Gene sets enriched in carpels, such as gamete formation, DNA replication and nucleosome assembly indicate that during pre-anthesis, carpels prepare to form megaspores by synthesizing DNA prior to meiosis.
The initial BLAST query to the Btau_3.1 assembly indicated that 88 prohormone gene candidates were likely to be present (E-value < 10-6).
A de novo repeat analysis of the reference genome assembly indicated that long terminal repeat (LTR) retrotransposons and DNA transposons account for the largest percentages of repeat elements at 40.5% and 36%, respectively (Table 3 and Figure S1A−C).
However, over 700-2000 bp length range, average contig lengths of the combination assembly are less than that of the 454-pyrosequencing assembly indicating that contigs longer than 700 bp of the combination assembly were mainly derived from the 454-pyroseqeuncing data, possibly because most of the 454-pyrosequencing reads were 400-600 bp.
Reliability evaluations on the final assemblies indicated that ACF bonding could give a very reliable electrical and mechanical interconnection.
A closer inspection of the assemblies indicates that GAML missed several possible joins.
This percentage is higher than for each of the single assemblies, indicating that the integrated assembly is of higher quality than the single assemblies.
Using the Bowtie2 read aligner [ 13] with the default settings we were able to align between 82.0 % and 96.2 % of sequenced reads as concordant pairs to the final genome assemblies, indicating that the genome assemblies are relatively complete.
However, our analysis of these regions using the Zv2, Zv3, Zv5 and Zv6 assemblies indicates that these apparent duplications represent artifacts caused by errors in the Zv4 genome assembly.
Mapping the positions of Bm Lep1 onto chromosome assemblies indicated that integrations are co-localized with protein-coding genes (Supplementary Fig. S1; chromosome 1 shown in Fig. 4), which agrees with seminal evidence of Lep1 being within gene intervals.
