Please cite our pre-print if this resource benefits your work: https://www.biorxiv.org/content/10.1101/2020.07.13.189936v1

Spreadsheet of known Ralstonia diversity, host range, and locations

Curated by Undergraduate Researchers in the Lowe-Power lab at UC Davis.

Kyle Chipman, Spring 2020

Jason Avalos, Fall 2020 - Spring 2021

Maria Charco Munoz, Fall 2020 - Spring 2021

Darrielle Williams, Summer 2021

Cloe Tom, Winter-Summer 2022

Yali Bai, Summer-Fall 2022

Scientific knowledge about Ralstonia diversity, host range, and geographic location is fragmented as individual papers in the publication record. Our goal is to consolidate the knowledge as a database that is frequently updated by undergraduate students at UC Davis.

Fig 1. Taxonomy of Ralstonia at the Species, Phylotype, and Sequevar level. The sequevars highlighted in red and purple text have conflicting reports in the literature. The conflicts are due to overlapping timing of paper publishing. Taxonomic classification of the Ralstonia species complex at the species, phylotype and sequevar levels. Sequevars highlighted in red or purple italics are assigned to strains in conflicting phylotypes. As a note, many of the phylotype I sequevars are polyphyletic (See Sharma et al 2022 for details), so the Ralstonia community needs to identify a cost-effective alternative for describing diversity of these strains. The clonal lineage that cause Blood Disease of Banana (BDB) are nested within phyl. IV-10 with non BDB phyl. IV strains.

The current classification scheme for Ralstonia is based on relative similarity of DNA sequences in the strains' genomes. Ralstonia is considered a species complex, i.e. a group of species that are closely inter-related. There are three formal species in the Ralstonia species complex: R. solanacearum, R. pseudosolanacearum, and R. syzygii. These three major divisions were recognized by Philippe Prior and Mark Fegan who built on earlier DNA-based phylogenetic groupings proposed by Doug Cook and Luis Sequiera. The three species were named in a 2015 publication by Safni et al.

The species are subdivided into phylotypes, and phylotypes are subdivided into sequevars. The major divisions are Ralstonia solanacearum (phylotype II, which has IIA, IIB, and IIC branches), Ralstonia pseudosolanacearum (phylotype I and III), and Ralstonia syzygii (phylotype IV). Sequevar is determined by the DNA sequence of the egl gene, which encodes an endoglucanase that is essential for Ralstonia's ability to degrade plant cell walls. Sequevars are numbered based on the timeline in which they were discovered. As of 2022, there are at least 71 sequevars.

• Ralstonia was historically named “Pseudomonas solanacearum” and, briefly, “Burkholderia solanacearum”.
• Before phylotype/sequevar, earlier methods attempted to classify Ralstonia strains by host range (“Race”) and sugar utilization patterns (“Biovars”). However, the host-range and sugar utilization patterns do not correspond to DNA-based phylogeny.

This is a work in progress! Papers often say that the Ralstonia host range includes over 250 plant species in over 50 botanical families. We will see what we find!

As of 2022, we have identified at least 394 host species reported in the literature.

Email Dr. Tiffany Lowe-Power and ask whether she will advise you for your thesis practicum. Advice for writing professional emails is in this article.. Include information that is helpful to Dr. Lowe-Power:

• When is your estimated graduation date
• Why did you choose to be a GDB major?
• What are your career goal(s)?
• Why are you interested in the Global Ralstonia Diversity database?
• Mention that you read this GitHub page.

• Link to the chapter

• Save the spreadsheet (above) on your computer. To avoid losing your work in case your laptop dies or is stolen, I strongly recommend that you keep the file in folder that is automatically backed up to Box.com or Google Drive.

• Explore the spreadsheet on your own. Try to figure out how it is organized. Then set up a meeting with Dr. Lowe-Power or a member of her lab for them to walk you through the spreadsheet.

• For your practicum, I ask that you add information from at least 25 papers into the spreadsheet. Then we will discuss meta-analyses that you can do to for your report.

• You are building on the previous work by Dr. Lowe-Power and other GDB students. Teamwork, yeah!

