Phylogenetic Analysis Using PHYLIP

Retief, Jacques D.

doi:10.1385/1-59259-192-2:243

Cited by 264 publications

(240 citation statements)

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“…A phylogenetic tree of Lr22a and known wheat resistance proteins was made using the PROTPARS tool of the PHYLIP package with 100 bootstrap replicates 46 . The amino acid sequences of known wheat NLRs were downloaded from the NCBI repository.…”

Section: Methodsmentioning

confidence: 99%

Rapid cloning of genes in hexaploid wheat using cultivar-specific long-range chromosome assembly

et al. 2017

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Cereal crops such as wheat and maize have large repeat-rich genomes that make cloning of individual genes challenging. Moreover, gene order and gene sequences often differ substantially between cultivars of the same crop species. A major bottleneck for gene cloning in cereals is the generation of high-quality sequence information from a cultivar of interest. In order to accelerate gene cloning from any cropping line, we report 'targeted chromosome-based cloning via long-range assembly' (TACCA). TACCA combines lossless genome-complexity reduction via chromosome flow sorting with Chicago longrange linkage to assemble complex genomes. We applied TACCA to produce a high-quality (N50 of 9.76 Mb) de novo chromosome assembly of the wheat line CH Campala Lr22a in only 4 months. Using this assembly we cloned the broad-spectrum Lr22a leaf-rust resistance gene, using molecular marker information and ethyl methanesulfonate (EMS) mutants, and found that Lr22a encodes an intracellular immune receptor homologous to the Arabidopsis thaliana RPM1 protein.DOI: https://doi.org/10.1038/nbt.3877Posted at the Zurich Open Repository and Archive, University of Zurich ZORA URL: https://doi.org/10.5167/uzh-144182 Journal Article Accepted Version Originally published at: Thind, Anupriya Kaur; Wicker, Thomas; Šimková, Hana; Fossati, Dario; Moullet, Odile; Brabant, Cécile; Vrána, Jan; Doležel, Jaroslav; Krattinger, Simon G (2017). Rapid cloning of genes in hexaploid wheat using cultivar-specific long-range chromosome assembly. Nature Biotechnology, 35(8) Using this assembly we cloned the broad-spectrum Lr22a leaf-rust resistance gene using molecular marker information and EMS mutants and found that Lr22a encodes an intracellular immune receptor homologous to the Arabidopsis RPM1 protein.While the world population continues to grow, the arable land per capita is decreasing 6 . To ensure food security, agriculture will require high-yielding crops that can withstand diseases, pests and adverse climatic conditions. A better understanding of genes that control these important traits may enable breeding of crop cultivars capable of feeding the 9-10 billion people expected by 2050. triticina isolates [13][14][15][16] . The Lr22a-mediated resistance is not present in young seedlings (<20 days) but is only visible in wheat plants from ~25 days of age.First, in order to evaluate the effectiveness of Lr22a against Swiss P. triticina isolates we inoculated the Lr22a-containing backcross line RL6044 ('Thatcher Lr22a') and the spring wheat cultivar 'Thatcher' with ten P. triticina isolates that were collected in Switzerland. The first leaves of RL6044 developed leaf rust pustules of similar size as the susceptible control 'Thatcher', while we observed complete to moderate resistance on the third leaves of 30-dayold RL6044 plants in comparison to 'Thatcher' (Fig. 1, Supplementary Fig. 1).Lr22a was previously mapped to the short arm of wheat chromosome 2D using microsatellite analysis of the Lr22a-containing wheat line 98B34-T4B 13 . In order to...

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Section: Methodsmentioning

confidence: 99%

Rapid cloning of genes in hexaploid wheat using cultivar-specific long-range chromosome assembly

et al. 2017

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“…The Jones-Taylor-Thornton (JTT) substitution model was used. One hundred bootstrap replicates were performed (13). Maximum likelihood analyses were performed by using TREE-PUZZLE version 5.1 for Unix (14).…”

Section: Methodsmentioning

confidence: 99%

Gene transfer in the evolution of parasite nucleotide biosynthesis

Striepen

Pruijssers

Huang

et al. 2004

Proc. Natl. Acad. Sci. U.S.A.

