Reading Group

Reading group

Candidate reading

CRISPR cas9

Arora, L. and Narula, A., 2017. Gene editing and crop improvement using CRISPR-Cas9 system. Frontiers in plant science, 8, p.1932. https://doi.org/10.3389/fpls.2017.01932

Dort, E.N., Tanguay, P. and Hamelin, R.C., 2020. CRISPR/Cas9 gene editing: an unexplored frontier for forest pathology. Frontiers in Plant Science, 11, p.1126. https://doi.org/10.3389/fpls.2020.01126

Drought tolerance

Fleury, D., Jefferies, S., Kuchel, H. and Langridge, P., 2010. Genetic and genomic tools to improve drought tolerance in wheat. Journal of experimental botany, 61(12), pp.3211-3222. https://doi.org/10.1093/jxb/erq152

Muhammad Ilyas1 · Mohammad Nisar1 · Nadeem Khan1 · Ali Hazrat1 · Aamir Hamid Khan 2 · Kashif Hayat3 · Shah Fahad4 · Aziz Khan5 · Abid Ullah. Drought Tolerance Strategies in Plants: A Mechanistic Approach. Vol.:(0123456789)1 3Journal of Plant Growth Regulation https://doi.org/10.1007/s00344-020-10174-5

Insights into Drought Stress Signaling in Plants and the Molecular Genetic Basis of Cotton Drought Tolerance

Genomics

Barbara McClintock. The origin and behavior of mutable loci in maize. June 1950. 36 (6) 344-355. https://doi.org/10.1073/pnas.36.6.344

Wild emmer genome architecture and diversity elucidate wheat evolution and domestication. Raz Avni, Moran Nave, Omer Barad, Kobi Baruch, Sven O. Twardziok, Heidrun Gundlach, Iago Hale, Martin Mascher, Manuel Spannagl, Assaf Distelfeld. https://doi.org/10.1126/science.aan0032

Hi-C

Belton, J.M., McCord, R.P., Gibcus, J.H., Naumova, N., Zhan, Y. and Dekker, J., 2012. Hi–C: a comprehensive technique to capture the conformation of genomes. Methods, 58(3), pp.268-276. https://doi.org/10.1016/j.ymeth.2012.05.001

Pal, K., Forcato, M. and Ferrari, F., 2019. Hi-C analysis: from data generation to integration. Biophysical reviews, 11(1), pp.67-78. https://doi.org/10.1007/s12551-018-0489-1

Kronenberg, Z.N., Rhie, A., Koren, S., Concepcion, G.T., Peluso, P., Munson, K.M., Porubsky, D., Kuhn, K., Mueller, K.A., Low, W.Y. and Hiendleder, S., 2021. Extended haplotype-phasing of long-read de novo genome assemblies using Hi-C. Nature communications, 12(1), pp.1-10. https://doi.org/10.1038/s41467-020-20536-y

Pathology

Thirty years of resistance: Zig-zag through the plant immune system. Bruno Pok Man Ngou, Pingtao Ding, Jonathan D G Jones. https://doi.org/10.1093/plcell/koac041

Plant disease resistance genes: Current status and future directions. Mayank Anand Gururani. Physiological and Molecular Plant Pathology 78 (2012) 51e65. https://doi.org/10.1016/j.pmpp.2012.01.002

Phytochemicals

Cannabinoids, Phenolics, Terpenes and Alkaloids of Cannabis. Mohamed M Radwan, Suman Chandra, Shahbaz Gul, Mahmoud A ElSohly https://doi.org/10.3390/molecules26092774

Secondary metabolism in Cannabis. Isvett Josefina Flores-Sanchez Æ Robert Verpoorte. Phytochem Rev (2008) 7:615–639. https://doi.org/10.1007/s11101-008-9094-4

Bautista, J.L., Yu, S. and Tian, L., 2021. Flavonoids in Cannabis sativa: Biosynthesis, bioactivities, and biotechnology. ACS omega, 6(8), pp.5119-5123. https://doi.org/10.1021/acsomega.1c00318

