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

BACKGROUND: The 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. RESULTS: Here 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. CONCLUSION: The 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

Parasitic Plants Striga and Phelipanche Dependent upon Exogenous Strigolactones for Germination Have Retained Genes for Strigolactone Biosynthesis

Abstract Strigolactones are plant hormones with multiple functions, including regulating various aspects of plant architecture such as shoot branching, facilitating the colonization of plant roots by arbuscular mycorrhizal fungi, and acting as seed germination stimulants for certain parasitic plants of the family Orobanchaceae. The obligate parasitic species Phelipanche aegyptiaca and Striga hermonthica require strigolactones for germination, while the facultative parasite Triphysaria versicolor does not. It has been hypothesized that P. aegyptiaca and S. hermonthica would have undergone evolutionary loss of strigolactone biosynthesis as a part of their mechanism to enable specific detection of exogenous strigolactones. We analyzed the transcriptomes of P. aegyptiaca, S. hermonthica and T. versicolor and identified genes known to act in strigolactone synthesis (D27, CCD7, CCD8, and MAX1), perception (MAX2 and D14) and transport (PDR12). These genes were then analyzed to assess likelihood of function. Transcripts of all strigolactone-related genes were found M. Das et al. 1152 in P. aegyptiaca and S. hermonthica, and evidence points to their encoding functional proteins. Gene open reading frames were consistent with homologs from Arabidopsis and other strigolactone-producing plants, and all genes were expressed in parasite tissues. In general, the genes related to strigolactone synthesis and perception appeared to be evolving under codon-based selective constraints in strigolactone-dependent species. Bioassays of S. hermonthica root extracts indicated the presence of strigolactone class stimulants on germination of P. aegyptiaca seeds. Taken together, these results indicate that Phelipanche aegyptiaca and S. hermonthica have retained functional genes involved in strigolactone biosynthesis, suggesting that the parasites use both endogenous and exogenous strigolactones and have mechanisms to differentiate the two

PlantTribes: a gene and gene family resource for comparative genomics in plants

The PlantTribes database (http://fgp.huck.psu.edu/tribe.html) is a plant gene family database based on the inferred proteomes of five sequenced plant species: Arabidopsis thaliana, Carica papaya, Medicago truncatula, Oryza sativa and Populus trichocarpa. We used the graph-based clustering algorithm MCL [Van Dongen (Technical Report INS-R0010 2000) and Enright et al. (Nucleic Acids Res. 2002; 30: 1575–1584)] to classify all of these species’ protein-coding genes into putative gene families, called tribes, using three clustering stringencies (low, medium and high). For all tribes, we have generated protein and DNA alignments and maximum-likelihood phylogenetic trees. A parallel database of microarray experimental results is linked to the genes, which lets researchers identify groups of related genes and their expression patterns. Unified nomenclatures were developed, and tribes can be related to traditional gene families and conserved domain identifiers. SuperTribes, constructed through a second iteration of MCL clustering, connect distant, but potentially related gene clusters. The global classification of nearly 200 000 plant proteins was used as a scaffold for sorting 4 million additional cDNA sequences from over 200 plant species. All data and analyses are accessible through a flexible interface allowing users to explore the classification, to place query sequences within the classification, and to download results for further study

Complete plastid genome sequences suggest strong selection for retention of photosynthetic genes in the parasitic plant genus -5

<p><b>Copyright information:</b></p><p>Taken from "Complete plastid genome sequences suggest strong selection for retention of photosynthetic genes in the parasitic plant genus "</p><p>http://www.biomedcentral.com/1471-2229/7/57</p><p>BMC Plant Biology 2007;7():57-57.</p><p>Published online 24 Oct 2007</p><p>PMCID:PMC2216012.</p><p></p>ficantly higher /are marked with one (p < 0.01), two, (p < 0.001), or three asterisks (p < 0.0001). Values of and /on relevant branches are given in Table 3

Complete plastid genome sequences suggest strong selection for retention of photosynthetic genes in the parasitic plant genus -2

<p><b>Copyright information:</b></p><p>Taken from "Complete plastid genome sequences suggest strong selection for retention of photosynthetic genes in the parasitic plant genus "</p><p>http://www.biomedcentral.com/1471-2229/7/57</p><p>BMC Plant Biology 2007;7():57-57.</p><p>Published online 24 Oct 2007</p><p>PMCID:PMC2216012.</p><p></p>ns at the LSC/IRjunction and increases numerically counterclockwise around the genome. Genes are denoted as in Figure 1

Complete plastid genome sequences suggest strong selection for retention of photosynthetic genes in the parasitic plant genus -6

<p><b>Copyright information:</b></p><p>Taken from "Complete plastid genome sequences suggest strong selection for retention of photosynthetic genes in the parasitic plant genus "</p><p>http://www.biomedcentral.com/1471-2229/7/57</p><p>BMC Plant Biology 2007;7():57-57.</p><p>Published online 24 Oct 2007</p><p>PMCID:PMC2216012.</p><p></p>(and ) are particularly divergent in

Complete plastid genome sequences suggest strong selection for retention of photosynthetic genes in the parasitic plant genus -7

<p><b>Copyright information:</b></p><p>Taken from "Complete plastid genome sequences suggest strong selection for retention of photosynthetic genes in the parasitic plant genus "</p><p>http://www.biomedcentral.com/1471-2229/7/57</p><p>BMC Plant Biology 2007;7():57-57.</p><p>Published online 24 Oct 2007</p><p>PMCID:PMC2216012.</p><p></p>rasitism in Convolvulaceae. Constraint is further relaxed in and is most relaxed in , although photosynthetically related genes remain highly constrained. In general, genes present in are under higher levels of constraint than in , despite the retention of photosynthetic genes in