196

198

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Nucleotide metabolic pathways provide numerous successful targets for antiparasitic chemotherapy, but the human pathogen Cryptosporidium parvum thus far has proved extraordinarily refractory to classical treatments. Given the importance of this protist as an opportunistic pathogen afflicting immunosuppressed individuals, effective treatments are urgently needed. The genome sequence of C. parvum is approaching completion, and we have used this resource to critically assess nucleotide biosynthesis as a target in C. parvum. Genomic analysis indicates that this parasite is entirely dependent on salvage from the host for its purines and pyrimidines. Metabolic pathway reconstruction and experimental validation in the laboratory further suggest that the loss of pyrimidine de novo synthesis is compensated for by possession of three salvage enzymes. Two of these, uridine kinase-uracil phosphoribosyltransferase and thymidine kinase, are unique to C. parvum within the phylum Apicomplexa. Phylogenetic analysis suggests horizontal gene transfer of thymidine kinase from a proteobacterium. We further show that the purine metabolism in C. parvum follows a highly streamlined pathway. Salvage of adenosine provides C. parvum's sole source of purines. This renders the parasite susceptible to inhibition of inosine monophosphate dehydrogenase, the rate-limiting enzyme in the multistep conversion of AMP to GMP. The inosine 5 monophosphate dehydrogenase inhibitors ribavirin and mycophenolic acid, which are already in clinical use, show pronounced anticryptosporidial activity. Taken together, these data help to explain why widely used drugs fail in the treatment of cryptosporidiosis and suggest more promising targets.Cryptosporidium parvum ͉ horizontal gene transfer ͉ drug target ͉ thymidine kinase ͉ IMPDH

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“…This was necessary as sequences from a study on these stromatolite populations conducted by Papineau et al (2005), samples designated as HPDOM and HPIRR, targeted different regions of the 16S rRNA genes as compared with this study and the study by Burns et al (2004). Bootstrap values were obtained for branching patterns by using the PHYLIP software package (Retief, 2000), and values 450% were included for the main nodes of the tree. 16S rRNA gene sequences from earlier studies on the Shark Bay stromatolites (Burns et al, 2004;Papineau et al, 2005) were included for the determination of differences in the populations.…”

Section: Phylogenetic Sequence Analysismentioning

confidence: 99%

Determining the specific microbial populations and their spatial distribution within the stromatolite ecosystem of Shark Bay

et al. 2008

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The stromatolites at Shark Bay, Western Australia, are analogues of some of the oldest evidence of life on Earth. The aim of this study was to identify and spatially characterize the specific microbial communities associated with Shark Bay intertidal columnar stromatolites. Conventional culturing methods and construction of 16S rDNA clone libraries from community genomic DNA with both universal and specific PCR primers were employed. The estimated coverage, richness and diversity of stromatolite microbial populations were compared with earlier studies on these ecosystems. The estimated coverage for all clone libraries indicated that population coverage was comprehensive. Phylogenetic analyses of stromatolite and surrounding seawater sequences were performed in ARB with the Greengenes database of full-length non-chimaeric 16S rRNA genes. The communities identified exhibited extensive diversity. The most abundant sequences from the stromatolites were a-and c-proteobacteria (58%), whereas the cyanobacterial community was characterized by sequences related to the genera Euhalothece, Gloeocapsa, Gloeothece, Chroococcidiopsis, Dermocarpella, Acaryochloris, Geitlerinema and Schizothrix. All clones from the archaeal-specific clone libraries were related to the halophilic archaea; however, no archaeal sequence was identified from the surrounding seawater. Fluorescence in situ hybridization also revealed stromatolite surfaces to be dominated by unicellular cyanobacteria, in contrast to the sub-surface archaea and sulphate-reducing bacteria. This study is the first to compare the microbial composition of morphologically similar stromatolites over time and examine the spatial distribution of specific microorganismic groups in these intertidal structures and the surrounding seawater at Shark Bay. The results provide a platform for identifying the key microbial physiology groups and their potential roles in modern stromatolite morphogenesis and ecology.

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Phylogenetic Analysis Using PHYLIP

Cited by 264 publications

References 0 publications

Rapid cloning of genes in hexaploid wheat using cultivar-specific long-range chromosome assembly

Rapid cloning of genes in hexaploid wheat using cultivar-specific long-range chromosome assembly

Gene transfer in the evolution of parasite nucleotide biosynthesis

Determining the specific microbial populations and their spatial distribution within the stromatolite ecosystem of Shark Bay

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