Repertoire-wide gene structure analyses: a case study comparing automatically predicted and manually annotated gene models

Table 1 Summary statistics of the genomes, automatically annotated and manually annotated gene sets, and gene model properties for the seven analyzed species

		Holometabolous				Hemimetabolous
		Coleoptera		Hymenoptera		Hemiptera		Thysanoptera
		Anoplohora glabripennis	Leptinotarsa decemlineata	Athalia rosae	Orussus abietinus	Cimex lectularius	Oncopeltus fasciatus	Frankliniella occidentalis
	Assembly size [Mbp] (% determined nucleotides)	707.7 (85.1)	1170.2 (58.0)	163.8 (95.7)	201.2 (92.7)	650.5 (79.0)	1098.7 (70.4)	415.8 (63.4)
	AUTO	22,253	24,732	11,956	10,966	14,085	19,587	18,021
	OGS	22,035	24,671	11,894	10,959	13,953	19,615	17,553
	AUTO-	749	972	805	659	795	1013	1118
	SUB
	AUTO-SUB % of AUTO	3.4	3.9	6.7	6.0	5.6	5.2	6.2
	MAN-SUB	770	933	825	670	778	945	1127
	MAN-SUB % of OGS	3.5	3.8	6.9	6.1	5.6	4.8	6.4
	MAN-ADD	216	98	50	30	221	161	381
	MAN-ADD % of OGS	1.0	0.4	0.4	0.3	1.6	0.8	2.2
Median transcript length [bp]	AUTO-SUB	6183	8562.5	4340	5200	4362	9324	5001.5
Median transcript length [bp]	MAN-SUB	5789.5	9280	3208	3996	4360	11,244	4064
Median protein length [aa]	AUTO-SUB	358	255	445	430	358	257	419.5
Median protein length [aa]	MAN-SUB	389	300	423	419	372.5	320	419
Median exon count p.t.	AUTO-SUB	4	4	6	5	5	4	6
Median exon count p.t.	MAN-SUB	4	4	5	5.5	5	4	6
Median median exon length p.t. [bp]	AUTO-SUB	1210	984	2220	2151	1200	1086	1807.5
Median median exon length p.t. [bp]	MAN-SUB	1345.5	1127	1786	1828	1194.5	1347	1755
Median median intron length p.t. [bp]	AUTO-SUB	354.75	1192	107.5	1278.25	75	126.75	108
Median median intron length p.t. [bp]	MAN-SUB	359	1363	100.5	1434	74	123	100.75

Summary statistics on assemblies and manual annotation actions for each species and selected set-wide property values of MAN-SUB and AUTO-SUB
aa amino acids, bp base pairs, det. Nucs. determined nucleotides (i.e., not N), Mbp mega base pairs, OGS official gene set, p.t.: per transcript

ISSN: 1471-2164