Week of December 2-6; arranged by students
December 12, 2019: 1:30pm - 4:30pm, Loftsgard 260
In 2018 and 2019, there were eleven genome sequences published in Nature Genetics. Links to those papers and there supplements are provided below. It is time to do an update on published plant genomes with reference to these papers. We are only focusing on Nature Genetics publications because they are usually the most stringent with regards to what they believe are the relevance/quality of the research reported in the paper.
For this semester's CTIG session, you have two responsibility. First, all four of you are to meet the week of December 2-6. You need to meet as a group to complete this task. I will be out of town that week. If you have any questions, please contact me prior to December 1.
Next, during that session, you are collectively to complete the MS Excel file attached below. This file is similar to the one that I provided (or will provide) to you in PLSC 731 - Plant Molecular Genetics. This file will be a compilation of the relevant statistics for all of the papers. (I have included data compilied from four plant genome papers as a reference for the data expected in the table.) The majority of the statistics can be found in the paper, but in some cases it may be necessary to read the supplementary information to complete the table.
Sidebar: I am sure that you know by now the correct defintion of N50 and L50. You should be aware that the these papers generally use the terms incorrectly. You must provide the correct information in the table.
We will next meet on December 12, 2019 at 1:30 pm. We will first go over the table that you generated for the eleven species. During that session, as groups of two, you will lead the group in a discussion of six papers in detail. This will be a joint discussion lead by two students, and each group is responsible for three papers. Below you will see which two students are responsible for which three papers. In each group presentation you are to: 1) present the general details regarding the genome sequencing, assembly, and annotation; 2) describe in detail the biological question the paper is addressing with sufficient background information for all in the class to understand; 3) discuss the papers with regards to a polyploid event specific to each species; and 4) compare and contrast polyploidy between the three species you are discussing. This last discussion topic should be based on relevant genomic data presented in the papers.
The group not responsible for a specific paper, must develop two questions for each of the papers that the other group is discussing.
Remember, this is a group assignment. It is important to clearly communicate the expectations of your partner to ensure you prepare a quality presenation.
Relevant links:
CTIG Fall 2019 – Reference Genome Papers
2019 – Nature Genetics
Bertiolli et al. – Allotetraploid peanut (Reviewer: Amanda, Peter)
Paper
Supplement
Topic: Polyploid vs. diploid domestication
Chen et al – Pineapple (Reviewer: Jithin, Katherine)
Paper
Supplement
Topic: Domestication, selective sweeps
Edger et al – Octoploid strawberry (Reviewer: Jithin, Katherine)
Paper
Supplement
Topic: Dynamics among the four subgenomes
Hu et al – Tetraploid cotton comparison (Reviewer: Amanda, Peter)
Paper
Supplement
Topic: High fiber yield vs high fiber cotton genome comparisons
Kreplak et al – Pea
Paper
Supplement
Topic: Genome size expansion
Maccaferri et al – Durum wheat (Reviewer: Amanda, Peter)
Paper
Supplement
Topic: Diversity reduction and selection
Yang et al – Tropical maize
Paper
Supplement
Topic: Yield gene cloning
2018 – Nature Genetics
Raymond et al – Rose
Paper
Supplement
Topic: Biochemistry of color and fragrance
Springer et al – Maize W22
Paper
Supplement
Topic: Transposon history
Sun et al – Maize B73
Paper
Supplement
Topic: Variation between B73 and Mo17
Zhang et al – Sugar cane (Reviewer: Jithin, Katherine)
Paper
Supplement
Topic: Evolution of a polyploid genome