Abstract
BackgroundCaecilians, with a discrete lifestyle, are the least explored group of amphibians. Though with distinct traits, many aspects of their biology are poorly investigated. Obtaining the caecilian genomic sequences will offer new perspectives and aid the fundamental studies in caecilian biology. The caecilian genomic sequences are also important and practical in the comparative genomics of amphibians. Currently, however, only sparse genomic sequences of caecilians are available. Hox genes, an old family of transcription factors playing central roles in the establishment of metazoan body plan. Understanding their structure and genomic organization may provide insights into the animal’s genome, which is valuable for animals without a sequenced genome.ResultsWe sequenced and characterized the Hox clusters of Banna caecilian (Ichthyophis bannanicus) with a strategy combining long range PCR and genome walking. We obtained the majority of the four caecilian Hox clusters and identified 39 Hox genes, 5 microRNA genes and 1 pseudogene (ψHoxD12). There remained seven intergenic gaps we were unable to fill. From the obtained sequences, the caecilian Hox clusters contained less repetitive sequences and more conserved noncoding elements (CNEs) than the frog counterparts. We found that caecilian and coelacanth shared many more CNEs than frog and coelacanth did. Relative rate of sequence evolution showed that caecilian Hox genes evolved significantly more slowly than the other tetrapod species used in this study and were comparable to the slowly evolving coelacanth Hox genes. Phylogenetic tree of the four Hox clusters also revealed shorter branch length especially for the caecilian HoxA, HoxB and HoxD clusters. These features of the caecilian Hox clusters suggested a slowly evolving genome, which was supported by further analysis of a large orthologous protein dataset.ConclusionsOur analyses greatly extended the knowledge about the caecilian Hox clusters from previous PCR surveys. From the obtained Hox sequences and the orthologous protein dataset, the caecilian Hox loci and its genome appear evolving comparatively slowly. As the basal lineage of amphibians and land vertebrate, this characteristic of the caecilian genome is valuable in the study concerning the genome biology and evolution of amphibians and early tetrapods.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1684-0) contains supplementary material, which is available to authorized users.
Highlights
Caecilians, with a discrete lifestyle, are the least explored group of amphibians
Hox clusters in Banna caecilian Based on the Hox gene fragments from our previous PCR survey, we used a strategy that combined long-range PCR
The caecilian Hox clusters appear compact and have fewer repetitive sequences than the Hox clusters in the other organisms studied in this work
Summary
Caecilians, with a discrete lifestyle, are the least explored group of amphibians. Though with distinct traits, many aspects of their biology are poorly investigated. An old family of transcription factors playing central roles in the establishment of metazoan body plan Understanding their structure and genomic organization may provide insights into the animal’s genome, which is valuable for animals without a sequenced genome. Caecilians live in the tropical regions of southeast Asia, Africa, the Seychelles islands and Central and South America. Caecilians are placed in a key position on the vertebrate tree They are the basal lineage of modern amphibians [3,4,5,6], and are the most primitive group of land vertebrates. Only a sparse number of caecilian nucleotide sequences are available in public databases, and most of them are mitochondrial genes from phylogenetic studies.
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