Abstract:The functional equivalence of Pax6/eyeless genes across distantly related animal phyla has been one of central findings on which evo-devo studies is based. In this study, we show that Pax4, in addition to Pax6, is a vertebrate ortholog of the fly eyeless gene (and its duplicate, twin of eyeless [toy] gene, unique to Insecta). Molecular phylogenetic trees published to date placed the Pax4 gene outside the Pax6/eyeless subgroup as if the Pax4 gene originated from a gene duplication before the origin of bilateria… Show more
“…Primers were designed based on Pax6 transcript sequences of zebrafish (Ensembl ID: ENSDART00000148420 for pax6a and ENSDART00000145946 for pax6b ), X. laevis (NCBI: NM_001085944 for Pax6a and NM_001172195 for Pax6b ), and the green anole (Ensembl ID: ENSACAT00000002377). Zebrafish pax4 probe synthesis employed the cDNA fragment previously reported (Manousaki et al 2011). …”
Section: Methodsmentioning
confidence: 99%
“…The last common ancestor of bilaterians, the so-called “Urbilateria,” already possessed proto-orthologs of these four Pax classes, plus an additional class, the PaxA/Pox neuro class, restricted to invertebrates (Matus et al 2007). Preceding the radiation of vertebrates, each of the four classes was quadruplicated by the 2R-WGD (Wada et al 1998; Holland et al 1999; Ogasawara et al 1999; Manousaki et al 2011). F ig .…”
Section: Introductionmentioning
confidence: 99%
“…1 B ; Ravi et al 2013). Pax4 , the other close relative of Pax6 (Manousaki et al 2011), also shows a mosaic pattern of phylogenetic distribution, confined to mammals (Pilz et al 1993; Tamura et al 1994) and teleost fish (Hoshiyama et al 2007; Manousaki et al 2011), whereas the Pax6 gene is identified in every vertebrate genome sequenced to date (fig. 1 B ).…”
Section: Introductionmentioning
confidence: 99%
“…This indicates evolutionarily conserved roles of Pax6 and lineage-specific differences in the roles of Pax4 during pancreas development among vertebrates. The Pax4 genes of mammals and teleost fishes are not implicated in the development of eyes (Rath et al 2009; Manousaki et al 2011). However, mammalian Pax4 genes are expressed in photoreceptors in the outer nuclear layer of the adult mammalian retina in a diurnal rhythm (Rath et al 2009).…”
Section: Introductionmentioning
confidence: 99%
“…The Pax6 gene is expressed in other neuronal layers of the mature retina, namely the inner nuclear layer, the ganglion cell layer, and in several species including a shark, zebrafish, chicken, and mouse, and also in the horizontal cell layer (Belecky-Adams et al 1997; Macdonald and Wilson 1997; Wullimann and Rink 2001; Ferreiro-Galve et al 2011). The teleost pax4 gene has an expression domain that has not been attributed to any other Pax gene, namely the stomodeum which corresponds to the developing lip (Manousaki et al 2011). …”
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.
“…Primers were designed based on Pax6 transcript sequences of zebrafish (Ensembl ID: ENSDART00000148420 for pax6a and ENSDART00000145946 for pax6b ), X. laevis (NCBI: NM_001085944 for Pax6a and NM_001172195 for Pax6b ), and the green anole (Ensembl ID: ENSACAT00000002377). Zebrafish pax4 probe synthesis employed the cDNA fragment previously reported (Manousaki et al 2011). …”
Section: Methodsmentioning
confidence: 99%
“…The last common ancestor of bilaterians, the so-called “Urbilateria,” already possessed proto-orthologs of these four Pax classes, plus an additional class, the PaxA/Pox neuro class, restricted to invertebrates (Matus et al 2007). Preceding the radiation of vertebrates, each of the four classes was quadruplicated by the 2R-WGD (Wada et al 1998; Holland et al 1999; Ogasawara et al 1999; Manousaki et al 2011). F ig .…”
Section: Introductionmentioning
confidence: 99%
“…1 B ; Ravi et al 2013). Pax4 , the other close relative of Pax6 (Manousaki et al 2011), also shows a mosaic pattern of phylogenetic distribution, confined to mammals (Pilz et al 1993; Tamura et al 1994) and teleost fish (Hoshiyama et al 2007; Manousaki et al 2011), whereas the Pax6 gene is identified in every vertebrate genome sequenced to date (fig. 1 B ).…”
Section: Introductionmentioning
confidence: 99%
“…This indicates evolutionarily conserved roles of Pax6 and lineage-specific differences in the roles of Pax4 during pancreas development among vertebrates. The Pax4 genes of mammals and teleost fishes are not implicated in the development of eyes (Rath et al 2009; Manousaki et al 2011). However, mammalian Pax4 genes are expressed in photoreceptors in the outer nuclear layer of the adult mammalian retina in a diurnal rhythm (Rath et al 2009).…”
Section: Introductionmentioning
confidence: 99%
“…The Pax6 gene is expressed in other neuronal layers of the mature retina, namely the inner nuclear layer, the ganglion cell layer, and in several species including a shark, zebrafish, chicken, and mouse, and also in the horizontal cell layer (Belecky-Adams et al 1997; Macdonald and Wilson 1997; Wullimann and Rink 2001; Ferreiro-Galve et al 2011). The teleost pax4 gene has an expression domain that has not been attributed to any other Pax gene, namely the stomodeum which corresponds to the developing lip (Manousaki et al 2011). …”
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.
Identification of intragenomic conservation of gene compositions in multiple chromosomal segments led to evidence of whole genome (WGDs) duplications. The process by which WGDs have been maintained and decayed provides us with clues for understanding how the genome evolves. In this chapter, we summarize current understanding of phylogenetic distribution and evolutionary impact of WGDs, introduce basic procedures to detect conserved synteny, and discuss typical pitfalls, as well as biological insights.
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