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Genomic Resources---2021-06-16.md

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Genomic resources available for Sorghum bicolor BTx623

This guide demonstrates genomic resources available through SorghumBase.

The examples below focus on MSD2, a gene which encodes a lipoxygenase (LOX) that catalyzes the first committed step of jasmonic acid biosynthesis. For more info on this gene see Gladman et al (2019).

Using the genes search interface {#search-interface}

Watch the demo video on YouTube.

Searching for a gene given a gene id can be done in a couple of ways:

If you don't know the gene id you can search by pathway and taxonomy example:

  1. In the search box, start typing jasmonic acid biosynthesis and choose the matching Plant Reactome Pathway term
  2. To limit the search to genes in Sorghum bicolor BTx623, type sorghum in the search box and select the matching Taxonomy term

The search results page is organized into three areas:

  1. A panel on the left side shows the status of the search
  2. At the top is a visualization of the genomic locations of genes matching the search
  3. Below this is a paginated list of genes

Each gene has a set of tabs that can be expanded to explore more details:

  • Location - Lightweight genome browser showing gene structure
  • Expression - Baseline gene expression viewer from EBI-Expression Atlas
  • Homology - Gene family tree viewer (opens by default if only one gene is found)
  • Pathways - Associated pathways in Gramene’s Plant Reactome
  • Xrefs - Cross-references to other databases

LOX3 ortholog

Searching for a gene – Gene ID equivalences {#gene-search}

The SorghumBase search interface is not case sensitive and it allows you to search older sorghum gene identifiers (IDs) of the form SbXXX (MIPS/JGI Sbi1.4 in Phytozome) as well as Ensembl gene IDs of the form SORBI_3* and Sobic.* gene IDs (JGI v2.1). Thus, you may search for our exemplar MSD2 gene using SORBI_3006G095600, Sb06g018040, Sobic.006G095600.1 or Sobic.006G095600.2 (gene synonyms or different versions of the same gene model).

You may convert any Sobic.* to its corresponding SbXXX gene ID (JGI v2.1) using JGI’s conversion file (password-protected). The file provides mapping of S. bicolor gene IDs from MIPS/JGI Sbi1.4 to v2.1 and higher builds.

The file looks like this:

Sbi1.4 [Sobic.006G095600] ⇔ v2.1 [Sb06g018040]

#new-locusName old-locusName

Sobic.006G095600 Sb06g018040

#new-transcriptName old-transcriptName

Sobic.006G095600.1 Sb06g018040.1

The following rule applies for the conversion between Sobic.* and Ensembl gene nomenclature in use at SorghumBase:

Sobic.* => SORBI_3*

For example:

Sobic.006G095600 = SORBI_3006G095600

Gene page {#gene-page}

More detailed views available in the SorghumBase Ensembl genome browser include a gene page, transcript page, (SNP) variant page, and structural variant page.

Ensembl Gene Page

Add/remove data tracks or configure an image on the genome browser {#configure-image}

Find the spider gear icon on a browser page, it might precede a "Configure this page" or have a "Configure this image" title when you mouse over it (see image below). When you click on it, you will be able to select or turn on/off a data track (click on a category to disclose all the tracks under it, the number of data sets (tracks) is indicated to the right of each category, for example in the first release of SorghumBase, there are 4 data sets (tracks) under Variation: Sequence variants (all sources), Morris 2013 variants, Mace_2013 variants, and Sorghum_EMS_mutants variants. Click on the square to the left of each data set (track) to select from several options. For example, you may choose to turn the track off or display its data in a collapsed or expanded manner, with or without labels for each data point.

