Comparative genomic analysis uncovered phylogenetic diversity, evolution of virulence factors, and horizontal gene transfer events in tomato bacterial spot Xanthomonas euvesicatoria

Authors: Chien-Jui Huang, Ting-Li Wu, Yu-Lin Wu, Ruei-Shiuan Wang, Yao-Cheng Lin

Source: Frontiers in Microbiology, Vol 15 (2024)

Subject Terms: Xanthomonas euvesicatoria, bacterial spot, microbial evolution, comparative genomics, virulence factors, microbial diversity, Microbiology, QR1-502

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fmicb.2024.1487917/full; https://doaj.org/toc/1664-302X

Access URL: https://doaj.org/article/9519ecc16b084cbeab332e4f5d54a390

KASP Markers for Identifying Roselle (Hibiscus sabdariffa L.) Key Varieties Based on Genetic Polymorphisms Revealed by ddRAD-Seq

Authors: Shih-Jie Huang, Jheng-Yang Ou, Yao-Cheng Lin, Jing-Wen Chen, Kai-Yi Chen, Yu-Lin Wu, Chun-Hao Hu, Ju-Yin Lee, Jia-Wei Wu, Fu-Chiun Hsu

Source: Horticulturae, Vol 10, Iss 12, p 1325 (2024)

Subject Terms: variety identification, genotyping, double-digest restriction-associated DNA sequencing (ddRAD-seq), kompetitive allele-specific PCR (KASP), genetic diversity, SNP genotyping, Plant culture, SB1-1110

File Description: electronic resource

Relation: https://www.mdpi.com/2311-7524/10/12/1325; https://doaj.org/toc/2311-7524

Access URL: https://doaj.org/article/51dcb2eadf5148139b310489b261f6c1

Whole genome resequencing and complementation tests reveal candidate loci contributing to bacterial wilt (Ralstonia sp.) resistance in tomato

Authors: Derek W. Barchenger, Yu-ming Hsu, Jheng-yang Ou, Ya-ping Lin, Yao-cheng Lin, Mark Angelo O. Balendres, Yun-che Hsu, Roland Schafleitner, Peter Hanson

Source: Scientific Reports, Vol 12, Iss 1, Pp 1-12 (2022)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: https://doaj.org/toc/2045-2322

Access URL: https://doaj.org/article/d5183fd6abc14c6d874a7f16fab03417

Reference genome and comparative genome analysis for the WHO reference strain for Mycobacterium bovis BCG Danish, the present tuberculosis vaccine

Authors: Katlyn Borgers, Jheng-Yang Ou, Po-Xing Zheng, Petra Tiels, Annelies Van Hecke, Evelyn Plets, Gitte Michielsen, Nele Festjens, Nico Callewaert, Yao-Cheng Lin

Source: BMC Genomics, Vol 20, Iss 1, Pp 1-14 (2019)

Subject Terms: Tuberculosis, Live vaccines, BCG, Next-generation sequencing, Complete genomic sequence, Genetic differences, Biotechnology, TP248.13-248.65, Genetics, QH426-470

File Description: electronic resource

Relation: http://link.springer.com/article/10.1186/s12864-019-5909-5; https://doaj.org/toc/1471-2164

Access URL: https://doaj.org/article/80a9e6d5e2924e2f986096653914a404

Comparative Genomic Analysis Uncovered Evolution of Pathogenicity Factors, Horizontal Gene Transfer Events, and Heavy Metal Resistance Traits in Citrus Canker Bacterium Xanthomonas citri subsp. citri

Authors: Chien-Jui Huang, Ting-Li Wu, Po-Xing Zheng, Jheng-Yang Ou, Hui-Fang Ni, Yao-Cheng Lin

Source: Frontiers in Microbiology, Vol 12 (2021)

Subject Terms: Xanthomonas citri subsp. citri, copper resistance, whole-genome sequence, TALE, plasmid, plasticity, Microbiology, QR1-502

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fmicb.2021.731711/full; https://doaj.org/toc/1664-302X

Access URL: https://doaj.org/article/3d08a18ab356471fa526e9c6d430b6d1

A Comprehensive Analysis of Genes Encoding Small Secreted Proteins Identifies Candidate Effectors in Melampsora larici-populina (Poplar Leaf Rust)

Authors: Stéphane Hacquard, David L. Joly, Yao-Cheng Lin, Emilie Tisserant, Nicolas Feau, Christine Delaruelle, Valérie Legué, Annegret Kohler, Philippe Tanguay, Benjamin Petre, Pascal Frey, Yves Van de Peer, Pierre Rouzé, Francis Martin, Richard C. Hamelin, Sébastien Duplessis

Source: Molecular Plant-Microbe Interactions, Vol 25, Iss 3, Pp 279-293 (2012)

Subject Terms: Microbiology, QR1-502, Botany, QK1-989

File Description: electronic resource

Relation: https://doaj.org/toc/0894-0282; https://doaj.org/toc/1943-7706

Access URL: https://doaj.org/article/0409f3addc9c4287b79d3f468d91a851

Serendipitous Meta-Transcriptomics: The Fungal Community of Norway Spruce (Picea abies).

