References
Alfaro ME, Brock CD, Banbury BL, Wainwright PC (2009) Does evolutionary
innovation in pharyngeal jaws lead to rapid lineage diversification in
labrid fishes? BMC Evolutionary Biology 9 (1), 255.
Alfaro ME, Faircloth BC, Harrington RC, et al. (2018) Explosive
diversification of marine fishes at the Cretaceous–Palaeogene boundary.Nat Ecol Evol , 2(4):688-696
Aparicio S, Chapman J, Stupka E, et al. (2002) Whole-genome
shotgun assembly and analysis of the genome of Fugu rubripes.science 297 , 1301-1310.
Bairoch A, Bougueleret L, Altairac S, Amendolia V, Zhang J (2010) The
Universal Protein Resource (UniProt) 2009. Nucleic acids research37 , D169-D174.
Bannikov AF, Sorbini L (1990) Coris bloti, a new genus and species of
labrid fish (Perciformes, Labroidei) from the Eocene of Monte
Bolca,Italy. Studi E Ricerche Sui Giacimenti Terziari Di Bolca ,
133-148.
Bao W, Kojima K, Kohany O (2015) Repbase Update, a database of
repetitive elements in eukaryotic genomes. Mobile Dna 6 ,
11.
Beissbarth T, Speed T (2004) GOstat: find statistically overrepresented
Gene Ontologies within a group of genes. Bioinformatics20 , 1464-1465.
Benson G (1999) Tandem repeats finder: a program to analyze DNA
sequences. Nucleic acids research 27 , 573-580.
Brawand D, Wagner CE, Li YI, et al. (2014) The genomic substrate
for adaptive radiation in African cichlid fish. Nature513 , 375-381.
Burton JN, Adey A, Patwardhan RP, et al. (2013) Chromosome-scale
scaffolding of de novo genome assemblies based on chromatin
interactions. Nature Biotechnology 31 , 1119-1125.
Castresana J (2000) Selection of conserved blocks from multiple
alignments for their use in phylogenetic analysis. Mol Biol Evol17 , 540-552.
Chen S, Zhang G, Shao C, QF H (2014) Whole-genome sequence of a flatfish
provides insights into ZW sex chromosome evolution and adaptation to a
benthic lifestyle. Nature Genetics 46 , 253-260.
Chen S, Zhou Y, Chen Y, Jia G (2018) fastp: an ultra-fast all-in-one
FASTQ preprocessor. Bioinformatics 34 , i884-i890.
Cheng C, Flamarique I (2007) Chromatic organization of cone
photoreceptors in the retina of rainbow trout: single cones irreversibly
switch from UV (SWS1) to blue (SWS2) light sensitive opsin during
natural development. J Exp Biol 210 , 4123-4135.
Collin SP, Knight MA, Davies WL, et al. (2003) Ancient colour
vision: multiple opsin genes in the ancestral vertebrates. Curr
Biol 13 , R864-865.
Cortesi F, Musilová Z, Stieb S, Hart N (2015) Ancestral duplications and
highly dynamic opsin gene evolution in percomorph fishes. PNAS112 , 1493-1498.
Cowman PF, Bellwood DR, Herwerden LV (2009) Dating the evolutionary
origins of wrasse lineages (Labridae) and the rise of trophic novelty on
coral reefs. Molecular phylogenetics and evolution 52 ,
621-631.
Davies WL, Cowing JA, Carvalho LS, et al. (2007) Functional
characterization, tuning, and regulation of visual pigment gene
expression in an anadromous lamprey. FASEB J 21 ,
2713-2724.
De Bie T, Cristianini N, Demuth JP, Hahn MW (2006) CAFE: a computational
tool for the study of gene family evolution. Bioinformatics22 , 1269-1271.
Donaldson TJ, Sadovy Y (2001) Threatened fishes of the world: Cheilinus
undulatus Ruppell, 1835 (Labridae). Environmental Biology of
Fishes 62 , 428.
Fay JC, Wu CI (2003) Sequence divergence, functional constraint, and
selection in protein evolution. Annu Rev Genomics Hum Genet4 , 213-235.
Flicek P, Amode M, Barrell D, Beal K, Billis K (2014) Ensembl 2014.Nucleic acids research 42 , 749-755.
Garrison E, Marth G (2012) Haplotype-based variant detection from
short-read sequencing. Quantitative Biology , 1-9.
Graham KS, Boggs CH, DeMartini EE, Schroeder RE, Trianni MS (2015)
Status review report: humphead wrasse (Cheilinus undulatus), pp. 1-123,
Report to National Marine Fisheries Service, Office of Protected
Resources.
