Sequences of matK, a gene that had not been used previously for phylogenetic analyses, provided a sufficient number of reliable characters for phylogenetic analysis within Polemoniaceae.
The family as a whole was monophyletic with no support for the segregate family Cobaeaceae. The tropical genera were resolved as basal and paraphyletic within the family. There was no support for the current separation of temperate Polemoniaceae into two tribes. Several strongly supported groups include genera now placed in different tribes. The segregation of Ipomopsis and Allophyllum from Gilia was supported by the placement of each in distinct groups separate from a group of four species of Gilia. Several well supported groups allowed us to test hypotheses of relationship within Polemoniaceae. Phylogenetic analyses resulted in four equally parsimonious trees with a consistency index of 0.70. Sequences 661 bases in length were obtained from twenty species of Polemoniaceae. Nucleotide sequences of the plastid encoded gene matK were examined for their potential utility in phylogenetic analyses within angiosperm families. In combination with the pool of 500 previously mapped SSR markers, this release makes available a total of 2740 experimentally confirmed SSR markers for rice, or approximately one SSR every 157 kb. AT-rich microsatellites had the longest average repeat tracts, while GC-rich motifs were the shortest. The largest proportion of SSRs in this data set correspond to poly(GA) motifs (36%), followed by poly(AT) (15%) and poly(CCG) (8%) motifs. Fifty-six SSR markers (2.8%) hit BAC clones on two or more different chromosomes and appeared to be multiple copy.
Additional information based on genetic mapping and “nearest marker” information provided the basis for locating a total of 1825 (81%) of the newly designed markers along rice chromosomes. Using electronic PCR (e-PCR) to align primer pairs against 3284 publicly sequenced rice BAC and PAC clones (representing about 83% of the total rice genome), 65% of the SSR markers hit a BAC or PAC clone containing at least one genetically mapped marker and could be mapped by proxy. The majority (92%) of primer pairs were developed in regions flanking perfect repeats ≥ 24 bp in length. Duplicate primer pairs are reported for 7% (174) of the loci. A total of 2414 new di-, tri- and tetra-nucleotide non-redundant SSR primer pairs, representing 2240 unique marker loci, have been developed and experimentally validated for rice ( Oryza sativa L.).
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