Fall 2024

2024-12-04
2024-11-20
2024-11-20 Adal, A.M., Doshi, K., Holbrook, L. et al. Comparative RNA-Seq analysis reveals genes associated with masculinization in female Cannabis sativa. Planta 253, 17 (2021). https://doi.org/10.1007/s00425-020-03522-y
2024-11-13 Stefan Kusch, Lina Pesch, Ralph Panstruga, Comprehensive Phylogenetic Analysis Sheds Light on the Diversity and Origin of the MLO Family of Integral Membrane Proteins, Genome Biology and Evolution, Volume 8, Issue 3, March 2016, Pages 878–895, https://doi.org/10.1093/gbe/evw036
2024-11-06 Owen, L. C., Suchoff, D. H., & Chen, H. (2023). A Novel Method for Stimulating Cannabis sativa L. Male Flowers from Female Plants. Plants, 12(19), 3371. https://doi.org/10.3390/plants12193371
2024-10-30 Alexandra J. Weisberg et al., Unexpected conservation and global transmission of agrobacterial virulence plasmids. Science368, eaba5256(2020). DOI:10.1126/science.aba5256

Spring 2024

2024-06-18 Xiaoya Shi, Shuo Cao, Xu Wang, Siyang Huang, Yue Wang, Zhongjie Liu, Wenwen Liu, Xiangpeng Leng, Yanling Peng, Nan Wang, Yiwen Wang, Zhiyao Ma, Xiaodong Xu, Fan Zhang, Hui Xue, Haixia Zhong, Yi Wang, Kekun Zhang, Amandine Velt, Komlan Avia, Daniela Holtgräwe, Jérôme Grimplet, José Tomás Matus, Doreen Ware, Xinyu Wu, Haibo Wang, Chonghuai Liu, Yuling Fang, Camille Rustenholz, Zongming Cheng, Hua Xiao, Yongfeng Zhou, The complete reference genome for grapevine (Vitis vinifera L.) genetics and breeding, Horticulture Research, Volume 10, Issue 5, May 2023, uhad061, https://doi.org/10.1093/hr/uhad061
2024-06-04 Pedersen, G.B., Blaschek, L., Frandsen, K.E., Noack, L.C. and Persson, S., 2023. Cellulose synthesis in land plants. Molecular Plant, 16(1), pp.206-231.
2024-5-21 Nix, J., Ranney, T. G., Lynch, N. P., and Chen, H. (2024). Flow Cytometry for Estimating Plant Genome Size: Revisiting Assumptions, Sources of Variation, Reference Standards, and Best Practices. J. Amer. Soc. Hort. Sci. 149, 3, 131-141, available from: https://doi.org/10.21273/JASHS05376-24
2024-5-14 Chakraborty, S., Dutta, S. and Das, M., 2023. Genetics behind sexual incompatibility in plants: How much we know and what more to uncover?. Journal of Plant Growth Regulation, 42(11), pp.7164-7188.
2024-4-09 Davey, J.W., Hohenlohe, P.A., Etter, P.D., Boone, J.Q., Catchen, J.M. and Blaxter, M.L., 2011. Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nature Reviews Genetics, 12(7), pp.499-510.

Winter 2024

2024-3-12 https://bioconductor.org/packages/release/bioc/html/flowCore.html
2024-3-05 Wang, H., Ren, J., Zhou, S., Duan, Y., Zhu, C., Chen, C., Liu, Z., Zheng, Q., Xiang, S., Xie, Z. and Wang, X., 2024. Molecular regulation of oil gland development and biosynthesis of essential oils in Citrus spp. Science, 383(6683), pp.659-666.

