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 5 Significantly expressed KOG-annotated Ascomycota 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
Ascomycetes	All	Plant effect		All	Plant effect		All	Plant effect		All	Plant effect
Ascomycetes		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	71	0	0	28	2	0	769	89	30	729	6	274
Cell motility	0	0	0	0	0	0	1	0	0	0	0	0
Cell wall/membrane/envelope biogenesis	1	0	0	0	0	0	36	2	0	45	0	21
Cytoskeleton	7	0	0	7	2	0	96	13	7	74	1	19
Defense mechanisms	2	0	0	0	0	0	13	0	0	8	0	1
Extracellular structures	4	0	0	0	0	0	5	0	0	3	0	0
Intracellular trafficking, secretion, and vesicular transport	0	0	0	2	0	0	114	15	3	77	0	28
Nuclear structure	0	0	0	0	0	0	9	1	0	7	0	4
Posttranslational modification, protein turnover, chaperones	50	0	0	17	0	0	334	30	14	355	3	128
Signal transduction mechanisms	7	0	0	2	0	0	161	28	6	160	2	73
Information storage and processing	137	0	0	35	0	0	918	51	57	785	4	348
Chromatin structure and dynamics	7	0	0	4	0	0	40	2	2	35	0	22
Replication, recombination and repair	1	0	0	0	0	0	46	1	0	1	0	0
RNA processing and modification	1	0	0	0	0	0	128	13	2	34	1	14
Transcription	3	0	0	31	0	0	90	8	2	61	0	28
Translation, ribosomal structure and biogenesis	125	0	0	0	0	0	614	27	51	654	3	284
Metabolism	134	0	0	16	0	4	1083	113	50	763	3	319
Amino acid transport and metabolism	10	0	0	0	0	0	149	26	1	97	0	45
Carbohydrate transport and metabolism	16	0	0	4	0	0	179	32	7	162	2	91
Cell cycle control, cell division, chromosome partitioning	0	0	0	0	0	0	77	3	1	42	0	17
Coenzyme transport and metabolism	1	0	0	1	0	0	38	1	2	27	0	4
Energy production and conversion	65	0	0	8	0	4	309	19	35	267	0	88
Inorganic ion transport and metabolism	13	0	0	0	0	0	66	8	0	61	0	23
Lipid transport and metabolism	11	0	0	1	0	0	125	12	0	51	0	26
Nucleotide transport and metabolism	1	0	0	0	0	0	42	2	0	20	0	9
Secondary metabolites biosynthesis, transport and catabolism	17	0	0	2	0	0	98	10	4	36	1	16
Poorly characterized	31	0	0	1	0	0	434	67	8	253	0	96
Function unknown	2	0	0	0	0	0	85	6	0	13	0	4
General function prediction only	29	0	0	1	0	0	349	61	8	240	0	92
Total KOG annotated, expressed	373	0	0	80	2	3	3204	320	145	2528	13	1037

The number of significantly expressed KOG-annotated Ascomycota 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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