Authors: Nicolas Delhomme, Görel Sundström, Neda Zamani, Henrik Lantz, Yao-Cheng Lin, Torgeir R Hvidsten, Marc P Höppner, Patric Jern, Yves Van de Peer, Joakim Lundeberg, Manfred G Grabherr, Nathaniel R Street

Source: PLoS ONE, Vol 10, Iss 9, p e0139080 (2015)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: http://europepmc.org/articles/PMC4586145?pdf=render; https://doaj.org/toc/1932-6203

Access URL: https://doaj.org/article/3657a32464e348579de10f9082deed29

DNA-free CRISPR-Cas9 gene editing of wild tetraploid tomato Solanum peruvianum using protoplast regeneration.

Authors: Choun-Sea Lin, Chen-Tran Hsu, Yu-Hsuan Yuan, Po-Xing Zheng, Fu-Hui Wu, Qiao-Wei Cheng, Yu-Lin Wu, Ting-Li Wu, Lin, Steven, Jin-Jun Yue, Ying-Huey Cheng, Shu-I Lin, Ming-Che Shih, Jen Sheen, Yao-Cheng Lin

Source: Plant Physiology; Apr2022, Vol. 188 Issue 4, p1917-1930, 14p

Comparative in silico analysis of SSRs in coding regions of high confidence predicted genes in Norway spruce (Picea abies) and Loblolly pine Pinus taeda).

Authors: Ranade, Sonali Sachin¹, Yao-Cheng Lin², Van de Peer, Yves^2,3,4, García-Gil, María Rosario¹ M.Rosario.Garcia@slu.se

Source: BMC Genetics. 12/26/2015, Vol. 16, p1-9. 9p.

Subject Terms: *MICROSATELLITE repeats, *NUCLEOTIDE sequencing, *GENOMES, *NORWAY spruce, *LOBLOLLY pine

Use of an A-T-rich DNA clone for identification and detection of Peronosclerospora sorghi.

Authors: Yao, Cheng-Lin, Magill, Clint W., Frederiksen, Richard A.

Source: Applied & Environmental Microbiology; July 1991, Vol. 57, p2027-2032, 6p

Comparative in silico analysis of EST-SSRs in angiosperm and gymnosperm tree genera.

Authors: Ranade, Sonali Sachin¹ Sonali.Ranade@slu.se, Yao-Cheng Lin² yao-cheng.lin@psb.vib-ugent.be, Zuccolo, Andrea^3,4 azuccolo@appliedgenomics.org, Van de Peer, Yves^2,5 yves.vandepeer@psb.vib-ugent.be, del Rosario García-Gil, María¹ M.Rosario.Garcia@slu.se

Source: BMC Plant Biology. 2014, Vol. 14 Issue 1, p1-20. 20p. 3 Charts.

Subject Terms: *ANGIOSPERMS, *GYMNOSPERMS, *EXPRESSED sequence tag (Genetics), *GENOMES, *TREES

Pickup Probability of Sediment under Log-Normal Velocity Distribution.

Authors: Fu-Chun Wu, Yao-Cheng Lin

Source: Journal of Hydraulic Engineering. Apr2002, Vol. 128 Issue 4, p438. 5p. 1 Chart, 2 Graphs.

Subject Terms: *PROBABILITY theory, *SEDIMENTS, *DISTRIBUTION (Probability theory), *ERROR analysis in mathematics

Functional and evolutionary genomic inferences in Populus through genome and population sequencing of American and European aspen.

Authors: Yao-Cheng Lin^1,2,3, Jing Wang^4,5, Delhomme, Nicolas⁶, Schiffthaler, Bastian⁷, Sundström, Görel⁶, Zuccolo, Andrea⁸, Nystedt, Björn⁹, Hvidsten, Torgeir R.^7,10, de la Torre, Amanda^4,11, Cossu, Rosa M.⁸, Hoeppner, Marc P.^12,13, Lantz, Henrik^12,14, Scofield, Douglas G.^4,15,16, Zamani, Neda^6,12, Johansson, Anna⁹, Mannapperuma, Chanaka⁷, Robinson, Kathryn M.⁷, Mähler, Niklas⁷, Leitch, Ilia J.¹⁷, Pellicer, Jaume¹⁷

Source: Proceedings of the National Academy of Sciences of the United States of America. 11/13/2018, Vol. 115 Issue 46, pE10970-E10978. 9p.

Subject Terms: *POPLARS, *ASPEN (Trees), *HETEROZYGOSITY, *GENE expression, *NUCLEOTIDE sequencing, *PLANTS

Draft genome of Cercospora zeina, Fusarium pininemorale, Hawksworthiomyces lignivorus, Huntiella decipiens and Ophiostoma ips.

