Interspecific and host-related gene expression patterns in nematode-trapping fungi

BMC Genomics

Table 2 Characterization of the transcriptome libraries

Library^a	Ao(Mh)	Ao(Hs)	Ad(Mh)	Ad(Hs)	Mc(Hs)
Reads
Total number of reads	114 418	70 061	226 301	191 632	245 264
Filtered reads^b	97 770	58 208	183 433	141 506	206 854
Isotigs
Total number of isotigs	2 663	1 354	4 517	4 003	5 258
Fungal isotigs	2 514	1 261	4 021	3 560	4 741
Nematode isotigs	11	20	21	18	44
Others	0	5	8	4	16
Filtered isotigs^c	2 634	1 318	4 428	3 926	5 140
(Average size, bp)	(1 160)	(1 008)	(1 237)	(1 128)	(1 167)
Isotigs with Pfam	1 730	856	2 317	2 504	3 071
Number of unique Pfam	1 251	707	1 555	1 592	1 847
Isotigs with UniRef50	2 485	1 239	3 916	3 472	4 601
Unique UniRef50	2 326	1 174	3 101	3 230	3 981
Mapping to Ao genome
Number of mapped reads	73 623	40 051
Number of gene models^d	7 351	6 377

^aThe following five combinations of fungi and nematodes were characterized: A. oligospora and M. hapla (Ao(Mh)), A. oligospora and H. schachtii (Ao(Hs)), A. dactyloides and M. hapla (Ad(Mh)), A. dactyloides and H. schachtii (Ad(Hs)), and M. cionopagum and H. schachtii (Mc(Hs)).
^bNumber of reads after removal of rRNA sequences.
^cNumber of isotigs after removal of non-fungal sequences, low abundance isotigs (less than 5 reads), and short isotigs (<100 bp).
^dNumber of gene models that have ≥1 read.

ISSN: 1471-2164