509:
1499:
1467:
1461:
1460:
1450:
1414:
1408:
1407:
1397:
1365:
1359:
1358:
1348:
1312:
1306:
1305:
1295:
1263:
1257:
1256:
1246:
1210:
1204:
1203:
1193:
1161:
1155:
1154:
1110:
1104:
1103:
1093:
1083:
1051:
1045:
1044:
1034:
1002:
996:
995:
955:
946:
945:
921:
915:
914:
878:
869:
868:
866:
864:
850:
844:
843:
811:
634:
608:
586:
286:gene duplication
158:percent identity
40:gene duplication
21:
3578:
3577:
3573:
3572:
3571:
3569:
3568:
3567:
3543:
3542:
3541:
3518:(12): 1826–32.
3505:
3504:
3497:
3449:
3448:
3444:
3390:
3389:
3385:
3331:
3330:
3326:
3285:(7): e1003754.
3272:
3271:
3267:
3233:
3232:
3228:
3192:
3191:
3187:
3152:Nature Genetics
3149:
3148:
3144:
3109:Nature Genetics
3106:
3105:
3101:
3065:
3064:
3060:
3006:
3005:
3001:
2970:(17): 1059–62.
2964:Current Biology
2957:
2956:
2952:
2898:
2897:
2893:
2857:
2856:
2852:
2822:
2821:
2817:
2787:
2786:
2782:
2752:
2751:
2747:
2703:
2702:
2698:
2688:
2687:
2683:
2642:(6): e1002073.
2629:
2628:
2624:
2590:
2589:
2585:
2555:
2554:
2547:
2501:
2500:
2496:
2452:
2451:
2447:
2403:
2402:
2398:
2361:Genome Research
2354:
2353:
2349:
2303:
2302:
2298:
2294:
2250:
2249:
2245:
2201:
2200:
2196:
2192:
2146:
2145:
2141:
2137:
2101:
2100:
2096:
2092:
2067:
2042:
2041:
2037:
1993:
1992:
1988:
1984:
1940:
1939:
1935:
1899:
1898:
1894:
1840:
1839:
1835:
1831:
1816:
1795:
1794:
1790:
1754:
1753:
1749:
1745:
1699:
1698:
1694:
1650:
1649:
1645:
1601:
1600:
1596:
1587:
1585:
1577:
1576:
1572:
1531:(7): e1004394.
1518:
1517:
1513:
1469:
1468:
1464:
1420:
1419:
1415:
1411:
1367:
1366:
1362:
1318:
1317:
1313:
1309:
1265:
1264:
1260:
1216:
1215:
1211:
1207:
1163:
1162:
1158:
1129:(5338): 631–7.
1116:
1115:
1111:
1107:
1066:(3): e1000703.
1053:
1052:
1048:
1004:
1003:
999:
972:10.2307/2412448
957:
956:
949:
923:
922:
918:
880:
879:
872:
862:
860:
852:
851:
847:
813:
812:
801:
797:
744:
724:sex chromosomes
720:
688:
675:
654:
653:
652:
651:
650:
635:
626:
625:
624:
609:
600:
599:
598:
587:
576:
527:
508:
406:
299:
279:shared ancestor
210:to produce two
200:
122:
28:
23:
22:
15:
12:
11:
5:
3576:
3574:
3566:
3565:
3560:
3555:
3545:
3544:
3540:
3539:
3495:
3442:
3403:(20): 9270–4.
3383:
3324:
3265:
3226:
3205:(5): 1387–98.
3185:
3142:
3099:
3058:
2999:
2950:
2891:
2870:(9): 1145–59.
2850:
2815:
2780:
2745:
2696:
2681:
2622:
2583:
2545:
2494:
2445:
2396:
2347:
2310:Genome Biology
2292:
2243:
2190:
2135:
2114:(16): 2044–6.
2108:Bioinformatics
2090:
2066:978-0471250951
2065:
2035:
1982:
1953:(4): 861–862.
1933:
1892:
1829:
1814:
1788:
1767:(6): 699–707.
