Abstract:

This is the assembled and annotated genome sequence from the spleen of a male marsh rice rat (Oryzomys palustris) collected from Bay Jimmy in Barataria Bay, Louisiana on June 21st, 2015. This genome was sequenced with the intent that it would serve as a reference genome for future target enrichment, RNA-seq, and gene methylation studies. Extracted DNA was sequenced using the Chromium 10x platform and linked-reads sequencing technology on a Novaseq. The sequenced genome was then assembled de novo using Supernova. The genome was annotated using MAKER v. 2.31.10 and the Comparative Annotation Toolkit v. Github commit 2de995c865afb44357e0056667ffd009ace3592b. Ab initio gene predictions were made using the Mus musculus (GCF_000001635.26) and Rattus norvegicus (GCF_000001895.5 ) genomes available on NCBI. There are two folders labeled “ORPA_Genome_Version1_Published_2022-02-08” and “ORPA_Genome_Version2_Published_2023-10-23”. Version 2 contains an additional file (OryPal1.fa.gz) that has the sequenced genome of a male marsh rice rat (Oryzomys palustris) and is the most up-to-date data package.

Suggested Citation:

Perez-Umphrey, Anna. 2022. The assembled and annotated genome of a male marsh rice rat (Oryzomys palustris) collected from Barataria Bay, Louisiana in 2015. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/n7-zt7g-sq80

Publications:

Pérez-Umphrey, A. A., Settlecowski, A. E., Elbers, J. P., Williams, S. T., Jonsson, C. B., Bonisoli-Alquati, A., Snider, A. M., & Taylor, S. S. (2023). Genetic variants associated with hantavirus infection in a reservoir host are related to regulation of inflammation and immune surveillance. Infection, Genetics and Evolution, 116, 105525. https://doi.org/10.1016/j.meegid.2023.105525

Purpose:

The marsh rice rat (Oryzomys palustris) genome was sequenced and annotated to serve as a reference for future target enrichment, RNA-seq, and gene methylation studies. The genome was sequenced using new linked-read sequencing technology from 10x Genomics, and assembled using Supernova.

Data Parameters and Units:

The genome was sequenced at 40x coverage with 150bp paired end reads.

Methods:

A male marsh rice rat was trapped using a baited Sherman live trap and then dissected for tissue harvest. The marsh rice rat was euthanized by asphyxiation with isoflurane followed by decapitation and its spleen tissue was removed, placed in a cryovial, and flash frozen in liquid nitrogen. Extracted DNA from the collected spleen tissue was sequenced using the Chromium 10x platform and linked-reads sequencing technology on a Novaseq. The sequenced genome was then assembled de novo using Supernova. This sample was collected on June 21st, 2015 from Bay Jimmy in Barataria Bay, Plaquemines Parish, LA.

Instruments:

Sherman live traps: Used to trap marsh rice rats Liquid nitrogen tank: Used to flash freeze collected blood and tissue samples Cryovials: Tubes to store tissue and blood samples in liquid nitrogen Dissection scissors: Laboratory scissors used to decapitate and remove tissues from the body cavity of marsh rice rats Dissection tweezers: Laboratory tweezers used to remove tissues from the body cavity of marsh rice rats Novaseq: Next-generation sequencing system

Individual Files: