short tandem repeats in v. 3.0 was lower than the
fraction in TAC end sequences, reflecting that the
highly repetitive heterochromatic regions are
underrepresented in the v. 3.0 genome sequence.
4.5 Resequencing of Wild
Accessions and Species
Polymorphism information from resequencing of
bothL. japonicusaccessions and different Lotus
species is a valuable resource that will facilitate
genetic mapping, including linkage mapping in
bi-parental populations and genome-wide asso-
ciation studies (GWAS). Currently, a whole-
genome resequencing strategy is being used to
sequence 130 JapaneseL. japonicusaccessions
and a number of, mainly diploid, different Lotus
species includingL. burttii,L. corniculatus,L.
filicaulis,L. glaber,L. japonicus,L. peduncula-
tus,L. preslii,L. subbiflorus,L. tenuis,L. uligi-
nosusandL. krylovii. The polymorphism density
and rate linkage disequilibrium decay within the
Japanese population sample appear compatible
with GWAS studies (Sato et al. 2014 ), and the
large number of inter-species polymorphism will
allow global studies of molecular gene evolution.
4.6 Future Perspectives
By integrating sequencing data from NGS plat-
forms, the gene space coverage reached 98 %,
and thus the genome sequence information of
version 3.0 should serve as a solid basis for gene
annotation, expression analysis, and insertion
mutant identification. Further improvement of
the genome sequence information is planned to
be carried out in the following two ways: (1)
assignment of unanchored contigs onto pseudo-
molecules by resequencing recombinant inbred
lines to generate high-resolution genetic map
information for the SNPs located on the unan-
chored contigs; (2)filling the gaps between the
contigs by applying long read data generated by
the Pacific Biosciences RS third generation
sequencer.
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