Detection and Phylogenetic Assessment of Conserved Synteny Derived from Whole Genome Duplications

Kuraku, Shigehiro; Meyer, Axel

doi:10.1007/978-1-61779-582-4_14

Cited by 23 publications

(18 citation statements)

References 52 publications

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“…Synteny analyses have been widely used as reliable tool to identify traces of WGD (Kuraku and Meyer 2012 and references therein). It is particularly useful when molecular phylogenies of the involved genes cannot be reliably reconstructed.…”

Section: Discussionmentioning

confidence: 99%

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Evolution of the Vertebrate Pax4/6 Class of Genes with Focus on Its Novel Member, the Pax10 Gene

Feiner

Meyer

Kuraku

2014

Genome Biology and Evolution

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The members of the paired box (Pax) family regulate key developmental pathways in many metazoans as tissue-specific transcription factors. Vertebrate genomes typically possess nine Pax genes (Pax1–9), which are derived from four proto-Pax genes in the vertebrate ancestor that were later expanded through the so-called two-round (2R) whole-genome duplication. A recent study proposed that pax6a genes of a subset of teleost fishes (namely, acanthopterygians) are remnants of a paralog generated in the 2R genome duplication, to be renamed pax6.3, and reported one more group of vertebrate Pax genes (Pax6.2), most closely related to the Pax4/6 class. We propose to designate this new member Pax10 instead and reconstruct the evolutionary history of the Pax4/6/10 class with solid phylogenetic evidence. Our synteny analysis showed that Pax4, -6, and -10 originated in the 2R genome duplications early in vertebrate evolution. The phylogenetic analyses of relationships between teleost pax6a and other Pax4, -6, and -10 genes, however, do not support the proposed hypothesis of an ancient origin of the acanthopterygian pax6a genes in the 2R genome duplication. Instead, we confirmed the traditional scenario that the acanthopterygian pax6a is derived from the more recent teleost-specific genome duplication. Notably, Pax6 is present in all vertebrates surveyed to date, whereas Pax4 and -10 were lost multiple times in independent vertebrate lineages, likely because of their restricted expression patterns: Among Pax6-positive domains, Pax10 has retained expression in the adult retina alone, which we documented through in situ hybridization and quantitative reverse transcription polymerase chain reaction experiments on zebrafish, Xenopus, and anole lizard.

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Section: Discussionmentioning

confidence: 99%

“…The search for conserved intragenomic synteny (Kuraku and Meyer 2012) in the green anole focused on up to 10-Mb genomic regions flanking the Pax6 and - 10 genes. Referring to the Ensembl “Gene Tree,” the duplication patterns of neighboring gene families were investigated.…”

Section: Methodsmentioning

confidence: 99%

Evolution of the Vertebrate Pax4/6 Class of Genes with Focus on Its Novel Member, the Pax10 Gene

Feiner

Meyer

Kuraku

2014

Genome Biology and Evolution

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“…Evolutionary considerations aside, practical work on targeting two or more ohnologs requires identification of the most complete set of ohnolog pairs or groups. Currently, the most robust methods are based on identification of large-scale regions of conserved synteny between species [ 38 , 39 ]. The set of ohnologs identified in the latest zebrafish reference genome paper [ 27 ] was chosen to test the applicability of CRISPR MultiTargeter to design sgRNAs targeting similar genes.…”

Section: Resultsmentioning

confidence: 99%

CRISPR MultiTargeter: A Web Tool to Find Common and Unique CRISPR Single Guide RNA Targets in a Set of Similar Sequences

