First identification of long non-coding RNAs in fungal parasite Nosema ceranae

Abstract

Nosema ceranae is a unicellular fungal parasite of honey bees and causes huge losses for apiculture. Until present, no study on N . ceranae long non-coding RNAs (lncRNAs) was documented. Here, we sequenced purified spores of N . ceranae using strand-specific library construction and high-throughput RNA sequencing technologies. In total, 83 novel lncRNAs were predicted from N . ceranae spore samples, including lncRNAs, long intergenic non-coding RNAs (lincRNAs), and sense lncRNAs. Moreover, these lncRNAs share similar characteristics with those identified in mammals and plants, such as shorter length and fewer exon number and transcript isoforms than protein-coding genes. Finally, the expression of 12 lncRNAs was confirmed with RT-PCR, confirming their true existence. To our knowledge, this is the first evidence of lncRNAs produced by a microsporidia species, offering novel insights into basic biology such as regulation of gene expression of this widespread taxonomic group.RNA-seq / long non-coding RNA / Nosema ceranae / honey bee

Transcriptome-wide expression profiling of Sporothrix schenckii yeast and mycelial forms and the establishment of the Sporothrix Genome DataBase

“…These results are in contrast with the very few findings dealing with lncRNAs in other fungi [43,45,46], in which intergenic regions appear to be the main sources of these RNA molecules. However, our data are in line with the results of two recent studies in Schizosaccharomyces pombe [41] and Nosema ceranae [47], where most of the discovered lncRNAs were transcribed as natural antisense transcripts (NATs). NATs are RNA molecules that originate from opposite DNA strands of the same genomic locus (cis-NAT) or unlinked loci (trans-NAT), and can be generically defined as coding RNAs or ncRNAs that are complementary to, and overlap with, either protein-encoding or non-coding transcripts [48].…”

Reconstruction and functional annotation of Ascosphaera apis full-length transcriptome via PacBio single-molecule long-read sequencing

“…In addition, the majority (72.37%) of the lncRNAs were single exons, and this percentage was obviously higher than that of mRNAs (20.51%) ( Figure 6C ). We additionally observed that when compared with protein-coding transcripts, non-coding transcripts had fewer exons, shorter exon and intron lengths, shorter transcript lengths, lower GC percentages, lower expression levels, and fewer comparison of alternative splicing (AS) events ( Figure 6D-I ), which are similar to findings in other species [26–29].…”

Genome-wide identification of long non-coding RNAs and their regulatory networks involved in Apis mellifera ligustica response to Nosema ceranae infection

“…In plants, 6,480 transcripts have been classified as lncRNAs in Arabidopsis [29]; 125 putative stress-responsive lncRNAs have been identified in wheat [30]. In microorganisms, our research group identified 379 novel lncRNAs in Ascosphaera apis (another common fungal pathogen of honeybee), 83 in N. ceranae, and revealed that these fungal lncRNAs shared similar characteristics with those in mammals and plants, such as shorter length and fewer exon number [31,32]. Recently, a number of lncRNAs were identified in insects such as Plutella xylostella [33], Anopheles gambiae [34], and Bombycis mori [35].…”

“…Fresh spores were isolated from naturally-infected foragers from a colony located at Fuzhou city, Fujian province, China, following the method described by Cornman et al [40] with some modifications [32]. (1) bees were kept in -20 °C for 5 min to anesthetize them, followed by separation of midguts with clean dissection tweezers, homogenization in distilled water, filtration in four layers of sterile gauze, and then three times of centrifugation at 8000 rpm for 5 min; (2) the supernatant was discarded as the spores remained in the sediment, the re-suspended pellet was further purified on a discontinuous Percoll gradient (Solarbio) consisting of 5 mL each of 25%, 50%, 75% and 100% Percoll solution, the spore suspension was overlaid onto the gradient and centrifuged at 14000 rpm for 90 min at 4 °C; (3) the spore pellet was carefully extracted with a sterile syringe and then centrifuged again on a discontinuous Percoll gradient to obtain clean spores ( Figure S1A), which were frozen in liquid nitrogen and stored at -80 °C until deep sequencing, RT-PCR, and real-time quantitative PCR (RT-qPCR).…”