Griffiths-Jones S, Moxon S, Marshall M, et al. (2005) Rfam:
annotating non-coding RNAs in complete genomes. Nucleic acids
research 33 , 121-124.
Guttman D, Dykhuizen DE (1994) Clonal divergence in Escherichia coli as
a result of recombination, not mutation. science 266 ,
1380-1383.
Haas BJ, Salzberg SL, Zhu W, Pertea… M (2008) Automated
eukaryotic gene structure annotation using EVidenceModeler and the
Program to Assemble Spliced Alignments. Genome Biology9 , 7.
Han Y, Wessler SR (2010) MITE-Hunter: a program for discovering
miniature inverted-repeat transposable elements from genomic sequences.Nucleic acids research 38 , e199.
Hedges S, Dudley J, Kumar S (2006) TimeTree: a public knowledge-base of
divergence times among organisms. Bioinformatics 22 ,
2971-2972.
Hofmann CM, Carleton KL (2009) Gene duplication and differential gene
expression play an important role in the diversification of visual
pigments in fish. Integr Comp Biol 49 , 630-643.
Howe K, Clark MD, Torroja CF, et al. (2013) The zebrafish
reference genome sequence and its relationship to the human genome.Nature 496 , 498-503.
Hu J, Fan J, Sun Z, Liu S (2020) NextPolish: a fast and efficient genome
polishing tool for long-read assembly. Bioinformatics36 , 2253-2255.
Huang da W, Sherman BT, Lempicki RA (2009) Bioinformatics enrichment
tools: paths toward the comprehensive functional analysis of large gene
lists. Nucleic Acids Res 37 , 1-13.
Huo R, Zhang B, Chen GH, et al. (2009) The karyotype of Cheilinus
undulates. Marine Sciences 33 , 94-97.
Jens K, Michael W, Erickson JL, et al. (2016) Using intron
position conservation for homology- based gene prediction. Nucleic
acids research , e89.
Kanehisa M, Goto S, Kawashima S, Nakaya A, S,, S. K. (2000) KEGG: kyoto
encyclopaedia of genes and genomes. Nucleic acids research28 , 27-30.
Karin L, Peter H, Andreas RE, et al. (2007) RNAmmer: consistent
and rapid annotation of ribosomal RNA genes. Nucleic acids
research 35 , 3100-3108.
Katoh K, Standley DM (2013) MAFFT multiple sequence alignment software
version 7: improvements in performance and usability. Mol Biol
Evol 30 , 772-780.
Kim D, Langmead B, Salzberg SL (2015) HISAT: a fast spliced aligner with
low memory requirements. Nature Methods 12 , 357-360.
Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018) MEGA X: Molecular
Evolutionary Genetics Analysis across Computing Platforms. Mol
Biol Evol 35 , 1547-1549.
Lagman D, Daza D, Widmark J, Abalo X (2013) The vertebrate ancestral
repertoire of visual opsins, transducin alpha subunits and
oxytocin/vasopressin receptors was established by duplication of their
shared genomic region in the two rounds of early vertebrate genome
duplications. BMC evolutionary biology 13 , 238.
Lagman D, Daza D, Widmark J, Abalo X, Sundstro¨m G (2014) The vertebrate
ancestral repertoire of visual opsins, transducin alpha subunits and
oxytocin/vasopressin receptors was established by duplication of their
shared genomic region in the two rounds of early vertebrate genome
duplications. BMC Evol Biol 13 , 238.
Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2.Nature Methods 9 , 357-359.
Lehmann R, Lightfoot DJ, Schunter C, Michell CT (2018) Finding Nemo’s
Genes: A chromosome‐scale reference assembly of the genome of the orange
clownfish Amphiprion percula. Mol Ecol Resour 00 , 1-16.
Li H, Durbin R (2010) Fast and accurate long-read alignment with
Burrows-Wheeler transform. Bioinformatics 26 , 589-595.
Li L, Stoeckert CJ, Roos DS (2003) OrthoMCL: identification of ortholog
groups for eukaryotic genomes. Genome research 13 ,
2178-2189.
Lin J, Wang F, Li W, Wang T (2017) The rises and falls of opsin genes in
59 ray-finned fish genomes and their implications for environmental
adaptation. Scientific reports 7 , 15568.
Liu D, Huang X, Tang W (2019) Advances in systematics of the Labridae.Marine Fisheries 41 , 107-117.
Liu D, Yang J, Tang W, et al. (2020) SINE Retrotransposon
variation drives Ecotypic disparity in natural populations of Coilia
nasus. Mob DNA 11 , 4.
