Abstract
We report here the complete genome sequence of Candida tropicalis no. 121. C. tropicalis no. 121 is a high-RNA-producing strain obtained by mutagenesis in our laboratory. The complete genome sequence was determined using the Illumina HiSeq 2000 and contains 6,415 genes. The genome size of C. tropicalis no. 121 is >15.3 Mb.
GENOME ANNOUNCEMENT
Candida tropicalis belongs to the genus Candida and is a diploid yeast that does not sexually reproduce (1). C. tropicalis is one of the more common Candida spp. causing human diseases in tropical countries. It is of medical, academic, and industrial interest. In the industrial field, C. tropicalis has been used for the production of long-chain dicarboxylic acids (2) and xylitol (3) and induced peroxisomal enzyme expression involved in the utilization of n-alkanes (4). In our study, C. tropicalis no. 121 was a high-yield strain used for RNA production in our laboratory and Nanjing BioTogether Co. Ltd. Under optimal conditions, the maximum RNA and dry cell weight (DCW) concentrations were >2.5 and 15 g liter-1 (5, 6), higher than those for Kluyveromyces marxianus (7). At the present, the genome sequence of C. tropicalis MYA-3404 is available at the National Center for Biotechnology Information (NCBI) (8). It contains 6,441 genes and has a genome size of 14.63 Mb.
Whole-genome sequencing of C. tropicalis no. 121 was performed using the high-throughput sequencing Illumina HiSeq 2000 platform (Beijing Genomics Institute [BGI], Shenzhen, China) by generating short-insert DNA libraries (500 bp, 6 kb, and 10 kb). The read length was 90 bp for these three libraries, resulting in 1,072 Mb to 477 Mb raw data. After the removal of adaptors, low-quality reads, poly-N sequences, error paired-end reads, and duplications, the clean data were assembled using SOAPdenovo version 1.05 and generated 150 contigs of >1,000 bp, with a total length of 14,979,840 bp. The total size of the resulting assembly is 15,326,821 bp, distributed on 150 scaffolds. The G+C content of the complete genome is 33.11%. The finished results were analyzed and annotated using GeneWise, SNAP, Genemarkers, RNAmmer, and tRNA-SE. The gene function annotation was predicted by using the Kyoto Encyclopedia of Genes and Genomes (KEGG), Clusters of Orthologous Groups (COG), Swiss-Prot, and Gene Ontology (GO).
The complete genome sequence of C. tropicalis no. 121 contains 6,415 coding sequences (CDSs), with an average length of 1,462.01 bp, and the total length of the CDSs is 9,378,801 bp. Among the 6,415 genes with an average length of 1,486.53 bp, the numbers of exons and introns are 6,929 and 514, respectively. There is no rRNA predicted by de novo prediction. Two hundred thirteen tRNAs, 49 small nuclear RNAs (snRNAs), and 2 micro-RNAs (miRNAs) were annotated and make up 0.1151%, 0.039%, and 0.0012% of the genome, respectively. In addition, there are 547,234-bp repeat sequences that were found in the genome based on the methods of Repbase, ProMask, De novo, and Tandem Repeats Finder (TRF). Furthermore, 217,480-bp transposons were involved in the whole genome.
Nucleotide sequence accession number.
This whole-genome shotgun project for C. tropicalis no. 121 has been deposited at DDBJ/EMBL/GenBank under the accession no. JGYC00000000.
ACKNOWLEDGMENTS
This work was supported by the Major Program of the National Natural Science Foundation of China (21390204), the National Outstanding Youth Foundation of China (grant 21025625), the National High-Tech Research and Development Program of China (863) (grant 2012AA021200), the National Basic Research Program of China (973) (grant 2011CBA00806), the National Key Technology R&D Program (2012BAI44G01), the Program Changjiang Scholars and Innovative in University (grant IRT1066), the National Natural Science Foundation of China, Youth Program (grant 21106070), Jiangsu Provincial Natural Science Foundation of China (grant BK2011031), the Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD), and the Jiangsu Provincial Graduate Student Innovation Project (CXZZ13_0457).
Footnotes
Citation Li B, Guo T, Chen Y, Xie J, Niu H, Liu D, Cheng J, Chen X, Wu J, Zhuang W, Zhu C, Ying H. 2014. Genome sequence of Candida tropicalis no. 121, used for RNA production. Genome Announc. 2(3):e00316-14. doi:10.1128/genomeA.00316-14.
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