Caecilian Genomes Reveal the Molecular Basis of Adaptation and Convergent Evolution of Limblessness in Snakes and Caecilians

We present genome sequences for the caecilians Geotrypetes seraphini (3.8Gb) and Microcaecilia unicolor (4.7Gb), representatives of a limbless, mostly soil-dwelling amphibian clade with reduced eyes, and unique putatively chemosensory tentacles. More than 69% of both genomes are composed of repeats, with retrotransposons the most abundant. We identify 1,150 orthogroups which are unique to caecilians and enriched for functions in olfaction and detection of chemical signals. There are 379 orthogroups with signatures of positive selection on caecilian lineages with roles in organ development and morphogenesis, sensory perception and immunity amongst others. We discover that caecilian genomes are missing the ZRS enhancer of Sonic Hedgehog which is also mutated in snakes. In vivo deletions have shown ZRS is required for limb development in mice, thus revealing a shared molecular target implicated in the independent evolution of limblessness in snakes and caecilians.

[1]  K. Sameith,et al.  Convergent and lineage-specific genomic differences in limb regulatory elements in limbless reptile lineages. , 2022, Cell reports.

[2]  Erez Lieberman Aiden,et al.  Complete vertebrate mitogenomes reveal widespread repeats and gene duplications , 2021, Genome Biology.

[3]  Stanley K. Sessions,et al.  Gigantic Genomes Provide Empirical Tests of Transposable Element Dynamics Models , 2021, Genom. Proteom. Bioinform..

[4]  Thomas M. Keane,et al.  Twelve years of SAMtools and BCFtools , 2020, GigaScience.

[5]  Ben Fulton,et al.  CAFE 5 models variation in evolutionary rates among gene families , 2020, Bioinform..

[6]  W. Chow,et al.  Significantly improving the quality of genome assemblies through curation , 2020, bioRxiv.

[7]  Sergey Koren,et al.  Towards complete and error-free genome assemblies of all vertebrate species , 2020, Nature.

[8]  Cédric Feschotte,et al.  RepeatModeler2 for automated genomic discovery of transposable element families , 2020, Proceedings of the National Academy of Sciences.

[9]  Astrid Gall,et al.  Ensembl 2020 , 2019, Nucleic Acids Res..

[10]  M. O'Keefe,et al.  A FBN1 variant manifesting as non-syndromic ectopia lentis with retinal detachment: clinical and genetic characteristics , 2019, Eye.

[11]  Jonathan Wood,et al.  Identifying and removing haplotypic duplication in primary genome assemblies , 2019, bioRxiv.

[12]  A. Viale,et al.  The Oncogenic Action of NRF2 Depends on De-glycation by Fructosamine-3-Kinase , 2019, Cell.

[13]  Daron M. Standley,et al.  MAFFT-DASH: integrated protein sequence and structural alignment , 2019, Nucleic Acids Res..

[14]  M. Wilkinson,et al.  Inadvertent Paralog Inclusion Drives Artifactual Topologies and Timetree Estimates in Phylogenomics , 2019, Molecular biology and evolution.

[15]  Anthony R. Borneman,et al.  Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies , 2018, BMC Bioinformatics.

[16]  Davide Heller,et al.  eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses , 2018, Nucleic Acids Res..

[17]  S. Kelly,et al.  OrthoFinder: phylogenetic orthology inference for comparative genomics , 2019, Genome Biology.

[18]  Brent S. Pedersen,et al.  GOATOOLS: A Python library for Gene Ontology analyses , 2018, Scientific Reports.

[19]  Michael Hiller,et al.  The axolotl genome and the evolution of key tissue formation regulators , 2018, Nature.

[20]  M. Michaelides,et al.  Leber Congenital Amaurosis Associated with Mutations in CEP290, Clinical Phenotype, and Natural History in Preparation for Trials of Novel Therapies , 2018, Ophthalmology.

[21]  Sergey Koren,et al.  Integrating Hi-C links with assembly graphs for chromosome-scale assembly , 2018, bioRxiv.

[22]  H. Kurumizaka,et al.  Structural diversity of the nucleosome. , 2018, Journal of biochemistry.

[23]  Michael Hiller,et al.  Author Correction: The axolotl genome and the evolution of key tissue formation regulators , 2018, Nature.

