Analysis of expressed sequence tags from the fungus Aspergillus oryzae cultured under different conditions

Abstract

We performed random sequencing of cDNAs from nine biologically or industrially important cultures of the industrially valuable fungus Aspergillus oryzae to obtain expressed sequence tags (ESTs). Consequently, 21 446 raw ESTs were accumulated and subsequently assembled to 7589 non-redundant consensus sequences (contigs). Among all contigs, 5491 (72.4%) were derived from only a particular culture. These included 4735 (62.4%) singletons, i.e. lone ESTs overlapping with no others. These data showed that consideration of culture grown under various conditions as cDNA sources enabled efficient collection of ESTs. BLAST searches against the public databases showed that 2953 (38.9%) of the EST contigs showed significant similarities to deposited sequences with known functions, 793 (10.5%) were similar to hypothetical proteins, and the remaining 3843 (50.6%) showed no significant similarity to sequences in the databases. Culture-specific contigs were extracted on the basis of the EST frequency normalized by the total number for each culture condition. In addition, contig sequences were compared with sequence sets in eukaryotic orthologous groups (KOGs), and classified into the KOG functional categories.

Figure 1

Sequence length distribution of raw ESTs and contigs. Hatched bar, raw EST (before assembly); Solid bar, contigs (after assembly).

Figure 2

Frequency distribution of the contigs. Contigs were generated by assembling raw ESTs, and they no longer overlapped with each other. The general tendency of frequency, i.e. redundancy of raw ESTs within a contig was analyzed. (A) Total EST contigs. (B) EST contigs of known sequence. (C) EST contigs with no significant similarity.

Figure 3

Dendrogram of culture conditions used for collecting ESTs. Culture conditions were classified based on the normalized frequency values of contigs by hierarchical clustering using the nearest neighbor-joining method.

Figure 4

Functional classification of contigs to major KOG categories. Contigs were compared with the KOG sequence set using BLASTX, and then classified into the major KOG major categories of most similar sequence (E-value < 10E-9). Categorical redundancy of contigs was not removed when they belonged to multiple KOG categories. (A) Total contigs, contigs from LCs, and contigs from SCs (B) contigs from each library.