Liu H, Liu J, Yang M, He Y, Wang Y (2019) SSR and SNP Polymorphic
Feature Analysis Based on Cheilinus undulatus Transcriptome.Genomics and Applied Biology 3 , 1-12.
Love MI, Huber W, Anders S (2014) Moderated estimation of fold change
and dispersion for RNA-seq data with DESeq2. Genome Biol15 , 550.
Lowe TM, Eddy SR (1997) tRNAscan-SE: A Program for Improved Detection of
Transfer RNA Genes in Genomic Sequence. Nucleic acids research25 , 955-964.
Mackin RD, Frey RA, Gutierrez C, et al. (2019) Endocrine
regulation of multichromatic color vision. PNAS 116 ,
16882-16891.
Mat Razali N, Cheah B, Nadarajah K (2019) Transposable Elements Adaptive
Role in Genome Plasticity, Pathogenicity and Evolution in Fungal
Phytopathogens. Int J Mol Sci 20 , 3597.
Mattingsdal M, Jentoft S, Torresen OK, et al. (2018) A continuous
genome assembly of the corkwing wrasse (Symphodus melops).Genomics 110 , 399-403.
Pertea M, Pertea GM, Antonescu CM, et al. (2015) StringTie
enables improved reconstruction of a transcriptome from RNA-seq reads.Nat Biotechnol 33 , 290-295.
Phillips GA, Carleton KL, Marshall NJ (2016) Multiple Genetic Mechanisms
Contribute to Visual Sensitivity Variation in the Labridae. Mol
Biol Evol 33 , 201-215.
Porath-Krause A, Palrett A, Fagglonato D, Birla B (2016) Structural
differences and differential expression among rhabdomeric opsins reveal
functional change after gene duplication in the bay scallop, Argopecten
irradians (Pectinidae). BMC evolutionary biology 16 ,
250.
Qi XZ, Yin SW, Luo J, Huo R (2013) Complete mitochondrial genome
sequence of the humphead wrasse, Cheilinus undulatus. Genetics &
Molecular Research Gmr 12 , 1095-1105.
Rennison DJ, Owens GL, Taylor JS (2012) Opsin gene duplication and
divergence in ray-finned fish. Mol Phylogenet Evol 62 ,
986-1008.
Robert VJ, Davis MW, Jorgensen EM, Bessereau JL (2008) Gene conversion
and end-joining- repair double-strand breaks in the Caenorhabditis
elegans germline. Genetics 180 , 673-679.
Rozas J, Ferrer-Mata A, Sánchez-DelBarrio JC, Guirao-Rico S (2017) DnaSP
6: DNA Sequence Polymorphism Analysis of Large Datasets. Mol.
Biol. Evol. 34 , 3299-3302.
Russell B (2004) Cheilinus undulatus. The IUCN Red List of
Threatened Species 2004 , e.T4592A11023949.
Sadovy Y (1998) Ciguatera hits Hong Kong live food-fish trade. SPC
Live Reef Fish Information Bulletin 4 , 51-53.
Sadovy Y, Kulbicki M, Labrosse P, et al. (2003) The humphead
wrasse, Cheilinus undulatus: Synopsis of a threatened and poorly known
giant coral reef fish. Reviews in Fish Biology & Fisheries13 , 327-364.
Sandkam BA, Joy JB, Watson CT, Breden F (2017) Genomic Environment
Impacts Color Vision Evolution in a Family with Visually Based Sexual
Selection. Genome Biol Evol 9 , 3100-3107.
Sarah H, Rolf A, Attwood TK, et al. (2009) InterPro: the
integrative protein signature database. Nucleic acids research37 , 211-215.
Sawyer S (1989) Statistical tests for detecting gene conversion.Mol Biol Evol 6 , 526-538.
Shao C, Li C, Wang N, et al. (2018) Chromosome-level genome
assembly of the spotted sea bass, Lateolabrax maculatus.GigaScience 7 .
Sharkey CR, Fujimoto MS, P.Lord NP, Shin S (2017) Overcoming the loss of
blue sensitivity through opsin duplication in the largest animal group,
beetles. Scientific reports 7 , 8.
Simão FA, Waterhouse RM, Panagiotis I, Kriventseva EV, Zdobnov EM (2015)
BUSCO: assessing genome assembly and annotation completeness with
single-copy orthologs. Bioinformatics 31 , 3210-3212.
Skorczyk-Werner A, Pawlowski P, Michalczuk M, et al. (2015)
Fundus albipunctatus: review of the literature and report of a novel
RDH5 gene mutation affecting the invariant tyrosine (p.Tyr175Phe).J Appl Genet 56 , 317-327.
