A repo for all scripts and associated files for the 2021 Virtual Nonmodel Genomics Workshop

The contributors to this workshop are: Jacob Landis ([email protected]) Fay-Wei Li ([email protected]) Adrian Powell ([email protected]) Bikash Shrestha ([email protected]) Suzy Strickler ([email protected]) Jing Zhang ([email protected])

The focus of the workshop is long-read genome sequencing, assembly, annotation, and downstream analyses. The taxonomic focus is Utricularia gibba, with a 78 MB genome and recent high quality published genome in the paper "Long-read sequencing uncovers the adaptive topography of a carnivorous plant genome" by Lan et al. 2017 in PNAS.

All the provided data was downloaded from SRA, including Illumina genome sequencing (SRR10676752), PacBio long-read data (from authors of Lan et al. 2017), and RNA-Seq (SRR10676739,SRR10676740, SRR10676741,SRR10676742,SRR10676743,SRR10676744,SRR10676745,SRR10676746,SRR10676747,SRR10676748, SRR10676749,SRR10676750,SRR5046448,SRR10676751).

The packaged data for the workshop can all be downloaded from the Discovery Environment of CyVerse using icommands and the following path: /iplant/home/shared/NMGWorkshop2021

The programs that are needed for workshop have all been downloaded to a virtual machine with the NMGWorkshop2021 image. A large3 instance (8 CPU, 64 GB RAM, and 480 GB storage), which is enough resources to run all the steps. Some of the programs that are used in this workshop are: BUSCO, fastp, Flye, fmlrc, hisat2, Maker, MaSuRCA, Nanoplot, Orthofinder, Stacks, Stringtie, Transdecoder, and VCFtools.

The structure of the workshop is as follows: Basic Linux commands, generating sequence data, genome assembly, genome annotation, and downstream analyses with CoGe and SNP calling. For both the genome assembly and annotation portion, small test data sets are provided to easily run all the steps. The full data sets are also provided for comparisons, but many of the analyses may take between 6-18 hours to run. For each section there is a presentation (found in slides), and walkthroughs (except for the sequencing section). For the assembly module, steps can be found in assembly/Genome_assembly_workshop_steps.pdf. Annotation scripts are numbered 1 to 6 to be done in order. The CoGe steps are in CoGe_overview.pdf. SNP calling steps are found in SNP_calling.pdf.

Additional data that is supplied in the shared NMGWorkshop2021 directory:

assemblies /Acarambola/ Genome fasta, proteins fasta, and gene model gff of Averrhoa carambola Data sources (Wu et al, 2020): https://www.nature.com/articles/s41438-020-0307-3 https://bigd.big.ac.cn/search/?dbId=gwh&q=GWHABKE00000000 /Acoerulea/ Genome fasta, protein fasta, and gene model gff of Aquilegia coerulea Data sources (Filiault et al, 2018): https://elifesciences.org/articles/36426 https://www.ncbi.nlm.nih.gov/genome/?term=aquilegia /Avesiculosa/ Genome fasta, protein fasta, and gene model gff of Aldrovanda vesiculosa Data sources (Palfalvi et al 2020): https://www.sciencedirect.com/science/article/pii/S0960982220305674 https://www.biozentrum.uni-wuerzburg.de/carnivorom/resources /Bvulgaris/ Genome fasta, protein fasta, and gene model gff of Beta vulgaris Data sources (Del Rio et al, 2019): https://pubmed.ncbi.nlm.nih.gov/31104348/ https://www.ncbi.nlm.nih.gov/genome/221 /Cfollicularis/ Genome fasta, protein fasta, and gene model gff of Cephalotus follicularis Data sources (Fukushima et al, 2017): https://www.nature.com/articles/s41559-016-0059 https://www.ncbi.nlm.nih.gov/genome/?term=Cephalotus /Dmuscipula/ Genome fasta, protein fasta, and gene model gff of Dionaea muscipula Data sources (Palfalvi et al 2020): https://www.sciencedirect.com/science/article/pii/S0960982220305674 https://www.biozentrum.uni-wuerzburg.de/carnivorom/resources /Dspatulata/ Genome fasta, protein fasta, and gene model gff of Drosera spatulata Data sources (Palfalvi et al 2020): https://www.sciencedirect.com/science/article/pii/S0960982220305674 https://www.biozentrum.uni-wuerzburg.de/carnivorom/resources /Gaurea/ Genome fasta, protein fasta, and gene model gff of Genlisea aurea Data sources (Leushkin et al., 2013): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3728226/ https://www.ncbi.nlm.nih.gov/genome/24580 /Sindicum/ Genome fasta, protein fasta, and gene model gff of Sesamum indicum Data sources (Wang et al., 2014): https://pubmed.ncbi.nlm.nih.gov/24576357/ https://www.ncbi.nlm.nih.gov/genome/11560 /Ugibba/ Genome fasta, protein fasta, and gene model gff of Utricularia gibba Data sources (Lan et al., 2017): https://www.pnas.org/content/114/22/E4435.short /Ureniformis/ Genome fasta, protein fasta, and gene model gff of Utricularia reniformis Data sources: https://www.ncbi.nlm.nih.gov/genome/44110

embryophyta_odb9 Lineage file for BUSCO

raw_data /Ugibba/genome/ Illumina (SRR10676752; ) and PacBio (Ugibba_PacBio_to_use; Lan et al., 2017) reads of Utricularia gibba /Ugibba/transcriptome/ Transcriptome (PRJNA595351) /Ureniformis/genome/ Illumina MiSeq reads of Utricularia reniformis Data sources: https://www.ncbi.nlm.nih.gov/sra/?term=SRR5349713 /Utricularia_spp/transcriptomes RNA-seq from five species of Utricularia Data source: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA354080