Improved methods and resources for paramecium genomics: transcription units, gene annotation and gene expression

BMC Genomics

Table 1 Annotation statistics

	P tetraurelia		P. biaurelia		P. sexaurelia		P. caudatum
	V1	V2	V1	V2	V1	V2	V1	V2
Genome size (nt)	72,094,543	72,102,941	75,777,660	74,348,537	67,662,147	67,662,147	29,932,356	29,932,356
Number of scaffolds	697	697	1426	1026	230	230	274	274
N50	412,884	412,881	156,715	159,040	430,207	430,207	312,370	312,370
Genomic GC content	0.28	0.28	0.25	0.25	0.24	0.24	0.28	0.28
Gene number	39,642	41,533	39,110	40,741	34,909	36,477	18,421	18,853
Gene length (nt)	1433.8	1409.91	1460.56	1430.22	1462.39	1430.91	1449.52	1448.91
Percent coding	75	75	71	73	71	73	85	86
Inter coding distance (TGA ↔ TGA)	285.23	244.88	304.13	275.83	362.68	331.12	109.29	87.73
Inter coding distance (ATG ↔ ATG)	451.27	388	462.77	410.36	565.88	501.34	143.39	120.63
Inter coding distance (TGA ↔ ATG)	332.03	286.77	357.91	333.08	433.5	393.35	131.64	116.84
Protein Coding Gene number	39,642	40,460	39,110	40,179	34,909	36,053	18,421	18,592
CDS length (nt)	1363.32	1330.35	1375.51	1359.78	1380.08	1367.54	1386.16	1385.68
Protein Coding Gene GC content	0.3	0.3	0.26	0.26	0.26	0.26	0.29	0.29
Non-coding gene number		1073		562		424		261
Exon number	130,216	136,527	141,873	135,427	126,637	124,022	63,789	62,173
Median exon length (nt)	230	222	200	221	202	213	216	232
Mean exon length (nt)	419.01	411.3	379.19	412.21	380.44	402.57	400.3	423.13
Exon per gene	3.28	3.29	3.63	3.32	3.63	3.4	3.46	3.3
Intron number	90,282	94,711	102,763	94,686	91,728	87,545	45,368	43,320
Median intron length (nt)	25	25	26	25	26	25	22	22
Mean intron length (nt)	25.14	25.31	32.37	25.82	31.32	25.91	25.72	23.3
Number of introns >40 nt	38	720	12,817	1366	9718	1218	2425	720

The genome assembly and v1 annotation of P. tetraurelia were published in [6]. The v2 annotation used the same assembly after polishing with Illumina reads, reported in [37]. The v1 genome assembly and annotation of P. biaurelia and P. sexaurelia were published in [7] and the v1 genome assembly and annotation of P. caudatum were published in [8]. The v2 annotations are those obtained in the present study. In the case of P. biaurelia, the reference genome was filtered to remove scaffolds of obvious bacterial origin before v2 annotation. All annotations are integrated into ParameciumDB and available for download as GFF3 files

ISSN: 1471-2164