Using online tools at the Bovine Genome Database to manually annotate genes in the new reference genome

Triant, D. A.; Le Tourneau, J. J.; Diesh, C. M.; Unni, D. R.; Shamimuzzaman, M.; Walsh, A. T.; Gardiner, J.; Goldkamp, A. K.; Li, Y.; Nguyen, H. N.; Roberts, C.; Zhao, Z.; Alexander, L. J.; Decker, J. E.; Schnabel, R. D.; Schroeder, S. G.; Sonstegard, T. S.; Taylor, J. F.; Rivera, R. M.; Hagen, D. E.; Elsik, C. G.

doi:10.1111/age.12962

Home/Archive/DOE OSTI

DOE OSTI · 1816108

Using online tools at the Bovine Genome Database to manually annotate genes in the new reference genome

View original source ↗Read source document ↗Export metadata ↓

Abstract

With the availability of a new highly contiguous Bos taurus reference genome assembly (ARS-UCD1.2), it is the opportune time to upgrade the bovine gene set by seeking input from researchers. Furthermore, advances in graphical genome annotation tools now make it possible for researchers to leverage sequence data generated with the latest technologies to collaboratively curate genes. For many years the Bovine Genome Database (BGD) has provided tools such as the APOLLO genome annotation editor to support manual bovine gene curation. The goal of this paper is to explain the reasoning behind the decisions made in the manual gene curation process while providing examples using the existing BGD tools. We will describe the sources of gene annotation evidence provided at the BGD, including RNAseq and Iso-Seq data. We will also explain how to interpret various data visualizations when curating gene models, and will demonstrate the value of manual gene annotation. The process described here can be applied to manual gene curation for other species with similar tools. With a better understanding of manual gene annotation, researchers will be encouraged to edit gene models and contribute to the enhancement of livestock gene sets.

Explore related subjects

59 BASIC BIOLOGICAL SCIENCES Bos taurus RNA-seq gene prediction genome annotation genome annotation tools

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

Triant, D. A., Le Tourneau, J. J., Diesh, C. M., Unni, D. R., Shamimuzzaman, M., Walsh, A. T., Gardiner, J., Goldkamp, A. K., Li, Y., Nguyen, H. N., Roberts, C., Zhao, Z., Alexander, L. J., Decker, J. E., Schnabel, R. D., Schroeder, S. G., Sonstegard, T. S., Taylor, J. F., Rivera, R. M., Hagen, D. E., Elsik, C. G.. 2020-06-14. Using online tools at the Bovine Genome Database to manually annotate genes in the new reference genome. https://doi.org/10.1111/age.12962

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related reports

DOE OSTI2026

Lines of Evidence Network Analysis of Yield-Associated Genes in Pennycress (Thlaspi arvense)

Functional network analysis of 112 GWAS-identified candidate genes for yield-related traits in pennycress ( Thlaspi arvense ). Uses RWRtools Lines of Evidence to propagate Arabidopsis orthologs through a nine-layer multiplex functional network.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Soil metagenomics umbrella narrative

Implementing accessible, authentic research experiences in introductory courses is challenging, particularly at institutions serving diverse student populations. To address this gap, we developed and deployed a Course-based Undergraduate Research Experience (CURE) focused on plant-microbe interactions in General Biology II at Northeastern Illinois University (NEIU), a minority-serving institution with a diverse student body. Students grew sugar beets (Beta vulgaris), extracted DNA from the rhizoplane, and used the Department of Energy Systems Biology Knowledgebase (KBase) for bioinformatic analysis to compare microbial relative abundance in fertilized versus unfertilized soil. Over five semesters, the CURE engaged 103 students and leveraged the intuitive KBase platform to make complex sequencing data accessible. Pre/post-course survey data revealed significant increases in student self-assessed research skills, including the ability to explain results and determine the types of data to collect. Furthermore, students reported significant gains in confidence related to experimental design and hypothesis development, alongside a strong increase in familiarity with KBase. Informal faculty feedback indicated high student engagement and appreciation for the real-world connections (e.g. food systems, agriculture, and health). This scalable, low-cost model effectively integrates data science tools into the foundational curriculum, demonstrating a potent strategy for boosting research skills and broadening participation in authentic scientific inquiry among diverse undergraduate students.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Genome-resolved insights into microbial diversity and elemental cycling in Winogradsky columns

We retained 18 MAGs with ≥50% completion and <10% contamination (i.e., at least medium quality). Of these, 10 had >90% completion and <5% contamination; however, only one (Paceibacteria Bin.003_MG) can be described as high-quality, as the others lacked a full suite of 5S, 16S, and 23S rRNA genes. To maximize the diversity of our recovered MAGs, we also retained one MAG (Chromatiaceae Bin.008_AM) with >40% (but less than 50%) completion and <5% contamination, as well as one (Rhodopseudomonas Bin.015_MK) with >90% completion and <20% (but>10%) contamination. Interestingly, significant chimerism was not detected in this MAG (40) , suggesting that the elevated contamination (20%) may instead reflect two closely related strains collapsing into a single bin. Consistent with this, contig coverage was bimodal, with roughly 17% of the assembly at ~115x and the remaining 83% at ~282x, while GC content remained uniform across both groups (~64%), arguing against contamination from a taxonomically distinct source.

59 BASIC BIOLOGICAL SCIENCES↗