Integration of mate pair sequences to improve shotgun assemblies of flow-sorted chromosome arms of hexaploid wheat

Table 4 Gene content in ABySS and SSPACE assemblies

Assembly	Arm	Brachypodium homologs	Brachypodium homolog coverage¹(mean)	GFI²	Full length genes
		Brachypodium homologs			Coverage*	Start-stop†
		(>30 aa, >70 pident)			Coverage*	Start-stop†
SSPACE k3	7BS	1029	0.49	0.09	449	193
SSPACE k3	7BL	1539	0.44	0.10	551	224
SSPACE k5	7BS	1038	0.49	0.09	445	193
SSPACE k5	7BL	1545	0.43	0.12	547	227
SSPACE k7	7BS	1032	0.49	0.09	449	196
SSPACE k7	7BL	1551	0.43	0.12	535	221
SSPACE k10	7BS	1038	0.49	0.09	447	195
SSPACE k10	7BL	1555	0.43	0.12	533	215
SSPACE k15	7BS	1040	0.48	0.12	436	186
SSPACE k15	7BL	1576	0.42	0.14	529	217
SSPACE k20	7BS	1048	0.47	0.13	433	183
SSPACE k20	7BL	1574	0.42	0.14	516	205
Contigs	7BS	1071	0.45	0.17	403	160
Contigs	7BL	1621	0.39	0.21	457	162

¹Mean coverage per sequence (contig/scaffold) of Brachypodium homologs based on blast analyses (see methods).
² Gene Fragmentation Index (GFI) is defined in the methods section.
* TBLASTN hits covering > =70% of a homologous Brachypodium protein in a single contig/scaffold.
† TBLASTN hits covering an entire Brachypodium protein (+ − 10aa) in a single contig/scaffold.

ISSN: 1471-2164