ABSTRACT
BACKGROUND: Hevea brasiliensis, a member of the Euphorbiaceae family, is the major commercial source of natural rubber (NR). NR is a latex polymer with high elasticity, flexibility, and resilience that has played a critical role in the world economy since 1876. RESULTS: Here, we report the draft genome sequence of H. brasiliensis. The assembly spans ~1.1 Gb of the estimated 2.15 Gb haploid genome. Overall, ~78% of the genome was identified as repetitive DNA. Gene prediction shows 68,955 gene models, of which 12.7% are unique to Hevea. Most of the key genes associated with rubber biosynthesis, rubberwood formation, disease resistance, and allergenicity have been identified. CONCLUSIONS: The knowledge gained from this genome sequence will aid in the future development of high-yielding clones to keep up with the ever increasing need for natural rubber.
Subject(s)
Genomics , Hevea/genetics , Sequence Analysis , Allergens/genetics , Disease Resistance/genetics , Evolution, Molecular , F-Box Proteins/genetics , Genome, Plant/genetics , Haploidy , Hevea/immunology , Hevea/metabolism , Latex/metabolism , Molecular Sequence Annotation , Phylogeny , Plant Growth Regulators/genetics , Rubber/metabolism , Signal Transduction/genetics , Transcription Factors/genetics , Wood/metabolismABSTRACT
Arabica coffee (Coffea arabica L.) is a self-compatible perennial allotetraploid species (2n=4x=44), whereas Robusta coffee (C. canephora L.) is a self-incompatible perennial diploid species (2n=2x=22). C. arabica (C(a) C(a) E(a) E(a) ) is derived from a spontaneous hybridization between two closely related diploid coffee species, C. canephora (CC) and C. eugenioides (EE). To investigate the patterns and degree of DNA sequence divergence between the Arabica and Robusta coffee genomes, we identified orthologous bacterial artificial chromosomes (BACs) from C. arabica and C. canephora, and compared their sequences to trace their evolutionary history. Although a high level of sequence similarity was found between BACs from C. arabica and C. canephora, numerous chromosomal rearrangements were detected, including inversions, deletions and insertions. DNA sequence identity between C. arabica and C. canephora orthologous BACs ranged from 93.4% (between E(a) and C(a) ) to 94.6% (between C(a) and C). Analysis of eight orthologous gene pairs resulted in estimated ages of divergence between 0.046 and 0.665 million years, indicating a recent origin of the allotetraploid species C. arabica. Analysis of transposable elements revealed differential insertion events that contributed to the size increase in the C(a) sub-genome compared to its diploid relative. In particular, we showed that insertion of a Ty1-copia LTR retrotransposon occurred specifically in C. arabica, probably shortly after allopolyploid formation. The two sub-genomes of C. arabica, C(a) and E(a) , showed sufficient sequence differences, and a whole-genome shotgun approach could be suitable for sequencing the allotetraploid genome of C. arabica.
Subject(s)
Coffea/genetics , Evolution, Molecular , Genome, Plant , Plant Proteins/genetics , Receptors, Cell Surface/genetics , Chromosomes, Artificial, Bacterial/genetics , DNA, Plant/genetics , Diploidy , Gene Library , Gene Rearrangement , Molecular Sequence Annotation , Mutagenesis, Insertional , Polyploidy , Retroelements , Sequence Analysis, DNA , Species SpecificityABSTRACT
The programmed senescence of flower petals has been shown to involve the fragmentation of nuclear DNA. Nuclear DNA fragmentation, as determined by the TUNEL assay, was detected in Petunia x hybrida corollas during both pollination-induced and age-related senescence. DNA fragmentation was detected late in the lifespan of the flower when corollas were wilting and producing ethylene. The induction of a 43 kDa nuclease (PhNUC1) correlated with increased DNA fragmentation. PhNUC1 is a glycoprotein with activity against DNA and RNA and a pH optimum of 7.5. EDTA was found to inhibit PhNUC1 activity, but the addition of Co2+ restored activity in the presence of the chelating agent. When total protein extracts from senescing petals were fractionated by differential centrifugation, PhNUC1 activity was detected in the nuclear but not the cytoplasmic fraction. Activity of PhNUC1 was induced in non-senescing corollas by treatment with ethylene. Delayed increases in PhNUC1 activity observed in ethylene-insensitive flowers (35S:etr1-1) suggest that ethylene modulates the timing of PhNUC1 induction, but that it is not an absolute requirement for its activation.