Transcriptomic analysis of lignocellulosic biomass degradation by the anaerobic fungal isolate Orpinomyces sp. strain C1A

Table 3 Transcriptional patterns of C1A CAZymes on various substrates

Transcripts	Number of transcripts when grown on
Transcripts	Alfalfa	Energy cane	Corn stover	Sorghum
Glycosyl hydrolases
Significantly upregulated^a	48	39	43	46
Upregulated^b	37	51	44	36
Downregulated^c	36	42	40	40
Significantly downregulated^d	54	61	66	53
No change^e	210	192	192	210
Polysaccharide lyases
Significantly upregulated^a	10	5	3	4
Upregulated^b	6	2	4	2
Downregulated^c	2	4	3	4
Significantly downregulated^d	3	1	5	5
No change^e	19	28	26	25
Carbohydrate esterases
Significantly upregulated^a	55	44	47	45
Upregulated^b	18	29	24	17
Downregulated^c	28	26	23	29
Significantly downregulated^d	35	31	40	22
No change^e	114	119	116	137

^aSignificantly upregulated refers to the number of transcripts with a differential expression p value <0.01 as calculated by the nbinomTest function in the R package DESeq [44]
^bUpregulated refers to the number of transcripts with a differential expression p value between 0.01 and 0.1 as calculated by the nbinomTest function in the R package DESeq [44]
^cDownregulated refers to the number of transcripts with a differential expression p value <0.01 as calculated by the nbinomTest function in the R package DESeq [44]
^dSignificantly downregulated refers to the number of transcripts with a differential expression p value between 0.01 and 0.1 as calculated by the nbinomTest function in the R package DESeq [44]
^eNo change refers to the number of transcripts with a differential expression p value >0.1 as calculated by the nbinomTest function in the R package DESeq [44]

ISSN: 2731-3654