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

Triant, Deborah A.; Tourneau, J. J. Le; Diesh, Colin; Unni, Deepak; Shamimuzzaman, Md.; Walsh, Amy T.; Gardiner, Jack M.; Goldkamp, Anna K; Li, Yahan; Nguyen, Hung N.; Roberts, Courtney; Zhao, Zhichao; Alexander, L. J.; Decker, Jared E.; Schnabel, Robert D.; Schroeder, Steven G.; Sonstegard, Tad S.; Taylor, Jeremy F.; Rivera, Rocío Melissa; Hagen, Darren E.; Elsik, Christine G.

doi:10.1111/age.12962

Cited by 3 publications

(7 citation statements)

References 25 publications

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“…Previous studies presented a comprehensive transcriptome survey based on ninety-five samples from three growth stages and one cell line [ 18 ] and identified a subset of functional enrichment of enhancer regions [ 19 ]. These effects promoted the establishment of a Bovine Genome Database (BGD) [ 20 ] and facilitated the deposition, curation, annotation, and integrated analysis of genomic data for global research communities [ 21 , 22 ].…”

Section: Introductionmentioning

confidence: 99%

Transcriptional atlas analysis from multiple tissues reveals the expression specificity patterns in beef cattle

et al. 2022

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Background A comprehensive analysis of gene expression profiling across tissues can provide necessary information for an in-depth understanding of their biological functions. We performed a large-scale gene expression analysis and generated a high-resolution atlas of the transcriptome in beef cattle. Results Our transcriptome atlas was generated from 135 bovine tissues in adult beef cattle, covering 51 tissue types of major organ systems (e.g., muscular system, digestive system, immune system, reproductive system). Approximately 94.76% of sequencing reads were successfully mapped to the reference genome assembly ARS-UCD1.2. We detected a total of 60,488 transcripts, and 32% of them were not reported before. We identified 2654 housekeeping genes (HKGs) and 477 tissue-specific genes (TSGs) across tissues. Using weighted gene co-expression network analysis, we obtained 24 modules with 237 hub genes (HUBGs). Functional enrichment analysis showed that HKGs mainly maintain the basic biological activities of cells, while TSGs were involved in tissue differentiation and specific physiological processes. HKGs in bovine tissues were more conserved in terms of expression pattern as compared to TSGs and HUBGs among multiple species. Finally, we obtained a subset of tissue-specific differentially expressed genes (DEGs) between beef and dairy cattle and several functional pathways, which may be involved in production and health traits. Conclusions We generated a large-scale gene expression atlas across the major tissues in beef cattle, providing valuable information for enhancing genome assembly and annotation. HKGs, TSGs, and HUBGs further contribute to better understanding the biology and evolution of multiple tissues in cattle. DEGs between beef and dairy cattle also fill in the knowledge gaps about differential transcriptome regulation of bovine tissues underlying economically important traits.

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Section: Introductionmentioning

confidence: 99%

Transcriptional atlas analysis from multiple tissues reveals the expression specificity patterns in beef cattle

et al. 2022

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“…We have previously described the general process of annotating a protein-coding gene, emphasizing the use of long-read transcriptome evidence to resolve split/merge discordances between Ensembl and RefSeq genes (Triant et al 2020 ). Here, we focus on short read RNAseq, because long-read transcript data are not available for all species.…”

Section: Gene Annotation Processmentioning

confidence: 99%

“…As previously described (Triant et al 2020 ), once a protein-coding gene annotation is complete, each new or modified isoform should be compared to a well-curated protein sequence database to check for congruency with known proteins. The sequence of an annotation is obtained by right clicking it and selecting Get Sequence .…”

Section: Gene Annotation Processmentioning

confidence: 99%

“…We have previously described genome annotation tools available at the Bovine Genome Database (BGD) that allow users to verify and manually refine genes of interest (Triant et al 2020 ). We have expanded upon those tools and have created a new resource called AgAnimalGenomes that includes additional animal species of interest to the FAANG Consortium.…”

Section: Introductionmentioning

confidence: 99%

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AgAnimalGenomes: browsers for viewing and manually annotating farm animal genomes

Triant,

Walsh,

Hartley

et al. 2023

Mamm Genome

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Current genome sequencing technologies have made it possible to generate highly contiguous genome assemblies for non-model animal species. Despite advances in genome assembly methods, there is still room for improvement in the delineation of specific gene features in the genomes. Here we present genome visualization and annotation tools to support seven livestock species (bovine, chicken, goat, horse, pig, sheep, and water buffalo), available in a new resource called AgAnimalGenomes. In addition to supporting the manual refinement of gene models, these browsers provide visualization tracks for hundreds of RNAseq experiments, as well as data generated by the Functional Annotation of Animal Genomes (FAANG) Consortium. For species with predicted gene sets from both Ensembl and RefSeq, the browsers provide special tracks showing the thousands of protein-coding genes that disagree across the two gene sources, serving as a valuable resource to alert researchers to gene model issues that may affect data interpretation. We describe the data and search methods available in the new genome browsers and how to use the provided tools to edit and create new gene models.

