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This is a final project for the Comparative Genomics seminar in the spring of 2019. The aim of this project is to begin the annotation process of a genome for the marine fish, Bluefin Trevally, in order to ultimately be able to map ddRAD loci onto the genome to identify loci under selection and determine their position in the genome relative to annotated gene regions. This will hopefully give us a functional genomic perspective on genetic differences between populations of this fish species in the Indo-Pacific.
The specific problem I seek to explore was annotating a genome of the Bluefin Trevally (Caranx melampygus).
The data are unpublished and are the result of a collaboration between myself and Dr. John Kauwe and his PhD candidate, Brandon Hassett, at Brigham Young University. The method used to sequence the genome was PacBio, using a Sequel machine. It generated 52.7 gigabases of sequence data across 10 SMRT cells. The raw PacBio reads assembled using the "self-correction" procedure in Canu. The estimated genome size was 782.4 Mb and the assembly size is 711 Mb. The N50 value is 1.4 Mb, and the NG50 value is 1.18 Mb. I have received the output of the Canu assembly in the form of a fastq file.
I do not have any transcriptome or proteome data for C. melampygus (yet) so I will be trying this assembly 'ab initio' just to get a hang of the program.
The motivation behind this project is to use the bluefin genome as a reference upon which to map ddRAD data. I have ddRAD data for Bluefins across their Indo-Pacific range, and have been using de novo assembly methods to examine population structure. I am particularly interested in identifying loci that are under selection and examining their function. In the future, I am also interested in examining hybridization between bluefin trevallies and a close relative, the Giant Trevally. We are also sequencing a Giant Trevally genome. I would like to learn the basic skills and understanding of genome annotation so that I can apply the same methods to the Giant Trevally.
Challenges as of 2/20/2019: I would like to explore heterozygosity in this dataset but am unsure how to start doing that.
Challenges as of 4/4/2019 It seems like transcriptome data are not available, so I will need to assemble the genome ab initio.
Updates: 4/09/2019: Began mapping ddRAD data to genome in demultiplex stage using ipyrad
4/10/2019: Having issues installing MAKER and all of its dependencies onto my Farnam account. Emailed Ben Evans for help.
Was it successful in achieving the initial goal?
What are the main obstacles encountered?
#1. Installing the software and all its dependencies
What would you have done differently?
What are future directions this could go in?
Maker Tutorials: MAKER GMOD: http://gmod.org/wiki/MAKER_Tutorial Deren Card: https://gist.github.com/darencard/bb1001ac1532dd4225b030cf0cd61ce2 Ian Gilman: https://github.com/isgilman/finalproject/wiki/Step-by-step-genome-annotation-for-Portulaca-amilis