Transcriptome Profile of the Green Odorous Frog (Odorrana margaretae)

Abstract

Transcriptome profiles provide a practical and inexpensive alternative to explore genomic data in non-model organisms, particularly in amphibians where the genomes are very large and complex. The odorous frog Odorrana margaretae (Anura: Ranidae) is a dominant species in the mountain stream ecosystem of western China. Limited knowledge of its genetic background has hindered research on this species, despite its importance in the ecosystem and as biological resources. Here we report the transcriptome of O . margaretae in order to establish the foundation for genetic research. Using an Illumina sequencing platform, 62,321,166 raw reads were acquired. After a de novo assembly, 37,906 transcripts were obtained, and 18,933 transcripts were annotated to 14,628 genes. We functionally classified these transcripts by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). A total of 11,457 unique transcripts were assigned to 52 GO terms, and 1,438 transcripts were assigned to 128 KEGG pathways. Furthermore, we identified 27 potential antimicrobial peptides (AMPs), 50,351 single nucleotide polymorphism (SNP) sites, and 2,574 microsatellite DNA loci. The transcriptome profile of this species will shed more light on its genetic background and provide useful tools for future studies of this species, as well as other species in the genus Odorrana. It will also contribute to the accumulation of amphibian genomic data.

Transcriptome analysis reveals the genetic basis underlying the seasonal development of keratinized nuptial spines in Leptobrachium boringii

“…In addition, the mapping rates of clean reads to the assembled unigenes for all samples ranged from 75.70% to 81.83% (Additional file 1: Table S1). Taken together, our de novo assemblies revealed a high quality compared with previous studies [5, 34, 35]. This high quality of sequence reads and assembly was the foundation of all our subsequent analyses [36].…”

“…All of these factors combined with the absence of genomic information for L. boringii would have caused the failure of functional annotation of a part of the identified unigenes. However, considering that previous studies successfully annotated approximately 25,000 genes in other non-model amphibian species, such as Odorrana margaretae , Megophrys sangzhiensis and Rhacophorus omeimontis [34, 37], our gene annotation results (more than 29,000 unigenes annotated) from L. boringii ’s transcriptome can be considered as high quality.…”

Analysis of embryonic development in the unsequenced axolotl: Waves of transcriptomic upheaval and stability

“…No complete genome assembly for the axolotl exists. Without such an assembly, gene identification was performed with one way alignments (Coppe et al, 2010; Qiao et al, 2013). Because of this caveat, our gene identification is only identifying the closest human homolog of the axolotl contig and thus should be considered tentative.…”

Amphibian molecular ecology and how it has informed conservation

“…Open shrub habitat and river crossings facilitate migration between populations, while elevation differences decrease gene flow Johansson et al (2005) Common frog (Rana temporaria) 7 microsats Agricultural fragmentation has markedly different impacts on the species in different parts of its range Funk et al (2005) Columbia spotted frog (R. luteiventris) 6 microsats There is a high degree of gene flow among low-elevation populations, and elevation changes serve as barriers to gene flow have recently been sequenced and assembled, including members of three salamander families [Hynobius chinensis (Che et al 2014), A. mexicanum , Notophthalmus viridescens (Looso et al 2013)] and three anuran families [X. tropicalis (Hellsten et al 2010;Tan et al 2013), X. laevis (Morin et al 2006), Pseudacris regilla/Rana (Lithobates) clamitans (Robertson & Cornman 2014), Rana chensinensis/Rana kukunoris (Yang et al 2012), Rana muscosa/Rana sierrae (Rosenblum et al 2012), Odorrana margaretae (Qiao et al 2013), Espadarana prosoblepon/Rana (Lithobates) yavapaiensis (Savage et al 2014)]. Several of these taxa are endangered in the wild, and the availability of these transcriptome resources will allow researchers to design target-capture arrays using DNA sequence data for a large variety of amphibian species.…”