1761:Bioinformatics
1743:
1692:
1643:
1594:
1570:
1511:
1462:
1409:
1360:
1307:
1258:
1205:
1156:
1105:
1046:
997:
947:
916:
870:
845:
798:
796:
793:
792:
791:
786:
781:
776:
774:Protein family
771:
766:
760:
755:
750:
743:
740:
719:
716:
687:
684:
674:
671:
636:
629:
628:
627:
610:
603:
602:
601:
588:
581:
580:
579:
578:
577:
575:
572:
554:and many more
552:homeobox genes
526:
523:
507:
504:
495:diverged from
405:
402:
401:
400:
397:
394:
387:
386:
381:
378:
367:
366:
363:
360:
357:
354:
351:OrthoInspector
348:
342:
337:
331:
328:
325:
303:bioinformatics
298:
295:
199:
196:
121:
118:
26:
24:
14:
13:
10:
9:
6:
4:
3:
2:
3575:
3564:
3561:
3559:
3558:Phylogenetics
3556:
3554:
3551:
3550:
3548:
3535:
3531:
3526:
3521:
3517:
3513:
3509:
3502:
3500:
3496:
3491:
3487:
3482:
3477:
3473:
3469:
3465:
3461:
3457:
3453:
3446:
3443:
3438:
3434:
3429:
3424:
3419:
3414:
3410:
3406:
3402:
3398:
3394:
3387:
3384:
3379:
3375:
3370:
3365:
3360:
3355:
3351:
3347:
3343:
3339:
3335:
3328:
3325:
3320:
3316:
3311:
3306:
3301:
3296:
3292:
3288:
3284:
3280:
3276:
3269:
3266:
3261:
3257:
3253:
3249:
3245:
3241:
3237:
3230:
3227:
3222:
3218:
3213:
3208:
3204:
3200:
3196:
3189:
3186:
3181:
3177:
3173:
3169:
3165:
3164:10.1038/75560
3161:
3157:
3153:
3146:
3143:
3138:
3134:
3130:
3126:
3122:
3121:10.1038/ng884
3118:
3114:
3110:
3103:
3100:
3095:
3091:
3086:
3081:
3078:(3): 351–62.
3077:
3073:
3069:
3062:
3059:
3054:
3050:
3045:
3040:
3035:
3030:
3026:
3022:
3018:
3014:
3010:
3003:
3000:
2995:
2991:
2987:
2983:
2978:
2973:
2969:
2965:
2961:
2954:
2951:
2946:
2942:
2937:
2932:
2927:
2922:
2918:
2914:
2910:
2906:
2902:
2895:
2892:
2887:
2883:
2878:
2873:
2869:
2865:
2861:
2854:
2851:
2846:
2842:
2838:
2834:
2830:
2826:
2819:
2816:
2811:
2807:
2803:
2799:
2796:(4): 345–51.
2795:
2791:
2784:
2781:
2776:
2772:
2768:
2764:
2760:
2756:
2749:
2746:
2741:
2737:
2732:
2727:
2723:
2719:
2715:
2711:
2707:
2700:
2697:
2692:
2685:
2682:
2677:
2673:
2668:
2663:
2658:
2653:
2649:
2645:
2641:
2637:
2633:
2626:
2623:
2618:
2614:
2610:
2606:
2602:
2598:
2594:
2587:
2584:
2579:
2575:
2571:
2567:
2564:(4): 359–66.
2563:
2559:
2552:
2550:
2546:
2541:
2537:
2532:
2527:
2522:
2517:
2513:
2509:
2505:
2498:
2495:
2490:
2486:
2481:
2476:
2472:
2468:
2464:
2460:
2456:
2449:
2446:
2441:
2437:
2432:
2427:
2423:
2419:
2415:
2411:
2407:
2400:
2397:
2392:
2388:
2383:
2378:
2374:
2370:
2367:(2): 327–35.
2366:
2362:
2358:
2351:
2348:
2343:
2339:
2334:
2329:
2324:
2319:
2315:
2311:
2307:
2301:
2296:
2293:
2288:
2284:
2279:
2274:
2270:
2266:
2262:
2258:
2254:
2247:
2244:
2239:
2235:
2230:
2225:
2221:
2217:
2213:
2209:
2205:
2199:
2194:
2191:
2186:
2182:
2177:
2172:
2167:
2162:
2158:
2154:
2150:
2144:
2139:
2136:
2131:
2127:
2122:
2117:
2113:
2109:
2105:
2099:
2094:
2091:
2086:
2082:
2077:
2072:
2068:
2062:
2058:
2054:
2050:
2046:
2039:
2036:
2031:
2027:
2022:
2017:
2013:
2009:
2005:
2001:
1997:
1991:
1986:
1983:
1978:
1974:
1969:
1964:
1960:
1956:
1952:
1948:
1944:
1937:
1934:
1929:
1925:
1920:
1915:
1912:(7): 1923–8.