Fall 2023

2023-11-14 Regularized multi-trait multi-locus linear mixed models for genome-wide association studies and genomic selection in crops Aurélie C. Lozano1, Hantian Ding2, Naoki Abe1 and Alexander E. Lipka3* BMC Bioinformatics (2023) 24:399 https://doi.org/10.1186/s12859-023-05519-2
2023-10-24 Genome-wide association mapping and genomic prediction for late blight and potato cyst nematode resistance in potato (Solanum tuberosum L.) Salej Sood1* Vinay Bhardwaj1 Aarti Bairwa1 Dalamu1 Sanjeev Sharma1 Ashwani K. Sharma1 Ashwani Kumar1 Mehi Lal2 Vinod Kumar1 Front. Plant Sci., 04 October 2023 Sec. Plant Pathogen Interactions Volume 14 - 2023 https://doi.org/10.3389/fpls.2023.1211472
2023-10-17 Genome-wide association mapping and genomic prediction for late blight and potato cyst nematode resistance in potato (Solanum tuberosum L.) Salej Sood1* Vinay Bhardwaj1 Aarti Bairwa1 Dalamu1 Sanjeev Sharma1 Ashwani K. Sharma1 Ashwani Kumar1 Mehi Lal2 Vinod Kumar1 Front. Plant Sci., 04 October 2023 Sec. Plant Pathogen Interactions Volume 14 - 2023 https://doi.org/10.3389/fpls.2023.1211472

Summer 2023

2023-09-05 Leveraging Single-Cell Populations to Uncover the Genetic Basis of Complex Traits Mark A.A. Minow, Alexandre P. Marand, Robert J. Schmitz Annual Review of Genetics 2023 57:1 https://doi.org/10.1146/annurev-genet-022123-110824
2023-08-22 “The Evolution of Plant Secretory Structures and Emergence of Terpenoid Chemical Diversity” https://doi.org/10.1146/annurev-arplant-043014-114639
2023-08-08 Berman, P., de Haro, L.A., Jozwiak, A. et al. Parallel evolution of cannabinoid biosynthesis. Nat. Plants 9, 817–831 (2023). https://doi.org/10.1038/s41477-023-01402-3
2023-07-25 Liao, WW., Asri, M., Ebler, J. et al. A draft human pangenome reference. Nature 617, 312–324 (2023). https://doi.org/10.1038/s41586-023-05896-x
2023-07-11 JBrowse 2: a modular genome browser with views of synteny and structural variation. Genome Biology (2023). https://doi.org/10.1186/s13059-023-02914-z
2023-06-27 Wang, D., Zheng, Z., Li, Y., Hu, H., Wang, Z., Du, X., … & Yang, Y. (2021). Which factors contribute most to genome size variation within angiosperms?. Ecology and Evolution, 11(6), 2660-2668 https://doi.org/10.1002/ece3.7222

Spring 2023

2023-05-18 Horvath, D. P., Clay, S. A., Swanton, C. J., Anderson, J. V., & Chao, W. S. (2023). Weed-induced crop yield loss: a new paradigm and new challenges. Trends in Plant Science. https://doi.org/10.1016/j.tplants.2022.12.014
2023-04-20 Amanda R Stahlke, Jennifer Chang, Sivanandan Chudalayandi, Chan C Heu, Scott M Geib, Brian E Scheffler, Anna K Childers, Jeffrey A Fabrick, Chromosome-scale genome assembly of the pink bollworm, Pectinophora gossypiella, a global pest of cotton, G3 Genes|Genomes|Genetics, Volume 13, Issue 4, April 2023, jkad040. https://doi.org/10.1093/g3journal/jkad040
2023-04-13 Keilwagen, J., Lehnert, H., Berner, T. et al. Detecting major introgressions in wheat and their putative origins using coverage analysis. Sci Rep 12, 1908 (2022). https://doi.org/10.1038/s41598-022-05865-w
2023-04-06 Jaegle, B., Pisupati, R., Soto-Jiménez, L.M. et al. Extensive sequence duplication in Arabidopsis revealed by pseudo-heterozygosity. Genome Biol 24, 44 (2023). https://doi.org/10.1186/s13059-023-02875-3

