Automated alignment-based curation of gene models in filamentous fungi

BMC Bioinformatics

Table 2 Gene models in six fungal species re-annotated by the ABFGP method

Species	Botrytis cinerea		Cladosporium fulvum		Dothistroma septosporum		Mycosphaerella fijiensis		Verticillium dahliae		Zymoseptoria tritici ¹
Sequence technology	Sanger		454		Illumina/454/Sanger		Sanger		Sanger		Sanger
Fold genome coverage	4.5		21		34		7.1		7.5		8.9
# Annotated genes	16,448		14,127		12,580		10,313		10,535		10,952
Annotation pipeline²	BROAD		GeneMark-ES		JGI		JGI		BROAD		JGI
Annotation year³	2005		2009		2010		≤2008		2008		2008
Reference	[21]		[20]		[20]		n.a.		[22]		[23]
Total eligible gene models	8,503		7,574		8,090		7,283		8,362		7,893
Bi Directional Best Hit	7,165		6,990		7,511		6,773		7,814		7,317
Gene Model Error	1,338		584		579		510		548		576
Confirmed/unchanged⁴	4,832	57%	5,823	77%	6,249	77%	4,775	66%	5,390	64%	5,262	67%
Revised⁴	3,505	41%	1,724	23%	1,770	22%	2,456	34%	2,870	34%	2,553	32%
Bi Directional Best Hit⁵	2,481	35%	1,304	19%	1,404	19%	2,064	30%	2,511	32%	2,137	29%
Gene Model Error⁵	1,024	77%	420	72%	366	63%	392	77%	359	66%	416	72%
Aborted⁴	166	2,0%	27	0,4%	71	0,9%	52	0,7%	102	1,2%	78	1,0%

¹Formerly named Mycosphaerella graminicola.
²Sequencing centre which sequenced and annotated this genome (BROAD institute or Joint Genome Institute); C. fulvum was sequenced at Wageningen University and annotated using GeneMark-ES version 2.2 [20].
³Estimated year the gene calling was performed.
⁴Number and percentage of all gene models in this category.
⁵Number and percentage of revised gene models in this category.

ISSN: 1471-2105