. 2012 Dec 26;4(1):e00428-12. doi: 10.1128/mBio.00428-12

TABLE 1 .

Statistics of P. jirovecii and P. carinii nuclear and mitochondrial genomes

Characteristic	Result
Characteristic	P. jirovecii	P. carinii^a
Assembly
Assembly size (Mb)	8.1	6.3
Mean 454 read depth	36	NA^b
Mean Illumina read depth	1,315	NA
No. of contigs	358	4,278
N₅₀ (kb)	41.6	2.2
Mean GC content (%)	28.4	32.5
Annotation
No. of CDSs	3,898	4,591^c
Coding regions (%)	68.9	50.0
No. of KEGG orthologs^d	269	252
No. of tRNA genes	77^e	36^f
Mean gene length (bp)	1,472	891
Mean exon length (nt)	211	223
Mean no. of introns per gene	4.5	2.3
Mean intron length (nt)	61	54
Repeat density (%)	9.86	5.71
Mitochondrial genome
Assembly size (kb)	27	23^g
No. of contigs	3	1
GC content in whole genome (%)	29.5	31.1
GC content in coding genes (%)	32.5	30.9
No. of protein coding genes (CDSs)	17	17
No. of rRNA genes	2	2
No. of tRNA genes	12	20

^{^a}

The P. carinii assembly was downloaded from the Pneumocystis genome project website (http://pgp.cchmc.org/) and corresponds to the sequences published by Slaven et al. (15). This assembly is known to be incomplete.

^{^b}

Not applicable.

^{^c}

Some of these peptides were derived from incomplete CDSs located at the extremity of a contig. Hence, the numbers of predicted peptides provide only a rough estimation of the proteome size.

^{^d}

The number of KEGG orthologs was computed as described previously (4).

^{^e}

Not including pseudo tRNAs.

^{^f}

Only complete copies are shown; the total number of tRNAs in the genome may be more important.

^{^g}

P. carinii mitochondrion data were computed from the published genome (16).