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1.  Variability among the Most Rapidly Evolving Plastid Genomic Regions is Lineage-Specific: Implications of Pairwise Genome Comparisons in Pyrus (Rosaceae) and Other Angiosperms for Marker Choice 
PLoS ONE  2014;9(11):e112998.
Plastid genomes exhibit different levels of variability in their sequences, depending on the respective kinds of genomic regions. Genes are usually more conserved while noncoding introns and spacers evolve at a faster pace. While a set of about thirty maximum variable noncoding genomic regions has been suggested to provide universally promising phylogenetic markers throughout angiosperms, applications often require several regions to be sequenced for many individuals. Our project aims to illuminate evolutionary relationships and species-limits in the genus Pyrus (Rosaceae)—a typical case with very low genetic distances between taxa. In this study, we have sequenced the plastid genome of Pyrus spinosa and aligned it to the already available P. pyrifolia sequence. The overall p-distance of the two Pyrus genomes was 0.00145. The intergenic spacers between ndhC–trnV, trnR–atpA, ndhF–rpl32, psbM–trnD, and trnQ–rps16 were the most variable regions, also comprising the highest total numbers of substitutions, indels and inversions (potentially informative characters). Our comparative analysis of further plastid genome pairs with similar low p-distances from Oenothera (representing another rosid), Olea (asterids) and Cymbidium (monocots) showed in each case a different ranking of genomic regions in terms of variability and potentially informative characters. Only two intergenic spacers (ndhF–rpl32 and trnK–rps16) were consistently found among the 30 top-ranked regions. We have mapped the occurrence of substitutions and microstructural mutations in the four genome pairs. High AT content in specific sequence elements seems to foster frequent mutations. We conclude that the variability among the fastest evolving plastid genomic regions is lineage-specific and thus cannot be precisely predicted across angiosperms. The often lineage-specific occurrence of stem-loop elements in the sequences of introns and spacers also governs lineage-specific mutations. Sequencing whole plastid genomes to find markers for evolutionary analyses is therefore particularly useful when overall genetic distances are low.
PMCID: PMC4236126  PMID: 25405773
2.  Development of nuclear microsatellites for the Arcto-Tertiary tree Zelkova carpinifolia (Ulmaceae) using 454 pyrosequencing1 
Applications in Plant Sciences  2014;2(3):apps.1300072.
• Premise of the study: The current study aimed at developing nuclear microsatellite markers for the relict tree species Zelkova carpinifolia, which is threatened in its natural range in the South Caucasus.
• Methods and Results: Pyrosequencing of an enriched microsatellite library on the Roche FLX platform using the 454 Titanium kit produced 86,058 sequence reads, most of which contained short tandem repeats. Eighty microsatellite loci identified using the software package QDD version 1 were selected and tested for proper PCR amplification. Of these, 13 allowed proper amplification and were shown to be polymorphic among a sample of 25 Z. carpinifolia specimens from various geographic origins.
• Conclusions: The set of microsatellite markers will be suitable for the assessment of genetic diversity in Z. carpinifolia. They will allow for an examination of phylogeographic patterns as well as of population structure and gene flow within this species.
PMCID: PMC4103100  PMID: 25202606
conservation genetics; microsatellites; phylogeography; pyrosequencing; Ulmaceae; Zelkova carpinifolia
3.  On the thermogenesis of the Titan arum (Amorphophallus titanum) 
Plant Signaling & Behavior  2009;4(11):1096-1098.
The Titan arum (Araceae) produces the largest bloom of all flowering plants. Its flowering period of two days is divided into a female flowering phase in the first night and a male flowering phase in the second night. Recently, we have documented thermogenesis in the spadix of the Titan arum during the female flowering phase. Here, we document a second thermogenic phase in which the male florets are heated during the male flowering phase. Obviously the two nocturnal thermogenic phases are linked with the two flowering periods. These observations now allow a more detailed understanding of the flowering behavior of the Titan arum.
PMCID: PMC2819525  PMID: 19838070
Amorphophallus titanum; araceae; thermogenesis; infrared thermography; pollination

Results 1-3 (3)