Configure_icon Configure_variation Track_display_options

Comparative Genomics {#comparative-genomics}

The following comparative genomics data for BTx623 are available in the SorghumBase Ensembl genome browser:

  • Gene trees - Example Ensembl GeneTree
  • Genome-wide alignment to Oryza sativa Japonica (see example region) Ensembl Alignment
  • Synteny maps with:
    • Rio
    • RTx430
    • TX2783
    • RTx436
    • Zea mays V4 (see example)
    • Oryza sativa Japonica

Ensembl Synteny

Regulation {#regulation}

RNA-Seq expression data related to root system morphology and architecture in sorghum BTx623 deposited under BioProject PRJNA454504 (Gladman et al, manuscript in prep.). Three repetitions available for each of seven samples: leaf lower (vegetative whorl), leaf upper (growing anthesis), panicle (upper anthesis), root bottom (anthesis), root top (vegetative), stem 1 cm (vegetative) and stem mid internode (anthesis).

  • The example below shows two samples with very similar patterns of gene expression for the msd2 gene region. MSD2

Baseline Gene Expression (Atlas) {#gene-expression}

Baseline gene expression data from seven sorghum BTx623 datasets curated and processed by the EMBL-EBI Expression Atlas [(Emms et al. 2016; Makita et al. 2015; Davidson et al. 2012; Turco et al. 2017; Wang et al. 2018; Olson et al. 2014) and BioProject PRJNA293229/SRP062564 by Thurber et al (2015)].

  • The example below shows Baseline gene expression for the msd2 gene. atlas

Variation {#variation}

Variation in SorghumBase is available for short variants (genetic variation, which in turn may be naturally occurring or chemically induced), longer than 50 nucleotides (structural variants) and QTL variants associated with physical traits.

Genetic Variation

Genetic variation data for a sorghum gene is available graphically and in tabular form, and for each variant, a Variant page provides more detailed information. Below are provided examples of each of these data representations.

  • An image of all the genetic variants mapping to the smaller transcript of the msd2 gene. variant image
  • A partial table of all the genetic variants mapping to the smaller transcript of the msd2 gene.
  • An example of a Variant summary page for a chemically induced variant (tmp_6_47487513_G_A) with a smaller inset of the genotype frequency panel showing the accession (ARS105) bearing the mutation (G|A).

Naturally occurring genetic variation - Single Nucleotide Polymorphisms (SNPs)

Currently in SorghumBase, there are two SNPs data sets for sorghum BTx623:

  • The Morris SNP dataset (Morris et al. 2013) consists of ~265,000 SNPs genotyped in 378 accessions from the US sorghum association panel (SAP).
  • The Mace SNP dataset (Mace et al. 2013) includes almost 6.5 million SNPs genotyped in 45 Sorghum bicolor lines including the BTx623 reference genome plus 2 S. propinquum lines reported by Mace and colleagues (Mace et al. 2013). The data were obtained by resequencing the genomes of the 44 S. bicolor lines representing the primary gene pool and spanning dimensions of geographic origin, end-use and taxonomic group (i.e., major races of cultivated S. bicolor, landraces, improved inbreds, progenitors, wild and weedy), and the first resequenced genome of S. propinquum, all of which were mapped to the BTx623 S. bicolor reference genome.

Chemically induced variation - Ethyl methanesulfonate (EMS)-induced mutations

Currently in SorghumBase, there is one collection of EMS-induced mutant lines. EMS is a chemical commonly used to cause point mutations, that is, to change single nucleotides in the DNA of a plant seed.

  • The Xin EMS dataset (Jiao et al. 2016) includes almost 1.5 million EMS-induced G/C to A/T transition mutations annotated from 252 M3 families selected from the 6,400 sorghum mutant library in BTx623 background described by Xin and colleagues (Xin et al. 2008). Genomic DNA used for sequencing was pooled from 20 M3 plants per M2 family (Jiao et al. 2016).

Structural Variation {#structural-variation}

Data for structural variation for the sorghum BTx623 reference has been imported from the Database of Genomic Variants Archive (dGVA) from a single study containing around 28 thousand structural variations described by (Zheng et al. 2011). Here is an example.

Phenotypic Variation - Quantitative Trait Locus (QTLs) {#qtls}

Data corresponding to 5,843 QTL features for 220 sorghum traits were imported from Sorghum QTL Atlas and are provided with predicted syntenic locations in maize and rice.

