Microbiome and ecotypic adaption of Holcus lanatus (L.) to extremes of its soil pH range, investigated through transcriptome sequencing

Young, Ellen; Carey, Manus; Meharg, Andrew A.; Meharg, Caroline

doi:10.1186/s40168-018-0434-3

Table 6 Significantly expressed KOG annotated Phialocephala transcripts in root and shoot in each soil

From: Microbiome and ecotypic adaption of Holcus lanatus (L.) to extremes of its soil pH range, investigated through transcriptome sequencing

	SA expressed at ≥ 5 reads in 3 out of 10 samples			SL expressed at ≥ 5 reads in 3 out of 9 samples			RA expressed at ≥ 5 reads in 3 out of 8 samples			RL expressed at ≥ 5 reads in 3 out of 9 samples
Phialocephala	All	Plant effect		All	Plant effect		All	Plant effect		All	Plant effect
Phialocephala	All	Up in a	Up in l	All	Up in a	Up in l	All	Up in a	Up in l	All	Up in a	Up in l
Cellular processes and signaling	1	0	0	0	0	0	370	61	0	6	0	2
Cell motility	0	0	0	0	0	0	1	0	0	0	0	0
Cell wall/membrane/envelope biogenesis	0	0	0	0	0	0	23	1	0	0	0	0
Cytoskeleton	0	0	0	0	0	0	37	6	0	0	0	0
Defense mechanisms	0	0	0	0	0	0	10	0	0	0	0	0
Extracellular structures	0	0	0	0	0	0	5	0	0	0	0	0
Intracellular trafficking, secretion, and vesicular transport	0	0	0	0	0	0	73	14	0	1	0	0
Nuclear structure	0	0	0	0	0	0	6	1	0	0	0	0
Posttranslational modification, protein turnover, chaperones	1	0	0	0	0	0	114	18	0	5	0	2
Signal transduction mechanisms	0	0	0	0	0	0	101	21	0	0	0	0
Information storage and processing	1	0	0	0	0	0	322	35	0	8	0	2
Chromatin structure and dynamics	0	0	0	0	0	0	18	1	0	0	0	0
Replication, recombination and repair	0	0	0	0	0	0	43	1	0	0	0	0
RNA processing and modification	0	0	0	0	0	0	86	10	0	0	0	0
Transcription	0	0	0	0	0	0	64	7	0	0	0	0
Translation, ribosomal structure and biogenesis	1	0	0	0	0	0	111	16	0	8	0	2
Metabolism	1	0	0	0	0	0	601	81	2	4	0	0
Amino acid transport and metabolism	0	0	0	0	0	0	117	24	0	1	0	0
Carbohydrate transport and metabolism	0	0	0	0	0	0	91	19	0	0	0	0
Cell cycle control, cell division, chromosome partitioning	0	0	0	0	0	0	46	2	0	0	0	0
Coenzyme transport and metabolism	0	0	0	0	0	0	25	1	0	0	0	0
Energy production and conversion	1	0	0	0	0	0	93	11	1	1	0	0
Inorganic ion transport and metabolism	0	0	0	0	0	0	38	7	0	0	0	0
Lipid transport and metabolism	0	0	0	0	0	0	85	6	0	0	0	0
Nucleotide transport and metabolism	0	0	0	0	0	0	33	2	0	1	0	0
Secondary metabolites biosynthesis, transport and catabolism	0	0	0	0	0	0	73	9	1	1	0	0
Poorly characterized	0	0	0	0	0	0	319	48	1	0	0	1
Function unknown	0	0	0	0	0	0	78	5	0	0	0	0
General function prediction only	0	0	0	0	0	0	241	43	1	0	0	1
Total KOG annotated	3	0	0	0	0	0	1612	225	3	18	0	5

The number of significantly expressed KOG-annotated Phialocephala transcripts (All) is defined as the number of transcripts that obtained ≥ 5 aligned reads in at least 3 samples from each of the following treatments: root acid bog soil (RA), root limestone soil (RL), shoot acid bog soil (SA) and shoot limestone soil (SL). Significant ecotype effects (absolute log₂FC ≤ − 1 or ≥ 1, FDR < 0.05) as identified by DESeq2 analysis are reported in subsequent columns for each treatment group under the heading plant effect

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ISSN: 2049-2618

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