The Lotus japonicus genome assembly build 2.5 was constructed
by adding genome sequence information on 460 TAC/BAC clones analyzed
after the release of previous build 1.0, and thus the length of the
pseudomolecules has been increased from 167 Mbp (build 1.0) to 201 Mbp
(build2.5).
(The LjSGA (Selected Genome shotgun Assembly) contig sequences
corresponding to added genomic clone sequences were replaced by the
pseudomolecules.)
By proceeding the sequence edit of the TAC/BAC clones in phase 1 draft stage in build 1.0, a total of 178 clones has updated to phase 3, and thus the total size of the finished sequences (phase 2 and 3) in the pseudomolecules has been increased from 97 Mbp (build 1.0) to 139 Mbp (build2.5).
The latest genetic map information was integrated to construct the pseudomolecules corresponding to 6 chromosomes, and thus the total size of mapped sequences in the pseudomolecules has been increased from 130 Mbp (build 1.0) to 195 Mbp (build2.5).
Regarding the code for the predicted genes, basically the same system as the previous release (build1.0) was applied for build 2.5. Therefore, the code "r2" is included in the build 2.5 annotation to distinguish from the code of build 1.0. So please keep in mind using the entire code to describe the predicted genes in build 2.5.
The gene code in build 2.5 also contains the suffix indicating the status of annotation as follows;
| .m | annotated on phase 2 and phase 3 sequences with manual curation. |
|---|---|
| .a | annotated on phase 2 and phase 3 sequences by automatic gene assignment program |
| .d | annotated on phase 1 draft sequences by automatic gene assignment program |