A Phylogenetic Study of Apiaceae Tribe Caucalideae

136 p.Thesis (Ph.D.)--University of Illinois at Urbana-Champaign, 1998.Since the tribe Caucalideae was established for those species of Apiaceae (Umbelliferae) with spines, tubercles or bristly hairs on the primary and/or secondary ridges of the fruits, there has been considerable disagreement as to its proper circumscription, the relationships among its members, and the delimitation of certain genera. Although Heywood and Jury (Heywood, 1982) provided a checklist of Caucalideae, recognizing 21 genera and 68 species, no rigorously constructed estimate of phylogeny exists for these taxa. Phylogenetic relationships within Caucalideae were assessed using nucleotide sequence variation in the internal transcribed spacer (ITS) regions of 18S-26S nuclear ribosomal DNA, detailed restriction site mapping of the chloroplast genome, and morphological and anatomical characters. Evolutionary patterns of selected (i.e., cytological, palynological, phytochemical and morphological) characters were interpreted by plotting their distribution on the ITS-based phylogeny, revealing that many of these characters are highly homoplastic. On the basis of these comparative data, the following results were obtained: (1) Phylogenies derived from three independent lines of evidence are largely congruent, suggesting that hybridization may not have been a factor in the evolution of this group; (2) There is little support for any existing system of classification for the tribe. Aphanopleura, Psammogeton and Kozlovia are excluded from the tribe, whereas representatives from tribe Laserpitieae are included. The genus Chaetosciadium is best treated within Torilis; (3) Fruit primary appendage characters are more useful than those of secondary appendages for delimiting generic boundaries; (4) Tribe Caucalideae sensu lato is provisionally established and consists of subtribes Daucinae (Daucus, Pseudorlaya, Pachyctenium, Agrocharis, Laserpitium, Orlaya, Ammodaucus, Cuminum, Polylophium and Artedia) and Caucalidinae (Astrodaucus, Turgeniopsis, Szovitsia, Torilis, Yabea, Caucalis, Turgenia and Lisaea).U of I OnlyRestricted to the U of I community idenfinitely during batch ingest of legacy ETD

Characterization of the complete chloroplast genome of Arabis stellari and comparisons with related species.

Arabis stellari var. japonica is an ornamental plant of the Brassicaceae family, and is widely distributed in South Korea. However, no information is available about its molecular biology and no genomic study has been performed on A. stellari. In this paper, the authors report the complete chloroplast genome sequence of A. stellari. The plastome of A. stellari was 153,683 bp in length with 36.4% GC and included a pair of inverted repeats (IRs) of 26,423 bp that separated a large single-copy (LSC) region of 82,807 bp and a small single-copy (SSC) region of 18,030 bp. It was also found to contain 113 unique genes, of which 79 were protein-coding genes, 30 were transfer RNAs, and four were ribosomal RNAs. The gene content and organization of the A. stellari chloroplast genome were similar to those of other Brassicaceae genomes except for the absence of the rps16 protein-coding gene. A total of 991 SSRs were identified in the genome. The chloroplast genome of A. stellari was compared with closely related species of the Brassicaceae family. Comparative analysis showed a minor divergence occurred in the protein-coding matK, ycf1, ccsA, accD and rpl22 genes and that the KA/KS nucleotide substitution ratio of the ndhA genes of A. stellari and A. hirsuta was 1.35135. The genes infA and rps16 were absent in the Arabis genus and phylogenetic evolutionary studies revealed that these genes evolved independently. However, phylogenetic analysis showed that the positions of Brassicaceae species are highly conserved. The present study provides A. stellari genomic information that may be found useful in conservation and molecular phylogenetic studies on Brassicaceae

Complete chloroplast genome of <i>Tetragonia tetragonioides</i>: Molecular phylogenetic relationships and evolution in Caryophyllales

<div><p>The chloroplast genome of <i>Tetragonia tetragonioides</i> (Aizoaceae; Caryophyllales) was sequenced to provide information for studies on phylogeny and evolution within Caryophyllales. The chloroplast genome of <i>Tetragonia tetragonioides</i> is 149,506 bp in length and includes a pair of inverted repeats (IRs) of 24,769 bp that separate a large single copy (LSC) region of 82,780 bp and a small single copy (SSC) region of 17,188 bp. Comparative analysis of the chloroplast genome showed that Caryphyllales species have lost many genes. In particular, the <i>rpl2</i> intron and <i>infA</i> gene were not found in <i>T</i>. <i>tetragonioides</i>, and core Caryophyllales lack the <i>rpl2</i> intron. Phylogenetic analyses were conducted using 55 genes in 16 complete chloroplast genomes. Caryophyllales was found to divide into two clades; core Caryophyllales and noncore Caryophyllales. The genus <i>Tetragonia</i> is closely related to <i>Mesembryanthemum</i>. Comparisons of the synonymous (Ks), nonsynonymous (Ka), and Ka/Ks substitution rates revealed that nonsynonymous substitution rates were lower than synonymous substitution rates and that Ka/Ks rates were less than 1. The findings of the present study suggest that most genes are a purified selection.</p></div

Molecular phylogenetic analyses of 55 protein-coding genes of Caryophyllales.

<p>The stability of each tree node was tested by bootstrap analysis with 1,000 replicates. Arabidopsis was used as the outgroup.</p

Comparison of nonsynonymous (Ka), synonymous (Ks), and Ka/Ks substitution rates of functional gene groups.

<p>Comparison of nonsynonymous (Ka), synonymous (Ks), and Ka/Ks substitution rates of functional gene groups.</p

The distribution, types and length of SSRs in <i>T</i>. <i>tetragonioides</i>.

<p>A: Presence of repeats in the LSC, SSC and IR regions. B: Presence of repeats in protein coding regions, intergenic spacers and intron regions. C: Numbers and length of SSRs.</p

Chloroplast genome of <i>Tetragonia tetragonioides</i>.

<p>Genes inside the circle are transcribed clockwise, and genes outside are transcribed counterclockwise. The dark gray inner circle corresponds to the GC content, and the light-gray circle corresponds to the AT content.</p

Comparison of <i>infA</i> gene and intron of <i>rpl2</i> sequences among Caryophyllales.

<p>A: <i>infA</i> gene region, B: <i>rpl2</i> intron region, C: lack of <i>rpl2</i> intron. The red word indicates <i>T</i>. <i>tetragonioides</i>.</p

Comparison of the borders of the LSC, SSC, and IR regions of Brassicaceae chloroplast genomes.

<p>Indicates a pseudogene. The figure is not drawn to scale.</p