For decades, more and more long non-coding RNAs (lncRNAs) have been confirmed to play important functions in key biological processes of different organisms. At present, most identified lncRNAs and those with known functional roles are from mammalian systems. However, lncRNAs have also been found in primitive eukaryotic fungi, and they have different functions in fungal development, metabolism, and pathogenicity. In this review, we highlight some recent researches on lncRNAs in the primitive eukaryotic fungi, particularly focusing on the identification of lncRNAs and their regulatory roles in diverse biological processes.
T he yeast Pachysolen tannophilus was first isolated from wood extracts used in leather tanning (2) and has gained interest due to its ability to utilize D-xylose (1,7,8) for fuel ethanol production (6,8,10). It can ferment the common sugars (glucose, mannose, and galactose) occurring in hemicellulose hydrolysate mixtures (8) and can produce ethanol from glycerol (4). The whole-genome sequencing of P. tannophilus was performed to provide genetic information as a necessary step toward engineering of the strain and its potential development as an industrial cell factory.Sequencing was performed by a whole-genome shotgun strategy with an Illumina genome analyzer (Beijing Genomics Institute, Shenzhen, China). The raw data of short reads were assembled into 279 contigs which were ordered into 34 scaffolds (Ͼ2 kb) with an N 50 size of 1.1 Mb by using the SOAPdenovo package (3). Augustus software, version 2.5 (9), trained for predicting genes in Debaryomyces hansenii, was utilized to identify protein-coding genes in the genome, and the putative amino acid sequences were used for subsequent gene function annotation analysis. The functional annotation was accomplished by BLASTP analysis (E-value Ͻ 1 ϫ 10 Ϫ5) of protein sequences in the databases (COG and KEGG), and the best hit was selected. Pulsed-field gel electrophoresis (PFGE) (5) was performed to predict the number and approximate sizes of chromosomes. The program for PFGE was 48 h at 3 V/cm with a 500-s switch time at an included angle of 106°with 0.5ϫ Tris-borate-EDTA (TBE) on 0.75% LMP (low melting point) agarose at 14°C.The total length of the sequenced genome was 12,238,196 bp (without N), with a GC content of 29.82%. A total of 1970.8 Mb of raw data was sequenced, representing around 145-fold coverage of the P. tannophilus genome. Five thousand three hundred fortysix protein-coding genes (coding sequences [CDSs]) were predicted, and 4,463 (83.5%) genes were annotated with function.Four coding sequences of P. tannophilus were retrieved from GenBank to compare with the annotated CDSs. There were 2-bp differences among 4,803 bp of length. Furthermore, 13 full-length coding sequences were PCR amplified and resequenced to estimate accuracy. The total resequenced length was 21,111 bp, with 100% similarity obtained.Based on PFGE results, six chromosomal bands were separated, with two of the bands probably migrating as doublets. The sizes of the chromosomal bands were estimated to be 2.9 Ϯ 0.05 Mb (mean Ϯ standard deviation), 2.1 Ϯ 0.04 Mb, 1.9 Ϯ 0.05 Mb, 1.6 Ϯ 0.08 Mb (doublet), 1.3 Ϯ 0.07 Mb (doublet), and 0.98 Ϯ 0.02 Mb based on comparison with the yeast marker Hansenula wingei. The estimated genome size of P. tannophilus was approximately 13.6 Ϯ 0.4 Mb with an estimated 8 chromosomes.Nucleotide sequence accession numbers. The draft genome sequences of P. tannophilus were deposited in EMBL with contig accession numbers CAHV01000001 to CAHV01000267. ACKNOWLEDGMENTS
Disease resistance (R) gene, RPP13, plays an important role in the resistance of plants to pathogen infections; its function in resistance of wheat to powdery mildew remains unknown. In this study, a RNA‐Seq technique was used to monitor expression of genes in susceptible wheat ‘Jing411’ and resistant near‐isogenic line ‘BJ‐1’ in response to powdery mildew infection. Overall, 413 differential expression genes were observed and identified as involved in disease resistance. RPP13 homologous gene on wheat chromosome 7D was preliminarily identified using the wheat 660K SNP chip. RPP13 was highly expressed in ‘BJ‐1’ and encodes 1,027 amino acids, including CC, NB and LRR domain, termed TaRPP13‐3. After inoculation with powdery mildew, expression of TaRPP13‐3 in resistant wheat changed with time, but average expression was higher when compared to susceptible variety, thus indicating that TaRPP13‐3 is involved in resistance to powdery mildew. Virus‐induced gene silencing (VIGS) was used to inhibit expression of TaRPP13‐3 in resistant parent ‘Brock’. Results indicated that silencing of TaRPP13‐3 led to decreased disease resistance in ‘Brock’. Overall results of this study indicate that TaRPP13‐3 gene is involved in the defence response of wheat to powdery mildew and plays a positive role in wheat powdery mildew interactions.
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