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Sequence homology

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Genephylogenyas red and blue branches within grey species phylogeny. Top: An ancestralgene duplicationproduces two paralogs (histone H1.1and1.2). A speciation event produces orthologs in the two daughter species (human and chimpanzee). Bottom: in a separate species (E. coli), a gene has a similar function (histone-like nucleoid-structuring protein) but has a separate evolutionary origin and so is ananalog.

Sequence homologyis thebiological homologybetweenDNA,RNA,orprotein sequences,defined in terms of shared ancestry in theevolutionary history of life.Two segments of DNA can have shared ancestry because of three phenomena: either aspeciationevent (orthologs), or aduplication event(paralogs), or else ahorizontal (or lateral) gene transferevent (xenologs).[1]

Homology among DNA, RNA, or proteins is typically inferred from theirnucleotideoramino acidsequence similarity. Significant similarity is strong evidence that two sequences are related by evolutionary changes from a common ancestral sequence.Alignmentsof multiple sequences are used to indicate which regions of each sequence are homologous.

Identity, similarity, and conservation[edit]

Asequence alignmentof mammalianhistoneproteins. Sequences are the middle 120-180amino acid residuesof the proteins. Residues that are conserved across all sequences are highlighted in grey. The key below denotesconserved sequence(*),conservative mutations(:), semi-conservative mutations (.), andnon-conservative mutations( ).[2]

The term "percent homology" is often used to mean "sequence similarity”, that is the percentage of identical residues (percent identity), or the percentage of residues conserved with similar physicochemical properties (percent similarity), e.g.leucineandisoleucine,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.[3]Sequences are either homologous or not.[3]This involves that the term "percent homology" is a misnomer.[4]

As with morphological and anatomical structures, sequence similarity might occur because ofconvergent evolution,or, as with shorter sequences, by chance, meaning that they are not homologous. Homologous sequence regions are also calledconserved.This is not to be confused with conservation inamino acidsequences, where the amino acid at a specific position has been substituted with a different one that has functionally equivalent physicochemical properties.

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 agene fusionevent.

Orthology[edit]

Top: An ancestral geneduplicatesto produce twoparalogs(Genes A and B). A speciation event producesorthologsin the two daughter species. Bottom: in a separate species, an unrelated gene has a similar function (Gene C) but has aseparate evolutionary originand so is ananalog.

Homologous sequences are orthologous if they are inferred to be descended from the same ancestral sequence separated by aspeciationevent: 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 thelast common ancestor.The term "ortholog" was coined in 1970 by themolecular evolutionistWalter Fitch.[5]

For instance, the plantFlu regulatory proteinis present both inArabidopsis(multicellular higher plant) andChlamydomonas(single cell green algae). TheChlamydomonasversion 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 simplerArabidopsisprotein, if transferred from algae to plant genome by means ofgenetic engineering.Significant sequence similarity and shared functional domains indicate that these two genes are orthologous genes,[6]inherited from theshared ancestor.

Orthology is strictly defined in terms of ancestry. Given that the exact ancestry of genes in different organisms is difficult to ascertain due togene duplicationand 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.[7]

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 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.[citation needed]

Databases of orthologous genes[edit]

Given their tremendous importance for biology andbioinformatics,orthologous genes have been organized in several specializeddatabasesthat provide tools to identify and analyze orthologous gene sequences. These resources employ approaches that can be generally classified into those that useheuristicanalysis of all pairwise sequence comparisons, and those that usephylogeneticmethods. Sequence comparison methods were first pioneered in the COGs database in 1997.[8]These methods have been extended and automated in twelve different databases the most advanced being AYbRAH Analyzing Yeasts by Reconstructing Ancestry of Homologs[9]as well as these following databases right now.

