| Miniaturization denotes extremely small body size within a lineage, and shows implications for the diversity of species. Miniaturized taxa are frequently characterized by a trend towards reduction and simplification on morphology; and they are also accompanied by morphological and behavior changes. This phenomenon is observed in all vertebrate lineages. In fish species, mature individuals fewer than20mm have been termed’ miniature fishes’. Paedocypris is a newly established genus of minifish and three species have been described, and it represents the smallest mature adult fish. By estimating the DNA content of one of species in Paedocypris, the result showed that its genome size was only315Mb, which is the smallest one in vertebrates so far. Species of this genus inhabit highly acidic condition, and have extremely simplified skeletal structure accompanied with a poorly ossified and many ’larval’characteristics associated with paedomorphic fish. Moreover, they do not show obvious sexual maturity, instead they show reproductive behavior during the physical development process. Thus, Paedocypris is excellent model for studying the mechanism of miniaturization.In this study, twenty-four individuals, which were a representative species of Paedocypris, were subjected to construct twelve cDNA libraries, and perform de novo transcriptome sequencing using the Illumina HiSeq2000platform. Finally, we obtained240Mbp trancriptomic data of P. carbunculus with N50of3,123bp. Our aim is to find out clues for genome miniaturization. Based on the reliable homogeneity of libraries, trancriptomic data was performed annotation.17,926Uniprot IDs in total were obtained, which was similar to18,523coding genes expressed in Fugu, but much less than26,459coding genes in zebrafish. Among them,13,640Uniprot IDs are homologous to known proteins or ORFs, and1,182ones were predicted as novel proteins. Gene Ontology (GO) analysis suggests that the functions of these genes mostly focus on biological processes of metabolism and cell processes, cellular components and also processes of enzyme activation and binding. According to the special morphological characteristics of Paedocypris, the expression of genes involved in bone formation were checked and compared with human and zebrafish. The results suggested there were less related genes in P. carbunculus. There are about109genes belong to12gene families involved in bone formation in zebrafish, but only62related genes belong to9gene families are expressed in P. carbunculus. It showed obviously decrease among these three species. The loss of other genes might be caused by sharp decrease in genome size during the evolution of miniaturization.After gene expression analysis, the top300high-expressed Uniprot IDs were selected and performed comprehensive functional annotation. Among them,160genes or gene families were identified. The functions of these genes focus on energy metabolism, cellular components, and biomolecules. Additionally, KEGG pathway analysis of these300genes involved in158KEGG pathways and the largest functional group was metabolic pathways. This revealed in need of high energy consumption for rapid movement and frequent mating. Interestingly, we found that some genes which usually might be found in juvenile development were identified and highly expressed. Including those related to organ development (e. g. nop56involved in heart development and rps4x related to brain development.). It might suggest special developmental pattern of these species, namely, reproductive behavior occurs during the physical development. This needs confirming and supporting by more experiments.This study provides valuable resources for further analyses on mechanism of miniaturization taxa, and also proves Paedocypris, which features a tiny genome, an unusual reproductive mode and truncated development, is excellent model for studying vertebrate genome miniaturization. |
PDF Full Text Request