Objective

Several species of filamentous fungi have been identified for their bioaccumulation or biosorption potentials [1,2,3,4]. Reduced cost and environmental-toxicity through microbial bioremediation approach makes it favorable over the conventional methods [5]. The genome of several A. flavus strain have been reported previously https://www.ncbi.nlm.nih.gov/genome/?term=aspergillus+flavus). The ability of the A. flavus isolate TERIBR1 to adapt and grow in tannery sludge highly contaminated with chromium inspired us to carry out its whole genome sequencing. The genome sequence reported here was utilized for comparative genomics study to understand the putative influence of the abundantly present non-synonymous SNP in TERIBR1 on the function of candidate genes involved in chromium tolerance [6].

Data description

Pure culture of A. flavus isolate TERIBR1 was recovered through an enrichment culture technique from tannery sludge [containing very high concentration of of Cr(III)] and molecularly characterized by the universal fungal primer set for Ascomycetes (ITS1: 5′ TCCGTAGGTGAACCTGCGG, 3′ (Eurofins India, Cat. No. 24-1023-5/6) and ITS4A: 5′ CGCCGTTACTGGGGCAATCCCTG 3′ (Eurofins India, Cat. No. 24-2002-1/6). Genomic DNA was extracted using the DNeasy plant maxi kit (QIAGEN, USA; cat. No. 68163). Using a whole-genome shotgun approach, two TruSeq paired-end (PE) libraries (insert sizes 180 bp and 500 bp) and a mate pair (MP) library (insert size ~ 5 Kb) was generated. An Illumina (HiSeq 2000) machine at a commercial facility (MOgene LC, USA) was used for sequencing. DNA libraries were loaded into Illumina flow-cells at concentrations of 1.4–1.75 pM. Cluster generation was performed in a cBOT automated cluster generation system. Real Time Analysis (RTA) software (rta_1–13) was used to process the image analysis and base calling. Sequencing of the DNA libraries yielded 5.4 Gb of PE reads and 2.6 Gb of MP reads. The raw reads were trimmed using Trimmomatic V 0.36 [7]. Quality-passed reads were assembled using the de novo genome assembler ALLPATHS-LG. PE reads with overlaps were first combined to form contigs. MP reads were used for gap filling in order to get sequences with minimal N’s and the longest length. Table 1 presents webpage links for genome assembly and annotation data files. The resulting 3,77,32,467 bp (100 X coverage) draft genome assembly [10] comprises of 322 contigs greater than 900 bp and has an N50 of 1,536,000 bp and an L50 of 9 contigs (Additional file 1). The GC content of the assembled genome is 48.30%. 225 out of 248 ultra-conserved eukaryotic genes were identified in the assembly through CEGMA ([8], Additional file 2). The MAKER v2.31.9 [9] genome annotation and curation pipeline predicted 13,587 protein coding genes as compared to 13,659 in NRRL3357. Using blastp search in the NCBI NR database, significant matches were identified for 11,120 protein-coding genes. An InterProScan analysis was also performed in order to further annotate the predicted genes with protein functional domains. 2551 proteins with InterProScan domains were identified (Additional file 3); major protein families included, Major facilitator superfamily (n = 334), fungal specific transcription factor domain (n = 190), Cytochrome P450 (n = 140), sugar (and other) transporters (n = 127), Protein kinase domain (n = 112), short chain dehydrogenase (n = 112) and fungal Zn(2)-Cys(6) binuclear cluster domain (n = 94) (Additional file 4). Genes were also annotated by using Blast2GO V5 basic [10] based on the term “biological function” in Gene Ontology (GO) (Additional file 5).

Table 1 Overview of data files
Full size table

Limitations

Illumina sequencing reads generated in this study were de novo assembled and annotated to understand the gene/protein repertoires in the chromium tolerant isolate of A. flavus. Since the whole genome sequencing project involved use of both PE and MP libraries for scaffold development, a high quality assembly with 100 X coverage could be generated. Therefore, we did not notice any serious limitations of the data.