1911:
1907:
1903:
1896:
1893:
1888:
1884:
1879:
1874:
1869:
1864:
1860:
1856:
1852:
1848:
1844:
1838:
1833:
1830:
1825:
1821:
1817:
1811:
1807:
1803:
1799:
1792:
1789:
1784:
1780:
1775:
1770:
1766:
1762:
1758:
1752:
1747:
1744:
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676:
655:
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568:human genome
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528:
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485:hemoglobin B
477:hemoglobin A
464:genes which
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440:
435:chromosome 7
418:
414:
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388:
371:phylogenetic
368:
315:phylogenetic
300:
291:
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270:
266:
260:
254:
248:
244:Walter Fitch
229:
223:
215:
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2410:GigaScience
1315:GreenPhylDB
666:Susumu Ohno
451:chromosomes
384:OrthoFinder
369:Tree-based
271:Arabidopsis
256:Arabidopsis
192:gene fusion
3547:Categories
3464:Cell Press
3158:(1): 3–4.
2911:(1): 184.
2831:: 155–61.
2316:(1): 238.
1853:(1): 241.
1751:OrthologID
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863:8 December
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795:References
738:in birds.
718:Gametology
698:to form a
686:Homoeology
542:clusters,
506:Regulation
493:angiogenin
473:hemoglobin
428:Vertebrate
396:HomoloGene
356:OrthologID
232:speciation
208:duplicates
185:amino acid
170:isoleucine
114:Alignments
110:amino acid
106:nucleotide
91:speciation
18:Orthologue
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942:0882-3383
936:(1): 55.
647:homoeolog
613:orthologs
536:paralogon
469:myoglobin
453:but also
431:Hox genes
399:Ortholuge
311:heuristic
307:databases
216:orthologs
198:Orthology
181:conserved
152:( ).
36:phylogeny
3534:11110898
3490:27021699
3437:20439718
3378:24368850
3319:25080083
3260:24530892
3221:23168259
3180:85257685
3172:10802639
3129:12032567
3094:11567626
3072:Immunity
3053:16801555
2994:32135432
2986:10996074
2945:18578868
2810:11144283
2755:Genomics
2740:28468957
2676:21695233
2617:19368988
2578:17644373
2540:16729895
2489:21097890
2440:29425291
2391:19029536
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2185:17346331
2130:16777906
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1824:19378138
1783:16410324
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1687:27899580
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1506:25429972
1457:19892828
1404:20864446
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1302:24297252
1253:19900971
1200:30893420
1170:Database
1100:20361041
1041:15630026
911:42949514
840:16285863
789:Syntelog
742:See also
673:Xenology
574:Ohnology
544:collagen
540:Hox gene
443:Homeobox
404:Paralogy
362:OrthoMCL
334:OHNOLOGS
212:paralogs
164:), e.g.
73:between
3481:4920642
3428:2889102
3405:Bibcode
3369:3890797
3346:Bibcode
3310:4117431
3287:Bibcode
3137:8263376
3044:1502464
3021:Bibcode
2936:2453138
2913:Bibcode
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2775:8486346
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2667:3111532
2644:Bibcode
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2076:3196566
2021:1347485
1968:6445298
1878:2249597
1855:Bibcode
1729:6323921
1678:5210582
1629:5753216
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1533:Bibcode
1497:4383983
1448:2808972
1395:3013755
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1123:Science
1091:2845645
1068:Bibcode
988:5449325
980:2412448
903:3621342
858:Clustal
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758:OrthoDB
704:meiosis
645:with a
621:xenolog
595:ohnolog
560:ParaHox
548:keratin
546:genes,
380:TreeFam
365:Roundup
345:OrthoDB
194:event.
166:leucine
134:histone
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3168:PMID
3125:PMID
3090:PMID
3049:PMID
2982:PMID
2941:PMID
2882:PMID
2841:PMID
2829:1994
2806:PMID
2771:PMID
2736:PMID
2672:PMID
2613:PMID
2574:PMID
2536:PMID
2485:PMID
2436:PMID
2387:PMID
2338:PMID
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2181:PMID
2126:PMID
2081:PMID
2061:ISBN
2026:PMID
1973:PMID
1924:PMID
1883:PMID
1820:PMID
1810:ISBN
1779:PMID
1734:PMID
1683:PMID
1634:PMID
1561:PMID
1502:PMID
1453:PMID
1400:PMID
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1196:PMID
1174:2019
1147:PMID
1096:PMID
1037:PMID
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226:.
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20:)
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