The Lotus japonicus Genome

space coverage of v. 3.0 is ~98 % based on the
placement of 57,916 de novo assembled RNA-
seq contigs and 25,694 tentative contigs (TCs,L.
japonicusGene Index v. 6.0) (Sato et al. 2014 ).

4.3 Gene Annotation

In early versions of the genome assembly, 1.0
and 2.5, annotation relied on ab initio predictions
and homology to available protein sequences. In

version 3.0 a hierarchical approach, prioritizing

transcription evidence was used instead (Sato

et al. 2014 ). The differences in annotation

approaches did not greatly influence the number

of annotated protein coding genes, which

remained around 40,000. However, the number

of annotated amino acids increased by 20 %

between v. 1.0 and 3.0, and this increase was

reflected by an increase in the number of

assigned peptides from proteomics data (Sato

et al. 2014 ).

Illumina reads

mate pair 38 bp

(2kb, 5kb)

Illumina reads

paired end 108 bp

(200bp, 500bp) ~ 14 Gbp ~ 3 Gbp

454 GS FLX paired end reads

(3kb, 8kb)

Filtering of repeat sequences against Lj_rep

Integration by mapping

(Megablast)

Combined assembly by PCAPrep

Version 2.5 phase

1 regions

LjSGA

de novo assembly by SOAPdenovo seqs

Upgraded pseudomolecules (build 3.0)

phase 2,3 sequences in version 2.5

additional finished TAC/BAC clones

Anchoring the scaffolds

(Marker-seq & pair-end info.)

Finished clone integrated contigs

Fig. 4.1 Summary of the hybrid assembly strategy used forL. japonicusgenome sequence version 3.0

Table 4.1 Assembly statistics ofL. japonicusgenome sequences in version 1.0, 2.5 and 3.0

Version 1.0 Version 2.5 Version 3.0

Total length of scaffolds (bases) 315,073,275 296,886,266 393,918,449

Anchored scaffolds

Number of anchored scaffolds 594 647 132

Length of anchored scaffolds (bases) 130,251,279 184,542,525 231,615,632

Unanchored scaffolds

Number of unanchored scaffolds 110,346 67,902 23,572

Length of unanchored scaffolds (bases) 184,821,996 112,343,741 162,302,817

4 Genome Sequencing 37