Authors: Wingfield, Brenda D., Berger, Dave K., Steenkamp, Emma T., Hye-Jin Lim, Duong, Tuan A., Bluhm, Burton H., De Beer, Z. Wilhelm, De Vos, Lieschen, Fourie, G., Naidoo, Kershney, Olivier, Nicky, Yao-Cheng Lin, Van De Peer, Yves, Joubert, Fourie, Crampton, Bridget G., Swart, Velushka, Soal, Nicole, Tatham, Catherine, Van Der Nest, Magriet A., Van Der Merwe, Nicolaas A.

Source: IMA Fungus; Dec2017, Vol. 8 Issue 2, p385-396, 12p

Subject Terms: CERCOSPORA diseases of plants, LEAF spots, FUSARIUM genetics, GENOME size, BACTERIA classification, PREVENTION

Expanding the repertoire of secretory peptides controlling root development with comparative genome analysis and functional assays.

Authors: Ghorbani, Sarieh^1,2, Yao-Cheng Lin^1,2, Parizot, Boris^1,2, Fernandez, Ana^1,2, Njo, Maria Fransiska^1,2, de Peer, Yves Van^1,2,3, Beeckman, Tom^1,2, Hilson, Pierre^1,2,4 pierre.hilson@versailles.inra.fr

Source: Journal of Experimental Botany. Aug2015 Special Issue, Vol. 66 Issue 17, p5257-5269. 13p.

Subject Terms: *PLANT genomes, *ROOT development, *PEPTIDE analysis, *CELL communication, *ARABIDOPSIS thaliana genetics, *PLANT phylogeny, *NUCLEOTIDE sequencing, *GENETIC transcription in plants

Evaluation of local area GPS quality monitoring algorithms in Taipei Flight Information Region.

Authors: Shuo-Ju Yeh, Hui-Chieh Hsu, An-Lin Tao, Yao-Cheng Lin, Shau-Shiun Jan

Source: Proceedings of SICE Annual Conference 2010; 2010, p342-348, 7p

Genome-Wide Analysis Reveals Diverged Patterns of Codon Bias, Gene Expression, and Rates of Sequence Evolution in Picea Gene Families.

Authors: De La Torre, Amanda R.¹ amanda.delatorre@emg.umu.se, Yao-Cheng Lin², Van de Peer, Yves^2,3, Ingvarsson, Pär K.^1,4

Source: Genome Biology & Evolution. Apr2015, Vol. 7 Issue 4, p1002-1015. 14p.

Subject Terms: *GENE expression, *GYMNOSPERMS, *NORWAY spruce, *WHITE spruce, *CHROMOSOME duplication

Obligate biotrophy features unraveled by the genomic analysis of rust fungi.

Authors: Duplessis, Sébastien, Cuomo, Christina A., Yao-Cheng Lin, Aerts, Andrea, Tisserant, Emilie, Veneault-Fourrey, Claire, Joly, David L., Hacquard, Stéphane, Amselem, Joëlle, Cantarel, Brandi L., Chiu, Readman, Coutinho, Pedro M., Feau, Nicolas, Field, Matthew, Frey, Pascal, Gelhaye, Eric, Goldberg, Jonathan, Grabherr, Manfred G., Kodira, Chinnappa D., Kohler, Annegret

Source: Proceedings of the National Academy of Sciences of the United States of America; 5/31/2011, Vol. 108 Issue 22, p9166-9171, 6p

Subject Terms: RUST fungi, BASIDIOMYCETES, PHYTOPATHOGENIC microorganisms, RUST diseases, PLANT genomes, GENETIC regulation

Development and implementation of a highlymultiplexed SNP array for genetic mapping in maritime pine and comparative mapping with loblolly pine.

Authors: Chancerel, Emilie, Lepoittevin, Camille, Le Provost, Grégoire, Yao-Cheng Lin, Jaramillo-Correa, Juan Pablo, Eckert, Andrew J., Wegrzyn, Jill L., Zelenika, Diana, Boland, Anne, Frigerio, Jean-Marc, Chaumeil, Philippe, Garnier-Géré, Pauline, Boury, Christophe, Grivet, Delphine, González-Martínez, Santiago C., Rouzé, Pierre, Van de Peer, Yves, Neale, David B., Cervera, Maria T., Kremer, Antoine

Source: BMC Genomics; 2011, Vol. 12 Issue 1, p368-381, 14p

Subject Terms: GENETIC polymorphisms, GENE mapping, HUMAN chromosomes, MOLECULAR genetics, GENETIC research

Genome sequence of the recombinant protein production host Pichia pastoris.

Authors: De Schutter, Kristof^1,2, Yao-Cheng Lin^3,4, Tiels, Petra^1,5, Hecke, Annelies Van^1,5, Glinka, Sascha⁶, Weber-Lehmann, Jacqueline⁶, Rouzé, Pierre^3,4, De Peer, Yves Van^3,4, Callewaert, Nico^1,5 Nico.Callewaert@dmbr.vib-UGent.be

Source: Nature Biotechnology. Jun2009, Vol. 27 Issue 6, p561-566. 6p. 2 Diagrams, 1 Chart, 1 Graph.

Subject Terms: *PICHIA pastoris, *PROTEINS, *PEROXISOMES, *METHANOL, *GENETIC engineering, *ALCOHOLS (Chemical class)