Detection of non-reference porcine endogenous retrovirus loci in the Vietnamese native pig genome

Ishihara, Shinya; Kumagai, Masahiko; Arakawa, Aisaku; Taniguchi, Masaaki; Cuc, Ngo Thi Kim; Pham, Lan Doan; Mikawa, Satoshi; Kikuchi, Kazuhiro

doi:10.1038/s41598-022-14654-4

Cited by 3 publications

(4 citation statements)

References 45 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In addition, 0.10–1.86% of the reads were singletons that were mapped to only one side. The analytical process was conducted in accordance with the methodology of previous studies [15, 16]. Initially, the author employed RetroSeq software [17] for the analysis and identified singleton and improper pairs among the read pairs supporting ERV during the RetroSeq “discover” step.…”

Section: Resultsmentioning

confidence: 99%

See 1 more Smart Citation

Detection for endogenous retroviral loci in Jungle fowl using whole-genome sequencing

Ishihara

2023

Preprint

Self Cite

View full text Add to dashboard Cite

Chickens harbor two primary families of endogenous retroviruses (ERVs): the avian leukosis virus (ALV) and endogenous avian retrovirus (EAV) families. Characterization of ERVs can provide crucial insights into avian evolution. This study aimed to identify novel ERV loci absent in the reference genome using whole-genome sequencing data of red junglefowl, gray junglefowl, Ceylon junglefowl, and green junglefowl. A total of 837 ERV loci were identified across the four Gallus species. The number of ERV loci detected in red junglefowl with its subspecies, gray junglefowl, Ceylon junglefowl, and green junglefowl, was 363, 217, 194, and 129 loci, respectively. The phylogenetic tree was congruent with previously reported trees, suggesting the potential for inferring relationships among past junglefowl populations from the identified ERV loci. Of the detected loci, 306 ERVs were identified near or within the genes, and some were associated with cell adhesion. The detected ERV sequences was in the long terminal repeat region and were classified as EAV-family, ALV-E, Ovex-1, and murine leukemia virus related ERVs. In addition, the sequence of the EAV family was divided into four patterns by combining the U3, R, and U5 regions. These findings contribute to a more comprehensive understanding of the characteristics of chicken ERVs.

show abstract

Section: Resultsmentioning

confidence: 99%

“…ERV detection was performed according to a previous method [15, 16]. We defined the types of read pairs that were mapped to the reference genome and extracted sequence reads that were useful for this study.…”

Section: Methodsmentioning

confidence: 99%

Detection for endogenous retroviral loci in Jungle fowl using whole-genome sequencing

Ishihara

2023

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

“…In addition, 0.10–1.86% of the reads were singletons that were mapped to only one side. The analytical process (see “ Methods ” section for more detail) was conducted in accordance with the methodology of previous studies 15 , 16 . The total number of candidate ERV-LTR insertion loci identified for each individual ranged from 39 to 2011 (Table S1 ) based on RetroSeq software 17 .…”

Section: Resultsmentioning

confidence: 99%

“…ERV detection was performed according to a previous method 15 , 16 . The types of read pairs mapped to the reference genome were defined and extracted sequence reads that were useful for this study.…”

Section: Methodsmentioning

confidence: 99%

Detection of long terminal repeat loci derived from endogenous retrovirus in junglefowl using whole-genome sequencing

Ishihara

2023

Sci Rep

Self Cite

View full text Add to dashboard Cite

Endogenous retroviruses (ERVs) are genetic elements present in the genome that retain traces of past viral infections. Characterization of ERVs can provide crucial insights into avian evolution. This study aimed to identify novel long terminal repeat (LTR) loci derived from ERVs (ERV-LTRs) absent in the reference genome using whole-genome sequencing data of red junglefowl, gray junglefowl, Ceylon junglefowl, and green junglefowl. In total, 835 ERV-LTR loci were identified across the four Gallus species. The numbers of ERV-LTRs loci detected in red junglefowl and its subspecies gray junglefowl, Ceylon junglefowl, and green junglefowl were 362, 216, 193, and 128, respectively. The phylogenetic tree was congruent with previously reported trees, suggesting the potential for inferring relationships among past junglefowl populations from the identified ERV-LTR loci. Of the detected loci, 306 ERV-LTRs were identified near or within the genes, and some were associated with cell adhesion. The detected ERV-LTR sequences were classified as endogenous avian retrovirus family, avian leukosis virus subgroup E, Ovex-1, and murine leukemia virus-related ERVs. In addition, the sequence of the EAV family was divided into four patterns by combining the U3, R, and U5 regions. These findings contribute to a more comprehensive understanding of the characteristics of junglefowl ERVs.

show abstract

Endogenous Retrovirus Loci and Induced Changes in Gene Expression in Japanese Indigenous Chickens

Ishihara,

Shiraishi,

Shimamoto

et al. 2024

Preprint

View full text Add to dashboard Cite

SummaryWhen retroviruses infect germ cells and are transmitted to offspring, they become endogenous retroviruses (ERVs), whose insertions influence the expression of nearby genes. This study aimed to identify the genomic loci of ERVs in commercial broiler (Ross308), Tosa-Jidori, and Yakido chickens as well as to elucidate their impact on neighboring gene expression. Whole-genome data were obtained using next-generation sequencing, and candidate ERV loci were identified using the RetroSeq software. The Integrative Genomics Viewer tool was used to confirm target site duplications (TSDs) as evidence of ERV insertions. All reads within 200 bp of these TSDs were extracted to create contigs, confirming the presence of ERV sequences in the contigs using BLASTN. Gene expression levels were estimated by focusing on genes located near the 172 identified ERV loci. Among these, 119 loci were detected in broiler chickens, 80 in Tosa-Jidori chickens, and 86 in Yakido chickens, with 28 loci shared among them. Moreover, of these 172 loci, 75 were located within or near genes. Significant differences in gene expression were observed for N-acetylated alpha-linked acidic dipeptidase 2, glypican 6, and phospholipid scramblase family member 5 depending on the presence of ERV insertions. These results suggest that ERV insertions may influence the expression of certain genes, providing insights into the genetic diversity and evolutionary background of commercial and indigenous chickens. Understanding the effects of ERV insertions on gene expression can inform future genetic research and poultry breeding programs aimed at improving health and productivity.Author SummaryRecently, endogenous retroviruses (ERVs) have gained significant attention as valuable markers for understanding genetic relationships and evolutionary processes among species. In this study, we investigated the loci and characteristics of ERVs in commercial and traditional Japanese chickens. ERVs are genetic remnants of ancient viral infections that can provide insights into avian evolution. We identified a total of 172 ERV loci in broiler, Tosa-Jidori, and Yakido chickens. Each chicken breed exhibited unique ERV insertion patterns. Notably, we found that ERV insertions near certain genes may influence gene expression. Our research enhances the understanding of how chickens have acquired traits, particularly through genetic mechanisms influenced by ERVs. These insights significantly contribute to our knowledge of biological evolution and the overall biodiversity of birds.

show abstract

Detection of non-reference porcine endogenous retrovirus loci in the Vietnamese native pig genome

Cited by 3 publications

References 45 publications

Detection for endogenous retroviral loci in Jungle fowl using whole-genome sequencing

Detection for endogenous retroviral loci in Jungle fowl using whole-genome sequencing

Detection of long terminal repeat loci derived from endogenous retrovirus in junglefowl using whole-genome sequencing

Endogenous Retrovirus Loci and Induced Changes in Gene Expression in Japanese Indigenous Chickens

Contact Info

Product

Resources

About