Example region with QTLs associated with multiple traits including greenbug resistance, fresh biomass, and flag leaf height.

You may need to turn on the QTLs track and select how you would like the data displayed on your browser. For the figure shown below, I selected "Collapsed" style, which limits the dispaly to only 5 QTLs in the image. Click on a track to disclose more information about that data point (for example, QTL name, location, associated phenotype and data source). In the example below, if you click on a phenotype/trait, such as "Green bug resistance", you will be taken to a page listing all the genomic locations of QTL features associated with Green bug resistance. See an example of such list for Panicle length.

Configure QTLs track

Hint: For additional regions with QTL data in the current sorghum assembly (v.3), use the physical or genetic (cM) coordinates kindly provided by the Sorghum QTL Atlas team.

References {#references}

Aken, Bronwen L., Sarah Ayling, Daniel Barrell, Laura Clarke, Valery Curwen, Susan Fairley, Julio Fernandez Banet, et al. 2016. "The Ensembl Gene Annotation System." Database: The Journal of Biological Databases and Curation. PMID: 27337980. https://doi.org/10.1093/database/baw093.

Brenton, Zachary W., Elizabeth A. Cooper, Mathew T. Myers, Richard E. Boyles, Nadia Shakoor, Kelsey J. Zielinski, Bradley L. Rauh, William C. Bridges, Geoffrey P. Morris, and Stephen Kresovich. 2016. "A Genomic Resource for the Development, Improvement, and Exploitation of Sorghum for Bioenergy." Genetics 204 (1): 21–33. PMID: 27356613. https://doi.org/10.1534/genetics.115.183947.

Casa, Alexandra M., Gael Pressoir, Patrick J. Brown, Sharon E. Mitchell, William L. Rooney, Mitchell R. Tuinstra, Cleve D. Franks, and Stephen Kresovich. 2008. "Community Resources and Strategies for Association Mapping in Sorghum." Crop Science 48 (1): 30–40. https://doi.org/10.2135/cropsci2007.02.0080.

Davidson, Rebecca M., Malali Gowda, Gaurav Moghe, Haining Lin, Brieanne Vaillancourt, Shin-Han Shiu, Ning Jiang, and C. Robin Buell. 2012. "Comparative Transcriptomics of Three Poaceae Species Reveals Patterns of Gene Expression Evolution." The Plant Journal: For Cell and Molecular Biology 71 (3): 492–502. PMID: 22443345. https://doi.org/10.1111/j.1365-313X.2012.05005.x.

Emms, David M., Sarah Covshoff, Julian M. Hibberd, and Steven Kelly. 2016. "Independent and Parallel Evolution of New Genes by Gene Duplication in Two Origins of C4 Photosynthesis Provides New Insight into the Mechanism of Phloem Loading in C4 Species." Molecular Biology and Evolution 33 (7): 1796–1806. PMID: 27016024. https://doi.org/10.1093/molbev/msw057.

Gladman, N. et al. "Sorghum root epigenetic landscape during limiting phosphorus conditions." Manuscript in preparation.

Goodstein, David M., Shengqiang Shu, Russell Howson, Rochak Neupane, Richard D. Hayes, Joni Fazo, Therese Mitros, et al. 2012. "Phytozome: A Comparative Platform for Green Plant Genomics." Nucleic Acids Research 40 (Database issue): D1178–86. PMID: 22110026. https://doi.org/10.1093/nar/gkr944.

Jiao, Yinping, John J. Burke, Ratan Chopra, Gloria Burow, Junping Chen, Bo Wang, Chad Hayes, Yves Emendack, Doreen Ware, and Zhanguo Xin. 2016. "A Sorghum Mutant Resource as an Efficient Platform for Gene Discovery in Grasses." The Plant Cell. PMID: 27354556. https://doi.org/10.1105/tpc.16.00373.

