The oak gene expression atlas: insights into Fagaceae genome evolution and the discovery of genes regulated during bud dormancy release

Table 1 Description of oak transcriptomic assemblies

A/ Assembly			Long-reads	Short-reads	OCV3
Number of trimmed sequences considered in the assembly			2,888,537	417,337,626	/
Number of trimmed sequences incorporated in the assembly			2,003,295	417,337,626	274,867
Number of contigs > 100bp, after redundancy reduction			44,272	230,595	192,097
Number of singletons			300,373	40,119,145	/
Consensus (total bp)			/	/	199,278,344
Average contig size (bp)			937	877	1,037
B/			OCV1	OCV2	OCV3
Number of contigs			69,154	65,712	192,097
Mean length (bp)			705	1,003	1,037
Median (bp)			606	734	597
N50 (bp)			908	1,545	1,879
Consensus (bp)			48,751,826	65,913,455	199,278,344
Nb of annotated contigs in SwissProt			34,614	38,292	63,857
Nb of unique SwissProt ID			13,333	16,429	17,476
C/	Number of contigs > 100bp, after redundancy reduction	Assembly (total bp)	Mean contig size (bp)	Median contig size (bp)	N50 (bp)
OCV3-91k	90,786	148,088,893	1,631	1,292	2,329
OCV3-101k	101,311	51,187,294	505	328	697
OCV3	192,097	199,278,344	1,037	597	1,879

A Characteristics of the long-reads, short-reads and meta assemblies (OCV3).
B Side-by-side comparison of oak unigene sets (OCV1: assembly from Ueno et al. [8], OCV2: assembly from Tarkka et al. [22], and OCV3: this paper). N50 length is defined as the length for which the collection of all contigs of that length or longer contains at least half of the total of the lengths of the contigs.
C Comparison between OCV3-91k (Unigenes with BlastX hit) and OCV3-101k (Unigenes without BlastX hit) subsets: assembled sequences (in bp), mean and median contig sizes, N50.

ISSN: 1471-2164