Community transcriptomics reveals universal patterns of protein sequence conservation in natural microbial communities

Table 2 Mean percentage amino acid identity of 454 reads matching database reference genes (NCBI-nr) shared between and unique to DNA and RNA samples

			Percentage identity to reference genes present in^a
	Depth (m)	Data	DNA+RNA^b	DNA only^c	RNA only	All^d
OMZ	50	DNA	71.0	59.8	NA	60.8
		RNA	73.8	NA	72.2	72.7
	85	DNA	67.3	59.5	NA	59.8
		RNA	68.4	NA	67.9	68.1
	110	DNA	65.7	58.7	NA	59.7
		RNA	68.5	NA	71.1	70.2
	200	DNA	64.3	58.5	NA	59.1
		RNA	67.0	NA	65.9	66.4
BATS 216	20	DNA	72.5	59.5	NA	62.7
		RNA	75.6	NA	71.6	72.9
	50	DNA	76.4	61.5	NA	64.4
		RNA	78.3	NA	71.2	74.1
	100	DNA	76.8	60.5	NA	63.9
		RNA	78.6	NA	71.6	74.8
HOT 186	25	DNA	75.3	63.7	NA	65.7
		RNA	76.4	NA	69.1	72.0
	75	DNA	77.3	64.1	NA	65.6
		RNA	77.5	NA	69.1	72.9
	110	DNA	80.0	60.7	NA	62.4
		RNA	81.3	NA	73.0	77.1
	500	DNA	63.1	59.4	NA	59.6
		RNA	64.0	NA	66.0	65.0
Soil	Surface	DNA	58.9	55.0	NA	56.1
		RNA	59.8	NA	61.1	60.5

^aMean percentage identity across all genes (unique accession numbers) identified via BLASTX against NCBI-nr (HSP alignment regions only; bit score cutoff = 50). ^bGenes present in both DNA and RNA datasets, that is, 'expressed' genes. ^cGenes present only in the DNA dataset, that is, 'non-expressed' genes. ^dGenes shared between datasets (in DNA + RNA) plus genes unique to a dataset. BATS, Bermuda Atlantic Time Series; BLAST, Basic Local Alignment Search Tool; HOT, Hawaii Ocean Time Series; HSP, high-scoring segment pair; NA, not applicable; NCBI-nr, National Center for Biotechnology Information non-redundant protein database; OMZ, oxygen minimum zone; rRNA, ribosomal RNA.

ISSN: 1474-760X