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As shown in Table 3, 10 20% of the non- Mt legume transcript sequences could be mapped to Mt BACs and clustered to a total of 7,896 non-redundant genes, 81% of which have also Mt EST support.
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The mutations 620U>A (m.1267T>A) (63) and 676G>A (m.1323G>A) (64), mapping to mt-h34, have been identified in three cancer patients (see Supplementary Material, Table S1).
The legume transcript sequences were mapped to the Mt and Lj BAC sets using the two computer programs GeneSeqer [ 34] and GMAP [ 35].
A number of 5,903 Roche/454 GS FLX (454) EST sequencing reads (total number of aligned bases: 1.89 Mbp) mapped to the mt genome.
Under stringent conditions using Blat, including a threshold of 95% identity and 90% coverage, 20,067 (10,911 TCs and 9,156 singletons) unique sequences (37%) were mapped to the MT 3.5.1 genome sequence assembly.
A sequencing read would have more than one hit mapped to the whole genome (the mt genome plus the nuclear genome), while it would be with unique hits to the mt sequence when we excluded the nuclear DNA sequence.
Reads almost exclusively mapped to coding regions of the mt genome (proteins and rRNA genes) and all ORFs except ORF_03 were partially or fully covered by ESTs.
Of these 923,507 and 1,015,279 reads (i.e. 2 % of total reads) were mapped to the 16,353-bp-long mt genome (Fig. 2), with the average coverage of 5696× and 6248×, respectively.
The BAC clone contig map constructed for the assembly gap coinciding with Mt-FTQTL6 will be interesting in efforts to clone important loci mapped to the same region as Mt-FTQTL6 including a locus for resistance to Subterranean clover mottle virus[ 83] and a QTL for the number of secondary branches [ 84].
The present study aimed to identify positional candidate genes for a major freezing tolerance quantitative trait locus that was previously mapped to M. truncatula chromosome 6 (Mt-FTQTL6) using the LR3 population derived from a cross between the freezing-tolerant accession F83005-5 and the freezing-sensitive accession DZA045-5.
Finally, the locus MT-2 of the 2-methyl-6-phytyl-1,4-benzoquinone/2-methyl-6-solanyl-1,4-benzoquinone methyltransferase (MPBQ/MSBQ-MT) gene was mapped to LG 4 using the F24/R25 INDEL marker [ 20].
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