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“…The authors' current research hopes to aims if similar genetic and epigenetic misregulation is the culprit of S-LOS, a previously uncharacterized syndrome in cattle, and to shed light on the contribution of S-LOS to the 25% to 46% rate of perinatal death in cattle resulting from unknown causes and dystocia. This peer-reviewed article demonstrated online tools for bovine genome annotation developed by Dr. Elsik's laboratory (Triant et al, 2020). These tools allow users to modify the annotation of bovine genes based on their own sequencing data and also serve as a database.…”

Section: Discussionmentioning

confidence: 99%

Involvement of aberrant chromosome architecture and locus-specific vulnerability to DNA methylation epimutations in bovine large offspring syndrome

Li¹

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Large/abnormal offspring syndrome (LOS/AOS) and Beckwith-Wiedemann syndrome (BWS) are similar congenital overgrowth syndromes which occur naturally in ruminants and humans, respectively. The incidence of these syndromes increases when offspring are conceived with the use of assisted reproductive technologies (ART; i.e. in vitro oocyte maturation, in vitro fertilization, and embryo culture). Molecular defects reported in both syndromes include global gene misregulation, DNA methylome epimutations, and disruption of genomic imprinting (parental-allele-specific gene expression). Although we have reported that bovine LOS occurs spontaneously (SLOS) based on phenotypic similarities to ART-LOS, to date no study has been conducted to determine if SLOS has the same methylome epimutations as ART-LOS. One goal of my dissertation research is to characterize DNA methylation profiles in bovine SLOS and ART-LOS to determine whether there are conserved genomic loci with DNA methylation defects between these overgrowth conditions. In addition, while it is known that LOS is characterized by global alterations in DNA methylation, it is largely unknown how altered DNA methylation drives the development of LOS, as the methylation errors (i.e., differentially methylated regions; DMRs) observed in the syndrome only explain [less than] 4 percent of the gene misregulation in short range (the flanking 20,000 DNA bases from the DMR). Therefore, another goal of my dissertation research is to determine whether long-range regulatory mechanisms of gene expression, such as chromosome architecture, is altered in LOS as a result of aberrant DNA methylation. In this dissertation, Chapter 1 is the literature review and will introduce epigenetic regulation of gene expression including chromosome architecture and clinical features and molecular findings of LOS and BWS. Chapter 2 and 3 are the research chapters. In Chapter 2, I characterize allele-specific chromosome architecture of IGF2R imprinted domain in fibroblast cells derived from control bovine fetuses and identified disrupted chromosome architecture in LOS. I also observed genomic location-based clustering tendency of misregulated genes in LOS. This study has been published in the Journal iScience (https://doi.org/10.1016/j.isci.2022.104269) (Li et al., 2022). In Chapter 3, I determined that bovine SLOS has DNA methylation defects with some similarities and differences when compared to ART-LOS. I also identified vulnerable genomic loci for DNA methylation defects in LOS, which could serve as molecular markers for the diagnosis of the syndrome during early pregnancy. This study has been published in the journal Epigenetics (https://doi.org/10.1080/15592294.2022.2067938). Chapter 4 is the general discussion in which my research findings are incorporated into the general knowledge of the field and implications and directions of future studies are discussed. In Appendix 1, I briefly introduce our ongoing Hi-C (global chromosome architecture), methylome and transcriptome project in which samples from LOS and BWS will be analyzed together to further shed light into the etiology of these syndromes, knowledge that will equally help Agriculture and Biomedicine. I anticipate submitting this manuscript for peer review and publication in July of 2022, thus becoming the third primary literature manuscript from my dissertation research. Appendix 2 is a review paper in which I am main contributor author published in Veterinary Clinics of North America: Food Animal Practice in 2019 (PMID: 31103180, https://doi.org/10.1016/j.cvfa.2019.02.007). This review summarized clinical and molecular findings in LOS and for the first time reported the existence of SLOS. Lastly, Appendix 3 summarizes my contributions of five other publications in which I collaborated with groups in the Division, at Mizzou, and other Academic institutions in the USA during my tenure as a PhD student.

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

Cited by 3 publications

References 25 publications

Transcriptional atlas analysis from multiple tissues reveals the expression specificity patterns in beef cattle

Transcriptional atlas analysis from multiple tissues reveals the expression specificity patterns in beef cattle

AgAnimalGenomes: browsers for viewing and manually annotating farm animal genomes

Involvement of aberrant chromosome architecture and locus-specific vulnerability to DNA methylation epimutations in bovine large offspring syndrome

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