Time Scale for Cyclostome Evolution Inferred with a Phylogenetic Diagnosis of Hagfish and Lamprey cDNA Sequences

Kuraku, Shigehiro; Kuratani, Shigeru

doi:10.2108/zsj.23.1053

Cited by 189 publications

(176 citation statements)

References 78 publications

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“…Here, we used the synonymous substitution rate (dS), which reflects the molecular evolution in a neutral manner (29). First, 4,991 of 6,170 core genes common to the seven teleost genomes (Table 2) were selected according to the criterion that the dS of any orthologous pair was computable.…”

Section: Resultsmentioning

confidence: 99%

Evolutionary changes of multiple visual pigment genes in the complete genome of Pacific bluefin tuna

Nakamura

Mori

Saitoh

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

109

112

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Tunas are migratory fishes in offshore habitats and top predators with unique features. Despite their ecological importance and high market values, the open-ocean lifestyle of tuna, in which effective sensing systems such as color vision are required for capture of prey, has been poorly understood. To elucidate the genetic and evolutionary basis of optic adaptation of tuna, we determined the genome sequence of the Pacific bluefin tuna (Thunnus orientalis), using next-generation sequencing technology. A total of 26,433 protein-coding genes were predicted from 16,802 assembled scaffolds. From these, we identified five common fish visual pigment genes: red-sensitive (middle/long-wavelength sensitive; M/LWS), UV-sensitive (short-wavelength sensitive 1; SWS1), blue-sensitive (SWS2), rhodopsin (RH1), and green-sensitive (RH2) opsin genes. Sequence comparison revealed that tuna's RH1 gene has an amino acid substitution that causes a short-wave shift in the absorption spectrum (i.e., blue shift). Pacific bluefin tuna has at least five RH2 paralogs, the most among studied fishes; four of the proteins encoded may be tuned to blue light at the amino acid level. Moreover, phylogenetic analysis suggested that gene conversions have occurred in each of the SWS2 and RH2 loci in a short period. Thus, Pacific bluefin tuna has undergone evolutionary changes in three genes (RH1, RH2, and SWS2), which may have contributed to detecting blue-green contrast and measuring the distance to prey in the blue-pelagic ocean. These findings provide basic information on behavioral traits of predatory fish and, thereby, could help to improve the technology to culture such fish in captivity for resource management.tuna genome | visual system | animal opsin

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Section: Resultsmentioning

confidence: 99%

Evolutionary changes of multiple visual pigment genes in the complete genome of Pacific bluefin tuna

Nakamura

Mori

Saitoh

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

109

112

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“…The tree was drawn respecting the proposed divergence times (million years ago) of the vertebrate lineages represented according to the mean of different studies given by http://www.timetree.org/: Elasmobranchii-Euteleostomi (±488 MYA); Actinopterygii-Sarcopterygii (±436 MYA); Latimeria-Tetrapoda (±413 MYA); Lepisosteiformes-Teleostei (±325 MYA); and Aves-Mammalian (±320 MYA). Agnatha-Gnathostomes (±500 MYA) was taken from (Kuraku & Kuratani 2006). A full colour version of this figure is available at http://dx.doi.org/10.1530/JME-16-0051.…”

Section: Discussionmentioning

confidence: 99%

“…Two CRH family genes were found in the former and four in the latter. Although it is possible that P. marinus may have lost two of the pepti de genes, the recent divergence of these two species from each other only 10-30 Mya (Kuraku & Kuratani 2006) makes it more likely that two genes are missing in the Research j c r cardoso and others Evolution of the CRH family 57 1 :…”

Section: Elephant Shark and Lampreysmentioning

confidence: 99%

Corticotropin-releasing hormone family evolution: five ancestral genes remain in some lineages