[24]  P. Huppke,et al.  Activating de novo mutations in NFE2L2 encoding NRF2 cause a multisystem disorder , 2017, Nature Communications.

[25]  Nicolas Bailly,et al.  Phylogenetic classification of bony fishes , 2017, BMC Evolutionary Biology.

[26]  Sudhir Kumar,et al.  TimeTree: A Resource for Timelines, Timetrees, and Divergence Times. , 2017, Molecular biology and evolution.

[27]  Jacob M. Luber,et al.  HiGlass: web-based visual exploration and analysis of genome interaction maps , 2017, Genome Biology.

[28]  Axel Visel,et al.  Progressive Loss of Function in a Limb Enhancer during Snake Evolution , 2016, Cell.

[29]  M. Schatz,et al.  Phased diploid genome assembly with single-molecule real-time sequencing , 2016, Nature Methods.

[30]  William Chow,et al.  gEVAL — a web-based browser for evaluating genome assemblies , 2016, bioRxiv.

[31]  Raymond J. Moran,et al.  The Interrelationships of Placental Mammals and the Limits of Phylogenetic Inference , 2016, Genome biology and evolution.

[32]  Wen J. Li,et al.  Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation , 2015, Nucleic Acids Res..

[33]  O. Kohany,et al.  Repbase Update, a database of repetitive elements in eukaryotic genomes , 2015, Mobile DNA.

[34]  Serafim Batzoglou,et al.  Read clouds uncover variation in complex regions of the human genome , 2015, RECOMB.

[35]  Mihai Albu,et al.  C2H2 zinc finger proteins greatly expand the human regulatory lexicon , 2015, Nature Biotechnology.

[36]  A. von Haeseler,et al.  IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies , 2014, Molecular biology and evolution.

[37]  R. Mueller,et al.  Hellbender Genome Sequences Shed Light on Genomic Expansion at the Base of Crown Salamanders , 2014, Genome biology and evolution.

[38]  Dong Liu,et al.  Functional roles of Lgr4 and Lgr5 in embryonic gut, kidney and skin development in mice. , 2014, Developmental biology.

[39]  R. Zardoya,et al.  Life-history evolution and mitogenomic phylogeny of caecilian amphibians. , 2014, Molecular phylogenetics and evolution.

[40]  Ziheng Yang,et al.  PAMLX: a graphical user interface for PAML. , 2013, Molecular biology and evolution.

[41]  J. McInerney,et al.  Heterogeneous Models Place the Root of the Placental Mammal Phylogeny , 2013, Molecular biology and evolution.

[42]  Li Lai,et al.  Lgr4 in Ocular Development and Glaucoma , 2013, Journal of ophthalmology.

[43]  Aaron A. Klammer,et al.  Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data , 2013, Nature Methods.

[44]  R. A. Pyron,et al.  A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes , 2013, BMC Evolutionary Biology.

[45]  D. Gower,et al.  A New Species of Skin-Feeding Caecilian and the First Report of Reproductive Mode in Microcaecilia (Amphibia: Gymnophiona: Siphonopidae) , 2013, PloS one.

[46]  D. Olive,et al.  The butyrophilin (BTN) gene family: from milk fat to the regulation of the immune response , 2012, Immunogenetics.

[47]  M. Wilkinson.  Caecilians , 2012, Current Biology.

[48]  F. Delsuc,et al.  Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria) , 2012, BMC Biology.

[49]  Gabor T. Marth,et al.  Haplotype-based variant detection from short-read sequencing , 2012, 1207.3907.

[50]  Diego San Mauro,et al.  Discovery of a new family of amphibians from northeast India with ancient links to Africa , 2012, Proceedings of the Royal Society B: Biological Sciences.

[51]  Abdelkader Essafi,et al.  Opposing Functions of the ETS Factor Family Define Shh Spatial Expression in Limb Buds and Underlie Polydactyly , 2012, Developmental cell.

[52]  Simon Whelan,et al.  Measuring the distance between multiple sequence alignments , 2012, Bioinform..

[53]  Diego San Mauro,et al.  A nine-family classification of caecilians (Amphibia: Gymnophiona) , 2011 .

[54]  Ning Ma,et al.  BLAST+: architecture and applications , 2009, BMC Bioinformatics.