McCormick, Ryan F., Sandra K. Truong, Avinash Sreedasyam, Jerry Jenkins, Shengqiang Shu, David Sims, Megan Kennedy, et al. 2018. "The Sorghum Bicolor Reference Genome: Improved Assembly, Gene Annotations, a Transcriptome Atlas, and Signatures of Genome Organization." The Plant Journal: For Cell and Molecular Biology 93 (2): 338–54. PMID: 29161754. https://doi.org/10.1111/tpj.13781.

Mace, Emma S., Shuaishuai Tai, Edward K. Gilding, Yanhong Li, Peter J. Prentis, Lianle Bian, Bradley C. Campbell, et al. 2013. "Whole-Genome Sequencing Reveals Untapped Genetic Potential in Africa’s Indigenous Cereal Crop Sorghum." Nature Communications 4: 2320. PMID: 23982223. http://doi.org/10.1038/ncomms3320.

Makita, Yuko, Setsuko Shimada, Mika Kawashima, Tomoko Kondou-Kuriyama, Tetsuro Toyoda, and Minami Matsui. 2015. "MOROKOSHI: Transcriptome Database in Sorghum Bicolor." Plant & Cell Physiology 56 (1): e6. PMID: 25505007. https://doi.org/10.1093/pcp/pcu187.

Morris, Geoffrey P., Punna Ramu, Santosh P. Deshpande, C. Thomas Hash, Trushar Shah, Hari D. Upadhyaya, Oscar Riera-Lizarazu, et al. 2013. "Population Genomic and Genome-Wide Association Studies of Agroclimatic Traits in Sorghum." Proceedings of the National Academy of Sciences of the United States of America 110 (2): 453–58. PMID: 23267105. https://doi.org/10.1073/pnas.1215985110.

Olson, Andrew, Robert R. Klein, Diana V. Dugas, Zhenyuan Lu, Michael Regulski, Patricia E. Klein, and Doreen Ware. 2014. "Expanding and Vetting Sorghum Bicolor Gene Annotations through Transcriptome and Methylome Sequencing." The Plant Genome 7 (2): plantgenome2013.08.0025. https://doi.org/10.3835/plantgenome2013.08.0025.

Paterson, A. H., J. E. Bowers, R. Bruggmann, I. Dubchak, J. Grimwood, H. Gundlach, G. Haberer, et al. 2009. "The Sorghum Bicolor Genome and the Diversification of Grasses." Nature 457 (7229): 551–56. PMID: 19189423. https://doi.org/10.1038/nature07723.

Turco, Gina M., Kaisa Kajala, Govindarajan Kunde-Ramamoorthy, Chew-Yee Ngan, Andrew Olson, Shweta Deshphande, Denis Tolkunov, et al. 2017. "DNA Methylation and Gene Expression Regulation Associated with Vascularization in Sorghum Bicolor." The New Phytologist 214 (3): 1213–29. PMID: 28186631. https://doi.org/10.1111/nph.14448.

Xin, Zhanguo, Ming Li Wang, Noelle A. Barkley, Gloria Burow, Cleve Franks, Gary Pederson, and John Burke. 2008. "Applying Genotyping (TILLING) and Phenotyping Analyses to Elucidate Gene Function in a Chemically Induced Sorghum Mutant Population." BMC Plant Biology. PMID: 18854043. https://doi.org/10.1186/1471-2229-8-103.

Wang, Bo, Michael Regulski, Elizabeth Tseng, Andrew Olson, Sara Goodwin, W. Richard McCombie, and Doreen Ware. 2018. "A Comparative Transcriptional Landscape of Maize and Sorghum Obtained by Single-Molecule Sequencing." Genome Research 28 (6): 921–32. PMID: 29712755 https://doi.org/10.1101/gr.227462.117.

Zheng, Lei-Ying, Xiao-Sen Guo, Bing He, Lian-Jun Sun, Yao Peng, Shan-Shan Dong, Teng-Fei Liu, et al. 2011. "Genome-Wide Patterns of Genetic Variation in Sweet and Grain Sorghum (Sorghum Bicolor)." Genome Biology 12 (11): R114. PMID: 22104744. http://dx.doi.org/10.1186/gb-2011-12-11-r114.