et al. 2015

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Genome engineering has been revolutionized by the discovery of clustered regularly interspaced palindromic repeats (CRISPR) and CRISPR-associated system genes (Cas) in bacteria. The type IIB Streptococcus pyogenes CRISPR/Cas9 system functions in many species and additional types of CRISPR/Cas systems are under development. In the type II system, expression of CRISPR single guide RNA (sgRNA) targeting a defined sequence and Cas9 generates a sequence-specific nuclease inducing small deletions or insertions. Moreover, knock-in of large DNA inserts has been shown at the sites targeted by sgRNAs and Cas9. Several tools are available for designing sgRNAs that target unique locations in the genome. However, the ability to find sgRNA targets common to several similar sequences or, by contrast, unique to each of these sequences, would also be advantageous. To provide such a tool for several types of CRISPR/Cas system and many species, we developed the CRISPR MultiTargeter software. Similar DNA sequences in question are duplicated genes and sets of exons of different transcripts of a gene. Thus, we implemented a basic sgRNA target search of input sequences for single-sgRNA and two-sgRNA/Cas9 nickase targeting, as well as common and unique sgRNA target searches in 1) a set of input sequences; 2) a set of similar genes or transcripts; or 3) transcripts a single gene. We demonstrate potential uses of the program by identifying unique isoform-specific sgRNA sites in 71% of zebrafish alternative transcripts and common sgRNA target sites in approximately 40% of zebrafish duplicated gene pairs. The design of unique targets in alternative exons is helpful because it will facilitate functional genomic studies of transcript isoforms. Similarly, its application to duplicated genes may simplify multi-gene mutational targeting experiments. Overall, this program provides a unique interface that will enhance use of CRISPR/Cas technology.

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“…2), three of the 4 Irs genes were found to be in genomic neighborhoods that shared similar gene contents. The sharing of paralogus genes among genomic neighborhoods is consistent with these genes originating through genome duplications [65], which suggests that at least 3 of the 4 Irs genes originated via the two rounds of genome duplication that occurred in the common ancestral vertebrate lineage [41, 42]. Interestingly, both the insulin [38] and the insulin receptor [39, 40] gene families originated very early in vertebrate evolution, and potentially via the same genome duplications.…”

Section: Discussionmentioning

confidence: 88%

Evolution of the vertebrate insulin receptor substrate (Irs) gene family

Al-Salam

Irwin

2017

BMC Evol Biol

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BackgroundInsulin receptor substrate (Irs) proteins are essential for insulin signaling as they allow downstream effectors to dock with, and be activated by, the insulin receptor. A family of four Irs proteins have been identified in mice, however the gene for one of these, IRS3, has been pseudogenized in humans. While it is known that the Irs gene family originated in vertebrates, it is not known when it originated and which members are most closely related to each other. A better understanding of the evolution of Irs genes and proteins should provide insight into the regulation of metabolism by insulin.ResultsMultiple genes for Irs proteins were identified in a wide variety of vertebrate species. Phylogenetic and genomic neighborhood analyses indicate that this gene family originated very early in vertebrae evolution. Most Irs genes were duplicated and retained in fish after the fish-specific genome duplication. Irs genes have been lost of various lineages, including Irs3 in primates and birds and Irs1 in most fish. Irs3 and Irs4 experienced an episode of more rapid protein sequence evolution on the ancestral mammalian lineage. Comparisons of the conservation of the proteins sequences among Irs paralogs show that domains involved in binding to the plasma membrane and insulin receptors are most strongly conserved, while divergence has occurred in sequences involved in interacting with downstream effector proteins.ConclusionsThe Irs gene family originated very early in vertebrate evolution, likely through genome duplications, and in parallel with duplications of other components of the insulin signaling pathway, including insulin and the insulin receptor. While the N-terminal sequences of these proteins are conserved among the paralogs, changes in the C-terminal sequences likely allowed changes in biological function.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-017-0994-z) contains supplementary material, which is available to authorized users.

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Detection and Phylogenetic Assessment of Conserved Synteny Derived from Whole Genome Duplications

Cited by 23 publications

References 52 publications

Evolution of the Vertebrate Pax4/6 Class of Genes with Focus on Its Novel Member, the Pax10 Gene

Evolution of the Vertebrate Pax4/6 Class of Genes with Focus on Its Novel Member, the Pax10 Gene

CRISPR MultiTargeter: A Web Tool to Find Common and Unique CRISPR Single Guide RNA Targets in a Set of Similar Sequences

Evolution of the vertebrate insulin receptor substrate (Irs) gene family

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