[55]  A. Mesecar,et al.  Cul3-mediated Nrf2 ubiquitination and antioxidant response element (ARE) activation are dependent on the partial molar volume at position 151 of Keap1. , 2009, The Biochemical journal.

[56]  K. Ozato,et al.  TRIM family proteins and their emerging roles in innate immunity , 2008, Nature Reviews Immunology.

[57]  D. Wake,et al.  Are we in the midst of the sixth mass extinction? A view from the world of amphibians , 2008, Proceedings of the National Academy of Sciences.

[58]  Alexander Souvorov,et al.  Splign: algorithms for computing spliced alignments with identification of paralogs , 2008, Biology Direct.

[59]  Ziheng Yang.  PAML 4: phylogenetic analysis by maximum likelihood. , 2007, Molecular biology and evolution.

[60]  K. Yamamura,et al.  LGR4 Regulates the Postnatal Development and Integrity of Male Reproductive Tracts in Mice1 , 2007, Biology of reproduction.

[61]  H. Greven,et al.  Parental investment by skin feeding in a caecilian amphibian , 2006, Nature.

[62]  A. Spada,et al.  The Purkinje cell degeneration 5J mutation is a single amino acid insertion that destabilizes Nna1 protein , 2006, Mammalian Genome.

[63]  Alejandro A. Schäffer,et al.  WindowMasker: window-based masker for sequenced genomes , 2006, Bioinform..

[64]  C. Plessy,et al.  Enhancer sequence conservation between vertebrates is favoured in developmental regulator genes. , 2005, Trends in genetics : TIG.

[65]  James O. McInerney,et al.  Clann: investigating phylogenetic information through supertree analyses , 2005, Bioinform..

[66]  Robert C. Edgar,et al.  MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.

[67]  W. Himstedt,et al.  A molecular phylogeny of ichthyophiid caecilians (Amphibia: Gymnophiona: Ichthyophiidae): out of India or out of South East Asia? , 2002, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[68]  Joseph P Bielawski,et al.  Accuracy and power of bayes prediction of amino acid sites under positive selection. , 2002, Molecular biology and evolution.

[69]  J. D. Thompson,et al.  Towards a reliable objective function for multiple sequence alignments. , 2001, Journal of molecular biology.

[70]  H. Huang,et al.  Regulation of the antioxidant response element by protein kinase C-mediated phosphorylation of NF-E2-related factor 2. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[71]  J. Martinez-Barbera,et al.  Mutations in the homeobox gene HESX1/Hesx1 associated with septo-optic dysplasia in human and mouse , 1998, Nature Genetics.

[72]  R. Axel,et al.  A novel multigene family may encode odorant receptors: A molecular basis for odor recognition , 1991, Cell.

[73]  D. Wake,et al.  Declining amphibian populations: A global phenomenon? , 1990 .

[74]  M. Wake,et al.  Tentacle development in dermophis mexicanus (amphibia, gymnophiona) with an hypothesis of tentacle origin , 1987, Journal of morphology.

[75]  M. Wilkinson.  A new genus and species of rhinatrematid caecilian (Amphibia: Gymnophiona: Rhinatrematidae) from Ecuador , 2021 .

[76]  A. J. Crawford,et al.  Advancing Understanding of Amphibian Evolution, Ecology, Behavior, and Conservation with Massively Parallel Sequencing , 2018 .

[77]  S. Nagini,et al.  Cytochrome P450 Structure, Function and Clinical Significance: A Review. , 2018, Current drug targets.

[78]  D. Balasubramanian,et al.  Gamma crystallins of the human eye lens. , 2016, Biochimica et biophysica acta.

[79]  Jesús A. Ballesteros,et al.  A New Orthology Assessment Method for Phylogenomic Data: Unrooted Phylogenetic Orthology. , 2016, Molecular biology and evolution.

[80]  Ari Löytynoja,et al.  Phylogeny-aware alignment with PRANK. , 2014, Methods in molecular biology.

[81]  O. Oommen,et al.  A subterranean generalist predator: diet of the soil-dwelling caecilian Gegeneophis ramaswamii (Amphibia; Gymnophiona; Caeciliidae) in southern India. , 2004, Comptes rendus biologies.

[82]  B. Olsen,et al.  Collagen IX. , 1997, The international journal of biochemistry & cell biology.

[83]  E. H. Taylor.  The Caecilians of the World: A Taxonomic Review , 1968 .