Monocot plastid phylogenomics, timeline, net rates of species diversification, the power of multiâ gene analyses, and a functional model for the origin of monocots

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/146610/1/ajb21178-sup-0009-AppendixS9.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/146610/2/ajb21178-sup-0020-AppendixS20.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/146610/3/ajb21178.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/146610/4/ajb21178-sup-0019-AppendixS19.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/146610/5/ajb21178-sup-0010-AppendixS10.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/146610/6/ajb21178-sup-0002-AppendixS2.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/146610/7/ajb21178-sup-0006-AppendixS6.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/146610/8/ajb21178-sup-0012-AppendixS12.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/146610/9/ajb21178-sup-0017-AppendixS17.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/146610/10/ajb21178-sup-0007-AppendixS7.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/146610/11/ajb21178-sup-0001-AppendixS1.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/146610/12/ajb21178-sup-0003-AppendixS3.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/146610/13/ajb21178-sup-0016-AppendixS16.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/146610/14/ajb21178_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/146610/15/ajb21178-sup-0008-AppendixS8.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/146610/16/ajb21178-sup-0004-AppendixS4.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/146610/17/ajb21178-sup-0018-AppendixS18.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/146610/18/ajb21178-sup-0014-AppendixS14.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/146610/19/ajb21178-sup-0011-AppendixS11.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/146610/20/ajb21178-sup-0005-AppendixS5.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/146610/21/ajb21178-sup-0015-AppendixS15.pd

A sex-chromosome mutation in Silene latifolia

Silene latifolia is dioecious, yet rare hermaphrodites have been found, and such natural mutants can provide valuable insight into genetic mechanisms. Here, we describe a hermaphrodite-inducing mutation that is almost certainly localized to the gynoecium-suppression region of the Y chromosome in S. latifolia. The mutant Y chromosome was passed through the megaspore, and the presence of two X chromosomes was not necessary for seed development in the parent. This result supports a lack of degeneration of the Y chromosome in S. latifolia, consistent with the relatively recent formation of the sex chromosomes in this species. When crossed to wild-type plants, hermaphrodites performed poorly as females, producing low seed numbers. When hermaphrodites were pollen donors, the sex ratio of offspring they produced through crosses was biased towards females. This suggests that hermaphroditic S. latifolia would fail to thrive and potentially explains the rarity of hermaphrodites in natural populations of S. latifolia. These results indicate that the Y chromosome in Silene latifolia remains very similar to the X, perhaps mostly differing in the primary sex determination regions

Chloroplast DNA from lettuce and Barnadesia (Asteraceae): structure, gene localization, and characterization of a large inversion

We have cloned into plasmids 17 of 18 lettuce chloroplast DNA SacI fragments covering 96% of the genome. The cloned fragments were used to construct cleavage maps for 10 restriction enzymes for the chloroplast genomes of lettuce ( Lactuca sativa ) and Barnadesia caryophylla , two distantly related species in the sunflower family (Asteraceae). Both genomes are approximately 151 kb in size and contain a 25 kb inverted repeat. We also mapped the position and orientation of 37 chloroplast DNA genes. The mapping studies reveal that chloroplast DNAs of lettuce and Barnadesia differ by a 22 kb inversion in the large single copy region. Barnadesia has retained the primitive land plant genome arrangement, while the inversion has occurred in a lettuce lineage. The endpoints of the derived lettuce inversion were located by comparison to the well-characterized spinach and tobacco genomes. Both endpoints are located in intergenic spacers within tRNA gene clusters; one cluster being located downstream from the atpA gene and the other upstream from the psbD gene. The endpoint near the atpA gene is very close to one endpoint of a 20 kb inversion in wheat (Howe et al. 1983; Quigley and Weil 1985). Comparison of the restriction site maps gives an estimated sequence divergence of 3.7% for the lettuce and Barnadesia genomes. This value is relatively low compared to previous estimates for other angiosperm groups, suggesting a high degree of sequence conservation in the Asteraceae.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/46961/1/294_2004_Article_BF00384619.pd

Phylogeny of the tropical tree family Dipterocarpaceae based on nucleotide sequences of the chloroplast RBCL gene

The Dipterocarpaceae, well-known trees of the Asian rain forests, have been variously assigned to Malvales and Theales. The family, if the Monotoideae of Africa (30 species) and South America and the Pakaraimoideae of South America (one species) are included, comprises over 500 species. Despite the high diversity and ecological dominance of the Dipterocarpaceae, phylogenetic relationships within the family as well as between dipterocarps and other angiosperm families remain poorly defined. We conducted parsimony analyses on rbcL sequences from 35 species to reconstruct the phylogeny of the Dipterocarpaceae. The consensus tree resulting from these analyses shows that the members of Dipterocarpaceae, including Monotes and Pakaraimaea, form a monophyletic group closely related to the family Sarcolaenaceae and are allied to Malvales. The present generic and higher taxon circumscriptions of Dipterocarpaceae are mostly in agreement with this molecular phylogeny with the exception of the genus Hopea, which forms a clade with Shorea sections Anthoshorea and Doona. Phylogenetic placement of Dipterocarpus and Dryobalanops remains unresolved. Further studies involving representative taxa from Cistaceae, Elaeocarpaceae, Hopea, Shorea, Dipterocarpus, and Dryobalanops will be necessary for a comprehensive understanding of the phylogeny and generic limits of the Dipterocarpaceae