Jeffrey D. Palmer

Mark W. Chase, Douglas E. Soltis, Richard G. Olmstead, David Morgan, Donald H. Les, Brent D. Mishler, Melvin R. Duvall, Robert A. Price, Harold G. Hills, Yin-Long Qiu, Kathleen A. Kron, Jeffrey H. Rettig, Elena Conti, Jeffrey D. Palmer, James R. Manhart, Kenneth J. Sytsma, Helen J. Michaels, W. John Kress, Kenneth G. Karol, W. Dennis Clark, Mikael Hedren, Brandon S. Gaut, Robert K. Jansen, Ki-Joong Kim, Charles F. Wimpee, James F. Smith, Glenn R. Furnier, Steven H. Strauss, Qui-Yun Xiang, Gregory M. Plunkett, Pamela S. Soltis, Susan M. Swensen, Stephen E. Williams, Paul A. Gadek, Christopher J. Quinn, Luis E. Eguiarte, Edward Golenberg, Gerald H. Learn, Jr., Sean W. Graham, Spencer C. H. Barrett, Selvadurai Dayanandan, Victor A. Albert, Phylogenetics of Seed Plants: An Analysis of Nucleotide Sequences from the Plastid Gene rbcL, Annals of the Missouri Botanical Garden, Vol. 80, No. 3 (1993), pp. 528-548+550-580

Small subunit rRNA sequence data were generated for 27 strains of cyanobacteria and incorporated into a phylogenetic analysis of 1,377 aligned sequence positions from a diverse sampling of 53 cyanobacteria and 10 photosynthetic plastids. Tree inference was carried out using a maximum likelihood method with correction for site-to-site variation in evolutionary rate. Confidence in the inferred phylogenetic relationships was determined by construction of a majority-rule consensus tree based on alternative topologies not considered to be statistically significantly different from the optimal tree. The results are in agreement with earlier studies in the assignment of individual taxa to specific sequence groups. Several relationships not previously noted among sequence groups are indicated, whereas other relationships previously supported are contradicted. All plastids cluster as a strongly supported monophyletic group arising near the root of the cyanobacterial line of descent.

In the early 1990s an outbreak of papaya ringspot virus (PRSV) in the papaya groves in the Puna district of Hawaii caused severe damage to an important crop. Since then, the planting of two transgenic cultivars resistant to the virus — called 'SunUp' and 'Rainbow' — has helped to maintain yields. SunUp is a transgenic red-fleshed fruit that expresses the coat protein gene of a mild mutant of PRSV, conferring resistance via post-transcriptional gene silencing. Rainbow is a yellow-fleshed (and therefore more popular) F1 hybrid bred from SunUp. Now the draft genome sequence of the SunUp strain of papaya has been determined — a first for a commercial virus-resistant transgenic fruit tree. Comparison of this plant genome to those of Arabidopsis and others sheds light on the evolution of qualities such as biosynthesis, starch deposition, control of photosynthesis and pathways for creating the volatile compounds that contribute to the characteristic flavour of papaya. On the cover, the disease-free transgenic Rainbow and the severely infected, stunted and dying non-transgenic Sunrise grow in adjoining plots. Researchers from Hawaii and an international consortium have produced a draft genome assembly for 'SunUp', the first commercial virus-resistant transgenic fruit tree. Comparison of this plant genome to those of Arabidopsis and others sheds light on evolution of characteristics such as biosynthesis, starch deposition, control of photosynthesis and pathways for creating volatile compounds. Papaya, a fruit crop cultivated in tropical and subtropical regions, is known for its nutritional benefits and medicinal applications. Here we report a 3× draft genome sequence of ‘SunUp’ papaya, the first commercial virus-resistant transgenic fruit tree1 to be sequenced. The papaya genome is three times the size of the Arabidopsis genome, but contains fewer genes, including significantly fewer disease-resistance gene analogues. Comparison of the five sequenced genomes suggests a minimal angiosperm gene set of 13,311. A lack of recent genome duplication, atypical of other angiosperm genomes sequenced so far2,3,4,5, may account for the smaller papaya gene number in most functional groups. Nonetheless, striking amplifications in gene number within particular functional groups suggest roles in the evolution of tree-like habit, deposition and remobilization of starch reserves, attraction of seed dispersal agents, and adaptation to tropical daylengths. Transgenesis at three locations is closely associated with chloroplast insertions into the nuclear genome, and with topoisomerase I recognition sites. Papaya offers numerous advantages as a system for fruit-tree functional genomics, and this draft genome sequence provides the foundation for revealing the basis of Carica’s distinguishing morpho-physiological, medicinal and nutritional properties.

Orthologs and paralogs are two fundamentally different types of homologous genes that evolved, respectively, by vertical descent from a single ancestral gene and by duplication. Orthology and paralogy are key concepts of evolutionary genomics. A ...Read More