• Most sequevar papers cite the original Fegan and Prior chapter. You can use Google Scholar to find papers that cite Fegan & Prior:

• Google Scholar link to papers that (1) cite Fegan and Prior and (2) include the word sequevar. As of May 2020, 243 papers match the search criteria.

• Each GDB student will systematically add strains from 20-30 papers to the spreadsheet.

  • As of March 2021, all Ralstonia diversity papers published between 2013-2019 are recorded in the database. Some of 2012 and 2020 are included. Papers from 2005-2012 and 2021 need to be added.

General tips

• Before proceeding, read 3+ papers that are already in the spreadsheet and how previous students found everything. It is important to look through not only the main body of the paper, but also the supplementary tables. These supplemental tables usually contain all the details.
• Next, find 1-2 papers and add their information to the table. Send it to Tiffany or your mentor. She will look over the spreadsheet for mistakes. It is best to catch these early! Don't feel bad about the mistakes. We expect you to make some at the beginning. Then we expect you to learn to correct them yourself.
• If you use the drag-to-copy feature of Excel, be very careful to correct Excel's mistakes. Although Excel will perfectly copy words like "tomato" to 20 rows, it likes to add "1" to any cell that ends in a number. So years might count up. The URLs to the papers might count up. Make sure you correct these mistakes!
• Send weekly progress updates to Tiffany. Tiffany will provide feedback, look for signs of data entry mistakes, and suggest Excel and organization tricks to make work easier.

• After you have completed the data collection portion of the project, you will analyze the results by summarizing the data. Aggregating the raw data as tables or figures can allow us to see patterns in the data.

Here are a few ways we have looked at the data. You can choose to apply the same analyses we performed previously, but we also welcome creative ideas about the data.

• Kyle Chipman's visualizations in Spring 2020

This is a work in progress. This project could be taken to the next level by a GDB researcher who wants to learn to code in R / ggmap and help us develop a reproductible workflow for mapping the raw data to country distributions.

At a much less-efficient approach, students could color-in a world map in a graphic design software or use a web interface like https://www.amcharts.com/visited_countries/

For example, here is the (likely incomplete) distribution of phylotype I sequevar 18 strains. These strains include GMI1000, which is one of the best-studied Ralstonia strains.

Fig 2. Distribution of phylotype I sequevar 18 Ralstonia. This figure was last rendered in 2019.

Collectively, Ralstonia strains infect hundreds of plants in dozens of botanical families. However, individual lineages have more narrow host ranges.

Fig 3. Known host ranges for two sequevars of Ralstonia. This figure was last rendered in 2019.

Depending on your contributions, Tiffany will let you know whether you will be a co-author or acknowledged in the final manuscript.

Criteria:

• Co-authorship: Student researchers who make a significant contribution to the database (Strains from > 20 papers with data accurately recorded) will be included as co-authors on a peer-reviewed manuscript. Tiffany will be the first author and corresponding author. Co-authors will be listed alphabetically by last name.
• Acknowledged: Students who contribute less reliable data and/or data from fewer papers will still be acknowledged in the final manuscript, but will not be included as authors.

Regardless of whether you contribute to the Acknowledged or Co-author level, you will develop skills in reading/analyzing the literature, in reproducible data-entry practices, and data-analysis. It makes sense to include this on your Resume or C.V.

I recommend the following information:

Authors and Acknowledged: In a "Research Experience" Heading on your C.V.

• Include the start/end date, "Advisor: Dr. Tiffany Lowe-Power (Dept Plant Pathology, UC Davis)

Co-Authors only In a "Non-refereed Publications" Heading on your C.V.

• Once Tiffany adds you as a co-author on the pre-print, you can include it on your C.V. (The goal will be to do this within 3 months from when you complete your work). Use a standard format for Scientific References to cite the BioRxiv "preprint". Pre-prints are not yet peer-reviewed. When Tiffany submits the manuscript to a peer-reviewed journal, she will email you (make sure to keep her updated on your email address). She will also email you when the final version is published in a peer-review journal. At that point, remove the pre-print from your C.V. and replace it with the final paper information in a section titled "Publications".