Cardoso¹,

Bergqvist²,

Félix³

et al. 2016

Journal of Molecular Endocrinology

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The evolution of the peptide family consisting of corticotropin-releasing hormone (CRH) and the three urocortins (UCN1-3) has been puzzling due to uneven evolutionary rates. Distinct gene duplication scenarios have been proposed in relation to the two basal rounds of vertebrate genome doubling (2R) and the teleost fish-specific genome doubling (3R). By analyses of sequences and chromosomal regions, including many neighboring gene families, we show here that the vertebrate progenitor had two peptide genes that served as the founders of separate subfamilies. Then, 2R resulted in a total of five members: one subfamily consists of CRH1, CRH2, and UCN1. The other subfamily contains UCN2 and UCN3. All five peptide genes are present in the slowly evolving genomes of the coelacanth Latimeria chalumnae (a lobe-finned fish), the spotted gar Lepisosteus oculatus (a basal ray-finned fish), and the elephant shark Callorhinchus milii (a cartilaginous fish). The CRH2 gene has been lost independently in placental mammals and in teleost fish, but is present in birds (except chicken), anole lizard, and the nonplacental mammals platypus and opossum. Teleost 3R resulted in an additional surviving duplicate only for crh1 in some teleosts including zebrafish (crh1a and crh1b). We have previously reported that the two vertebrate CRH/UCN receptors arose in 2R and that CRHR1 was duplicated in 3R. Thus, we can now conclude that this peptide-receptor system was quite complex in the ancestor of the jawed vertebrates with five CRH/UCN peptides and two receptors, and that crh and crhr1 were duplicated in the teleost fish tetraploidization.

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“…Although staging and methodological differences likely explain these discrepancies, it is formally possible that they reflect independent evolution of nested Dlx expression in P. marinus, or the loss of such patterning in L. japonicum. Despite a recent divergence time of 10-30 million years ago for the two species (27), differences in gene expression between them have been suggested (18,28).…”

Section: Discussionmentioning

confidence: 99%

“…Taken together, the tenuous phylogenetic positions of lamprey Dlxs leave open the precise relationships between agnathan and gnathostome Dlx paralogs. This may be due to the rapid evolution of lamprey genes relative to their gnathostome homologs (27). Assembly of the lamprey genome and identification of conserved vertebrate synteny groups should help to establish the timing of the duplications that generated the gnathostome and lamprey Dlx paralogs.…”

Section: Discussionmentioning

confidence: 99%

Evidence for the prepattern/cooption model of vertebrate jaw evolution

Cerny

Cattell²,

Sauka‐Spengler³

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

107

179

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The appearance of jaws was a turning point in vertebrate evolution because it allowed primitive vertebrates to capture and process large, motile prey. The vertebrate jaw consists of separate dorsal and ventral skeletal elements connected by a joint. How this structure evolved from the unjointed gill bar of a jawless ancestor is an unresolved question in vertebrate evolution. To understand the developmental bases of this evolutionary transition, we examined the expression of 12 genes involved in vertebrate pharyngeal patterning in the modern jawless fish lamprey. We find nested expression of Dlx genes, as well as combinatorial expression of Msx, Hand and Gsc genes along the dorso-ventral (DV) axis of the lamprey pharynx, indicating gnathostome-type pharyngeal patterning evolved before the appearance of the jaw. In addition, we find that Bapx and Gdf5/6/7 , key regulators of joint formation in gnathostomes, are not expressed in the lamprey first arch, whereas Barx , which is absent from the intermediate first arch in gnathostomes, marks this domain in lamprey. Taken together, these data support a new scenario for jaw evolution in which incorporation of Bapx and Gdf5/6/7 into a preexisting DV patterning program drove the evolution of the jaw by altering the identity of intermediate first-arch chondrocytes. We present this “Pre-pattern/Cooption” model as an alternative to current models linking the evolution of the jaw to the de novo appearance of sophisticated pharyngeal DV patterning.

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Time Scale for Cyclostome Evolution Inferred with a Phylogenetic Diagnosis of Hagfish and Lamprey cDNA Sequences

Cited by 189 publications

References 78 publications

Evolutionary changes of multiple visual pigment genes in the complete genome of Pacific bluefin tuna

Evolutionary changes of multiple visual pigment genes in the complete genome of Pacific bluefin tuna

Corticotropin-releasing hormone family evolution: five ancestral genes remain in some lineages

Evidence for the prepattern/cooption model of vertebrate jaw evolution

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