Complete plastid genome sequences of Drimys, Liriodendron, and Piper: implications for the phylogenetic relationships of magnoliids

BACKGROUND: The magnoliids with four orders, 19 families, and 8,500 species represent one of the largest clades of early diverging angiosperms. Although several recent angiosperm phylogenetic analyses supported the monophyly of magnoliids and suggested relationships among the orders, the limited number of genes examined resulted in only weak support, and these issues remain controversial. Furthermore, considerable incongruence resulted in phylogenetic reconstructions supporting three different sets of relationships among magnoliids and the two large angiosperm clades, monocots and eudicots. We sequenced the plastid genomes of three magnoliids, Drimys (Canellales), Liriodendron (Magnoliales), and Piper (Piperales), and used these data in combination with 32 other angiosperm plastid genomes to assess phylogenetic relationships among magnoliids and to examine patterns of variation of GC content. RESULTS: The Drimys, Liriodendron, and Piper plastid genomes are very similar in size at 160,604, 159,886 bp, and 160,624 bp, respectively. Gene content and order are nearly identical to many other unrearranged angiosperm plastid genomes, including Calycanthus, the other published magnoliid genome. Overall GC content ranges from 34–39%, and coding regions have a substantially higher GC content than non-coding regions. Among protein-coding genes, GC content varies by codon position with 1st codon > 2nd codon > 3rd codon, and it varies by functional group with photosynthetic genes having the highest percentage and NADH genes the lowest. Phylogenetic analyses using parsimony and likelihood methods and sequences of 61 protein-coding genes provided strong support for the monophyly of magnoliids and two strongly supported groups were identified, the Canellales/Piperales and the Laurales/Magnoliales. Strong support is reported for monocots and eudicots as sister clades with magnoliids diverging before the monocot-eudicot split. The trees also provided moderate or strong support for the position of Amborella as sister to a clade including all other angiosperms. CONCLUSION: Evolutionary comparisons of three new magnoliid plastid genome sequences, combined with other published angiosperm genomes, confirm that GC content is unevenly distributed across the genome by location, codon position, and functional group. Furthermore, phylogenetic analyses provide the strongest support so far for the hypothesis that the magnoliids are sister to a large clade that includes both monocots and eudicots

Comparative analyses of land plant plastid genomes

textThe availability of complete plastid genomes has been playing an important role in resolving phylogenetic relationships among the major clades of land plants and in improving our understanding of the evolution of genomic organization. The increased availability of complete genome sequences has enabled researchers to build large multi-gene datasets for phylogenetic and molecular evolutionary studies. In chapter 2 of this thesis a web-based multiple sequence web viewer and alignment tool (MSWAT) is developed to handle large amount of data generated from complete genome sequences for phylogenetic and evolutionary analyses. We expect that MSWAT will be of general interest to biologists who are building large data matrices for evolutionary analyses. The third chapter presents the sequenced plastid genomes of three magnoliids, Drimys (Canellales), Liriodendron (Magnoliales), and Piper (Piperales). Data from these genomes, in combination with 32 other angiosperm plastid genomes, were used to assess phylogenetic relationships of magnoliids to other angiosperms and to examine patterns of variation of GC content. Evolutionary comparisons of three new magnoliid plastid genome sequences, combined with other published angiosperm genomes, confirm that GC content is unevenly distributed across the genome by location, codon position, and functional group. Furthermore, phylogenetic analyses provide the strongest support so far for the hypothesis that the magnoliids are sister to a large clade that includes both monocots and eudicots. The fourth chapter presents the Trifolium subterraneum plastid genome sequence, which is unusual in genome size and organization relative to other angiosperm plastid genomes. The Trifolium plastid genome is an excellent model system to examine mechanisms of rearrangements and the evolution of repeats and unique DNA.Biological Sciences, School o

Identification of novel viruses using VirusHunter--an automated data analysis pipeline.

Quick and accurate identification of microbial pathogens is essential for both diagnosis and response to emerging infectious diseases. The advent of next-generation sequencing technology offers an unprecedented platform for rapid sequencing-based identification of novel viruses. We have developed a customized bioinformatics data analysis pipeline, VirusHunter, for the analysis of Roche/454 and other long read Next generation sequencing platform data. To illustrate the utility of VirusHunter, we performed Roche/454 GS FLX titanium sequencing on two unclassified virus isolates from the World Reference Center for Emerging Viruses and Arboviruses (WRCEVA). VirusHunter identified sequences derived from a novel bunyavirus and a novel reovirus in the two samples respectively. Further sequence analysis demonstrated that the viruses were novel members of the Phlebovirus and Orbivirus genera. Both Phlebovirus and Orbivirus genera include many economic important viruses or serious human pathogens

High Rate of Chimeric Gene Origination by Retroposition in Plant Genomes

Retroposition is widely found to play essential roles in origination of new mammalian and other animal genes. However, the scarcity of retrogenes in plants has led to the assumption that plant genomes rarely evolve new gene duplicates by retroposition, despite abundant retrotransposons in plants and a reported long terminal repeat (LTR) retrotransposon-mediated mechanism of retroposing cellular genes in maize (Zea mays). We show extensive retropositions in the rice (Oryza sativa) genome, with 1235 identified primary retrogenes. We identified 27 of these primary retrogenes within LTR retrotransposons, confirming a previously observed role of retroelements in generating plant retrogenes. Substitution analyses revealed that the vast majority are subject to negative selection, suggesting, along with expression data and evidence of age, that they are likely functional retrogenes. In addition, 42% of these retrosequences have recruited new exons from flanking regions, generating a large number of chimerical genes. We also identified young chimerical genes, suggesting that gene origination through retroposition is ongoing, with a rate an order of magnitude higher than the rate in primates. Finally, we observed that retropositions have followed an unexpected spatial pattern in which functional retrogenes avoid centromeric regions, while retropseudogenes are randomly distributed. These observations suggest that retroposition is an important mechanism that governs gene evolution in rice and other grass species

Phylogenetic analysis of Salanga and Heramatsu Orbivirus virus.

<p>Phylogenetic tree comparing RNA-dependent RNA polymerase of (A) Salanga virus with representative members of the <i>Phlebovirus</i> genus within the <i>Bunyaviridae</i> family and (B) Heramatsu Orbivirus with representative members of the <i>Orbivirus</i> genus within the <i>Reoviridae</i> family. Phylogenetic trees were constructed by using the neighbor-joining method in the MEGA5 program with 1000 bootstrap replicates. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test is shown next to the branches. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. </p

Genomic structure and coding strategy of Salanga virus.

<p>Predicted open reading frames indicated by boxes with arrows indicating the directionality of the open reading frame.</p

Workflow of VirusHunter.

<p>Workflow of VirusHunter.</p