Sotero-Caio C, Platt II RN, Suh A, Ray D (2017) Evolution and Diversity
of Transposable Elements in Vertebrate Genomes. Genome Biol. Evol91 , 161-177.
Springer MS, Emerling CA, Fugate N, Patel R (2016) Inactivation of
Cone-Specific Phototransduction Genes in Rod Monochromatic Cetaceans.Front. Ecol. Evol 4 , 61.
Stamatakis A (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic
analyses with thousands of taxa and mixed models. Bioinformatics22 , 2688-2690.
Stanke M, Schoffmann O, Morgenstern B, Waack S (2006) Gene prediction in
eukaryotes with a generalized hidden Markov model that uses hints from
external sources. BMC Bioinformatics 7 , 62.
Stieb SM, Cortesi F, Sueess L, et al. (2017) Why UV vision and
red vision are important for damselfish (Pomacentridae): structural and
expression variation in opsin genes. Mol Ecol 26 ,
1323-1342.
Sun H, Ding J, Piednoe M, Schneeberger K (2018) findGSE: estimating
genome size variation within human and Arabidopsis using k-mer
frequencies. Bioinformatics 34 , 550-557.
Tian Y, Li T, Sun M, et al. (2013) Neurexin regulates visual
function via mediating retinoid transport to promote rhodopsin
maturation. Neuron 77 , 311-322.
Tine M, Kuhl H, Gagnaire P, Louro B (2014) European sea bass genome and
its variation provide insights into adaptation to euryhalinity and
speciation. Nat Commun 5 , 5770.
Todd EV, Ortega-Recalde O, Liu H, et al. (2019) Stress, novel sex
genes, and epigenetic reprogramming orchestrate socially controlled sex
change. Sci Adv 5 , eaaw7006.
Trapnell C, Roberts A, Goff L, et al. (2012) Differential gene
and transcript expression analysis of RNA-seq experiments with TopHat
and Cufflinks. Nat Protoc 7 , 562-578.
Vurture GW, Sedlazeck FJ, Nattestad M, et al. (2017) GenomeScope:
fast reference-free genome profiling from short reads.Bioinformatics 33 , 2202-2204.
Wainwright P, Smith W, Price S, Tang K (2012) The Evolution of
Pharyngognathy: A Phylogenetic and Functional Appraisal of the
Pharyngeal Jaw Key Innovation in Labroid Fishes and Beyond.Systematic Biology 61 , 1001-1027.
Wang X, Lu P, Luo Z (2013) GMATo: A novel tool for the identification
and analysis of microsatellites in large genomes. Bioinformation9 , 541-544.
Waszak SM, Robinson GW, Gudenas BL, et al. (2020) Germline
Elongator mutations in Sonic Hedgehog medulloblastoma. Nature580 , 396-401.
Willingham A, Orth A, Batalov S, et al. (2005) A strategy for
probing the function of noncoding RNAs finds a repressor of NFAT.science 309 , 1570-1573.
Xiao Y, Xiao Z, Ma D, Liu J, Li J (2019) Genome sequence of the barred
knifejaw Oplegnathus fasciatus (Temminck & Schlegel, 1844): the first
chromosome-level draft genome in the family Oplegnathidae.GigaScience 8 , 1-8.
Xu S, Xiao S, Zhu S, et al. (2018) A draft genome assembly of the
Chinese sillago (Sillago sinica), the first reference genome for
Sillaginidae fishes. GigaScience 7 .
Yang J, Chen X, Bai J, Fang D (2016) The Sinocyclocheilus cavefish
genome provides insights into cave adaptation. BMC Biology14 .
Yang Z (1997) PAML: a program package for phylogenetic analysis by
maximum likelihood. Comput Appl Biosci 13 , 555-556.
Yokoyama S, Jia H (2020) Origin and adaptation of green-sensitive (RH2)
pigments in vertebrates. FEBS Open Bio 10 , 873-882.
You X, Bian C, Zan Q, Xu X (2014) Mudskipper genomes provide insights
into the terrestrial adaptation of amphibious fishes. Nature
Communications 5 , 5594.
Zdobnov EM, Rolf A (2001) InterProScan – an integration platform for
the signature-recognition methods in InterProScan. Bioinformatics17 , 847-848.
Zhu G, Wang L, Tang W, Liu D, Yang J (2014) De Novo Transcriptomes of
Olfactory Epithelium Reveal the Genes and Pathways for Spawning
Migration in Japanese Grenadier Anchovy (Coilia nasus). PloS one9 , e103832.