K. Arumuganathan

Construction of a bacterial artificial chromosome library from the spikemoss Selaginella moellendorffii: a new resource for plant comparative genomics

BackgroundThe lycophytes are an ancient lineage of vascular plants that diverged from the seed plant lineage about 400 Myr ago. Although the lycophytes occupy an important phylogenetic position for understanding the evolution of plants and their genomes, no genomic resources exist for this group of plants.ResultsHere we describe the construction of a large-insert bacterial artificial chromosome (BAC) library from the lycophyte Selaginella moellendorffii. Based on cell flow cytometry, this species has the smallest genome size among the different lycophytes tested, including Huperzia lucidula, Diphaiastrum digita, Isoetes engelmanii and S. kraussiana. The arrayed BAC library consists of 9126 clones; the average insert size is estimated to be 122 kb. Inserts of chloroplast origin account for 2.3% of the clones. The BAC library contains an estimated ten genome-equivalents based on DNA hybridizations using five single-copy and two duplicated S. moellendorffii genes as probes.ConclusionThe S. moellenforffii BAC library, the first to be constructed from a lycophyte, will be useful to the scientific community as a resource for comparative plant genomics and evolution.

Characterization of natural orchardgrass (Dactylis glomerata L.) populations of the Thrace Region of Turkey based on ploidy and DNA polymorphisms

Determining the ploidy and geneticdiversity of a germplasm is necessarybefore initiating breeding or geneticstudies. This study was conducted tocharacterize the ploidy level of 57 naturalpopulations of orchardgrass (Dactylisglomerata L.) collected from the ranges ofThrace region of Turkey and the diversityamong populations based on RAPD (RandomAmplified Polymorphic DNA) markers. Flowcytometry was used to determine nuclear DNAcontent (pg 2C-1 = DNA content of adiploid somatic nucleus) of 6 plants foreach population. Nuclear DNA contents werecorrelated to ploidy level with root tipchromosome counts on selected plants. Onthe basis of this study, mean nuclear DNAcontent of orchardgrass was determined as9.57 ± 0.33 (with 95% confidenceinterval) while all the plants used inchromosome counting were determined to betetraploid, with 2n = 28 mitoticchromosomes, suggesting that diploidorchardgrass plants are likely very rare orabsent in ranges of Thrace region ofTurkey. In the RAPD assay, over 40polymorphic fragments were generated whichallowed some populations to bedistinguished from the rest by uniquemarkers. A cluster analysis was performedusing Neis (1972) genetic distance indexwith an unweighted pair group method witharitmetic mean (UPGMA). The clusteranalysis indicated that there is a highlevel of gene flow among naturalorchardgrass populations and thereforegenes distributed quite homogeneouslythrough out the region. The results of thisstudy can be useful in the development ofDactylis germ plasm collectionstrategies in Thrace region for breedingpurpose.

Using partial genomic fosmid libraries for sequencing complete organellar genomes

Organellar genome sequences provide numerous phylogenetic markers and yield insight into organellar function and molecular evolution. These genomes are much smaller in size than their nuclear counterparts; thus, their complete sequencing is much less expensive than total nuclear genome sequencing, making broader phylogenetic sampling feasible. However; for some organisms, it is challenging to isolate plastid DNA for sequencing using standard methods. To overcome these difficulties, we constructed partial genomic libraries from total DNA preparations of two heterotrophic and two autotrophic angiosperm species using fosmid vectors. We then used macroarray screening to isolate clones containing large fragments of plastid DNA. A minimum tiling path of clones comprising the entire genome sequence of each plastid was selected, and these clones were shotgun-sequenced and assembled into complete genomes. Although this method worked well for both heterotrophic and autotrophic plants, nuclear genome size had a dramatic effect on the proportion of screened clones containing plastid DNA and, consequently, the overall number of clones that must be screened to ensure full plastid genome coverage. This technique makes it possible to determine complete plastid genome sequences for organisms that defy other available organellar genome sequencing methods, especially those for which limited amounts of tissue are available.