  • eggNOG[10][11]
  • GreenPhylDB[12][13]for plants
  • InParanoid[14][15]focuses on pairwise ortholog relationships
  • OHNOLOGS[16][17]is a repository of the genes retained from whole genome duplications in the vertebrate genomes including human and mouse.
  • OMA[18]
  • OrthoDB[19]appreciates that the orthology concept is relative to different speciation points by providing a hierarchy of orthologs along the species tree.
  • OrthoInspector[20]is a repository of orthologous genes for 4753 organisms covering the three domains of life
  • OrthologID[21][22]
  • OrthoMaM[23][24][25]for mammals
  • OrthoMCL[26][27]
  • Roundup[28]

Tree-basedphylogeneticapproaches aim to distinguish speciation from gene duplication events by comparing gene trees with species trees, as implemented in databases and software tools such as:

A third category of hybrid approaches uses both heuristic and phylogenetic methods to construct clusters and determine trees, for example:

Paralogy[edit]

Paralogous genes are genes that are related via duplication events in thelast common ancestor(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.[1]

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. 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.[1]

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 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.[1]

VertebrateHox genesare organized in sets of paralogs. Each Hox cluster (HoxA, HoxB, etc.) is on a different chromosome. For instance, the human HoxA cluster is onchromosome 7.The mouse HoxA cluster shown here has 11 paralogous genes (2 are missing).[37]

Paralogous genes can shape the structure of whole genomes and thus explain genome evolution to a large extent. Examples include theHomeobox(Hox) genes in animals. These genes not only underwent gene duplications withinchromosomesbut alsowhole genome duplications.As a result, Hox genes in most vertebrates are clustered across multiple chromosomes with the HoxA-D clusters being the best studied.[37]

Another example are theglobingenes whichencodemyoglobinandhemoglobinand are considered to be ancient paralogs. Similarly, the four known classes of hemoglobins (hemoglobin A,hemoglobin A2,hemoglobin B,andhemoglobin F) 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. Humanangiogenindiverged fromribonuclease,for example, and while the two paralogs remain similar in tertiary structure, their functions within the cell are now quite different.[citation needed]

It is often asserted that orthologs are more functionally similar than paralogs of similar divergence, but several papers have challenged this notion.[38][39][40]

Regulation[edit]

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,Bacillus subtilisencodes two paralogues ofglutamate dehydrogenase: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.[41]

Paralogous chromosomal regions[edit]

Sometimes, large regions of chromosomes share gene content similar to other chromosomal regions within the same genome.[42]They are well characterised in the human genome, where they have been used as evidence to support the2R hypothesis.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 paralogon.[43]Well-studied sets of paralogy regions include regions of human chromosome 2, 7, 12 and 17 containingHox geneclusters,collagengenes,keratingenes and other duplicated genes,[44]regions of human chromosomes 4, 5, 8 and 10 containing neuropeptide receptor genes, NK classhomeobox genesand many moregene families,[45][46][47]and parts of human chromosomes 13, 4, 5 and X containing theParaHoxgenes and their neighbors.[48]TheMajor histocompatibility complex(MHC) on human chromosome 6 has paralogy regions on chromosomes 1, 9 and 19.[49]Much of thehuman genomeseems to be assignable to paralogy regions.[50]

Ohnology[edit]

Awhole genome duplicationevent produces a genome with twoohnologcopies of each gene.
A speciation event producesorthologsof a gene in the two daughter species. Ahorizontal gene transferevent from one species to another adds axenologof the gene to its genome.
A speciation event produces orthologs of a gene in the two daughter species. Subsequenthybridisationof those species generates ahybrid genomewith ahomoeologcopy of each gene from both species.

Ohnologous genes are paralogousgenesthat have originated by a process ofwhole-genome duplication.The name was first given in honour ofSusumu Ohnoby Ken Wolfe.[51]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, and pathogenic copy number variations.[52][53][54][55][56]

Xenology[edit]

Homologs resulting fromhorizontal gene transferbetween 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.[5]

Homoeology[edit]

Homoeologous (also spelled homeologous) chromosomes or parts of chromosomes are those brought together followinginter-species hybridizationandallopolyploidizationto form ahybrid genome,and whose relationship was completely homologous in an ancestral species.[57]In allopolyploids, the homologous chromosomes within each parental sub-genome should pair faithfully duringmeiosis,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 totetrasomic inheritance(four chromosomes pairing at meiosis), intergenomicrecombination,and reduced fertility.[citation needed]

Gametology[edit]

Gametology denotes the relationship between homologous genes on non-recombining, oppositesex chromosomes.The term was coined by García-Moreno and Mindell.[58]2000. Gametologs result from the origination of geneticsex determinationand barriers to recombination between sex chromosomes. Examples of gametologs includeCHDWandCHDZin birds.[58]

See also[edit]

References[edit]

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