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Each group was represented by multiple genera and congeneric species with multiple accessions in each species.
In the absence of whole-genome draft sequences, high-throughput sequencing of genome representations of multiple accessions in parallel using CRoPS will supply sufficient genetic (single nucleotide) polymorphisms to allow marker-assisted selection using existing genotyping platforms.
Our study of complete plastid genomes of multiple accessions in M. truncatula revealed a significant intraspecies ptDNA variation.
The other novel variant, DQ2.5-glia-α2 variant 4, was found in multiple accessions in varying abundances (ranging from 0.1 to 11).
However, relationships within the Malagasy Canarium clade were mostly poorly resolved, and species with multiple accessions in the tree were not always monophyletic, possibly due to lineage sorting or hybridization (confident resolution of these relationships will require additional data).
We predict, based on our finding of two stable plastid genomes in M. truncatula, that a survey of multiple accessions in these legume species is likely to uncover multiple genome configurations.
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Fourthly, it could indicate that taxa whose multiple accessions are appearing in diverse clades represent cryptic species, where broad morphological concepts on species are masking genetic patterns.
aType strain bNCBI sequence entries with multiple accession numbers in RDP data bases have been mentioned within the parentheses In our quest to validate the phylogenetic framework sequences, different phylogenetic trees were drawn on the basis of 404 rrs sequences belonging to 15 different Clostridium species along with 56 reference sequences.
Of nine species, six of them such as O. rufipogon (AA), O. nivara (AA), O. glumaepatula (AA), O. glaberrima (AA), O. sativa (AA), and O. punctata (BB) contained both SUB1B- and SUB1C-like genes side by side on chromosome 9 (Chr 9), as shown in Fig. 1a and b, which is consistent with the observations in multiple accessions of O. sativa (AA) (Singh et al., 2010; Xu et al., 2006).
The monophyly of multiple accessions of each species in our tree is well-supported, with the exception of M. pulvinaris whose monophyly is not, however, contradicted.
At the beginning, for each protein (or protein group with multiple accession numbers) in the combined lists, the total number of MS/MS spectra that were assigned a peptide mapping to that protein was calculated.
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