Project description:Background Banna caecilian (Ichthyophis bannanicus) is the only species of Gymnophiona in China, with unique lifestyles and characteristics. Although there have been some studies on distribution and morphological characteristics in I. bannanicus, little research focused on the molecular level. A comprehensive analysis of gene expression profiling across tissues can provide necessary information for an in-depth understanding of their biological functions. Result To provide new insights into molecular mechanisms of ecological adaptation in I. bannanicus, we performed gene expression analysis across 10 tissues including skin, blood, spleen, liver, kidney, lung, heart, stomach, testis and ovary. By integrating 27 newly generated RNA-seq datasets with 21 publicly available transcriptomes, we performed a systematic gene expression analysis across tissues representing 19 major organ systems, thereby generating a comprehensive and high-resolution transcriptomic atlas for I. bannanicus. We identified 5,092 housekeeping genes (HKGs) and 2,169 tissue-specific genes (TSGs), and conducted weighted gene co-expression network analysis to determine the modules most relevant to each tissue. Functional enrichment indicated that HKGs support basic cellular activities, while TSGs and the module genes are associated with tissue differentiation and specific physiological processes. Our comparative genomic analysis of I. bannanicus and Xenopus tropicalis revealed genes potentially lost in I. bannanicus, including RCVRN.1, GNAT2, SAG, GRK7, SMURF1, NOG, and MAPK14, which may be associated with degeneration of its visual system and limb structures. Notably, cross-species comparison of HKGs, TSGs, and co-expression modules highlighted an enhanced and unique immune capacity in I. bannanicus. Conclusion Our findings demonstrate that HKGs, TSGs, and co-expression module genes offer valuable perspectives on tissue specialization and evolutionary divergence. The comparative transcriptomic analysis across multiple species and diverse tissue types provides valuable clues into the molecular features that may contribute to ecological adaptation in I. bannanicus.

Project description: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.

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Ichthyophis bannanicus

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