Winter 2023

2023-03-23 Jaegle, B., Pisupati, R., Soto-Jiménez, L.M. et al. Extensive sequence duplication in Arabidopsis revealed by pseudo-heterozygosity. Genome Biol 24, 44 (2023). https://doi.org/10.1186/s13059-023-02875-3
2023-03-16 Healey, A.L., Piatkowski, B., Lovell, J.T. et al. Newly identified sex chromosomes in the Sphagnum (peat moss) genome alter carbon sequestration and ecosystem dynamics. Nat. Plants 9, 238–254 (2023). https://doi.org/10.1038/s41477-022-01333-5
2023-03-09 Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads https://doi.org/10.1038/s41587-020-0719-5
2023-03-02 Semi-automated assembly of high-quality diploid human reference genomes https://doi.org/10.1038/s41586-022-05325-5
2023-02-23 Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm https://doi.org/10.1038/s41592-020-01056-5
2023-02-16 Genome architecture and tetrasomic inheritance of autotetraploid potato https://doi.org/10.1016/j.molp.2022.06.009
2023-02-09 Fertility and Reproductive Pathways of Triploid Flowering Pears (Pyrus sp.) https://doi.org/10.21273/HORTSCI.51.8.968
2023-02-02 The Biochemistry of Phytocannabinoids and Metabolic Engineering of Their Production in Heterologous Systems https://doi.org/10.3390/ijms22052454

Winter break 2022

2022-12-15 Chromosome-scale and haplotype-resolved genome assembly of a tetraploid potato cultivar https://doi.org/10.1038/s41588-022-01015-0

Fall 2022

2022-12-01 Phased, chromosome-scale genome assemblies of tetraploid potato reveal a complex genome, transcriptome, and predicted proteome landscape underpinning genetic diversity https://doi.org/10.1016/j.molp.2022.01.003
2022-11-17 Genome assembly of six polyploid potato genomes https://www.nature.com/articles/s41597-020-0428-4
2022-11-10 Design and validation issues in RNA-seq experiments https://doi.org/10.1093/bib/bbr004
2022-11-04 Haplotype-phased genome and evolution of phytonutrient pathways of tetraploid blueberry https://doi.org/10.1093/gigascience/giz012
2022-10-27 Haplotype-phased genome and evolution of phytonutrient pathways of tetraploid blueberry https://doi.org/10.1093/gigascience/giz012
2022-10-20 Methods: Improved pea reference genome and pan-genome highlight genomic features and evolutionary characteristics https://doi.org/10.1038/s41588-022-01172-2
2022-10-13 Improved pea reference genome and pan-genome highlight genomic features and evolutionary characteristics https://doi.org/10.1038/s41588-022-01172-2
2022-10-06 Reading resources, how to find things to read
https://www.sciencenews.org/
https://www.science.org/journal/science
https://www.nature.com/
https://scholar.google.com/
https://www.google.com/alerts
https://apsjournals.apsnet.org/
https://journals.ashs.org/
https://twitter.com/ - follow authors and journals

Summer 2022

2022-09-15 Lieberman-Aiden, E., Van Berkum, N.L., Williams, L., Imakaev, M., Ragoczy, T., Telling, A., Amit, I., Lajoie, B.R., Sabo, P.J., Dorschner, M.O. and Sandstrom, R., 2009. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. science, 326(5950), pp.289-293. https://doi.org/10.1126/science.1181369
2022-08-18 Avni, R., Nave, M., Barad, O., Baruch, K., Twardziok, S.O., Gundlach, H., Hale, I., Mascher, M., Spannagl, M., Wiebe, K. and Jordan, K.W., 2017. Wild emmer genome architecture and diversity elucidate wheat evolution and domestication. Science, 357(6346), pp.93-97. https://doi.org/10.1126/science.aan0032
2022-07-07 Twenty years of plant genome sequencing: achievements and challenges. Yanqing Sun, Lianguang Shang, Qian-Hao Zhu, Longjiang Fan, Longbiao Guo. https://doi.org/10.1016/j.tplants.2021.10.006
2022-06-23 How to read a scientific paper

Spring 2022

2022-05-26 Allen et al. 2019 Genomic characterization of the complete terpene synthase gene family from Cannabis sativa
2022-05-12 Petit et al. 2020 Elucidating the Genetic Architecture of Fiber Quality in Hemp (Cannabis sativa L.) Using a Genome-Wide Association Study
2022-04-28 Ejigu and Jung 2020 Review on the Computational Genome Annotation of Sequences Obtained by Next-Generation Sequencing
2022-03-31 Garfinkel et al. 2021. SNP in Potentially Defunct Tetrahydrocannabinolic Acid Synthase Is a Marker for Cannabigerolic Acid Dominance in Cannabis sativa L.