What’s in your next-generation sequence data? An exploration of unmapped DNA and RNA sequence reads from the bovine reference individual

Whitacre, Lynsey K.; Tizioto, P. C.; Kim, JaeWoo; Sonstegard, Tad S.; Schroeder, Steven G.; Alexander, L. J.; Medrano, Juan F.; Schnabel, Robert D.; Taylor, Jeremy F.; Decker, Jared E.

doi:10.1186/s12864-015-2313-7

Cited by 33 publications

(49 citation statements)

References 37 publications

(30 reference statements)

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“…However, these differences could also partially be artifacts since the bovine assembly is an early-stage draft assembly while the human assembly is essentially complete. Whitacre et al (32) predicted that 42% of bovine genes are either missing or misassembled in the UMD3.1 (32) assembly and this may have produced the domain differences that we found. Thus, we decided to classify these genes as “c” class until further information can be added in the literature and the assembly improved.…”

Section: Discussionmentioning

confidence: 64%

“…Expression of bovine TFs and TcoFs in 14 tissues was examined using RNA-seq data from the L1 Hereford cow Dominette 01449 described in Whitacre et al (32). Tissues included in the analysis were ampulla, white blood cells, cerebral cortex, endometrium, caruncular regions contralateral (car con) and ipsilateral (car ips) to the corpeus luteum, gallbladder, heart, jejunum, kidney, liver, mesenteric lymph nodes, pons, semitendinosus muscle, and spleen.…”

Section: Methodsmentioning

confidence: 99%

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A comprehensive manually-curated Compendium of Bovine Transcription Factors

Souza

Vaquerizas

Zerlotini

et al. 2018

Preprint

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Transcription factors (TFs) are pivotal regulatory proteins that control gene expression in a context-dependent and tissue-specific manner. In contrast to human, where comprehensive curated TF collections exist, bovine TFs are only rudimentary recorded and characterized. In this article, we present a manually-curated compendium of 865 sequence-specific DNA-binding bovines TFs, which we analyzed for domain family distribution, evolutionary conservation, and tissue-specific expression. In addition, we provide a list of putative transcription cofactors derived from known interactions with the identified TFs. Since there is a general lack of knowledge concerning the regulation of gene expression in cattle, the curated list of TF should provide a basis for an improved comprehension of regulatory mechanisms that are specific to the species.

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Section: Discussionmentioning

confidence: 64%

Section: Methodsmentioning

confidence: 99%

A comprehensive manually-curated Compendium of Bovine Transcription Factors

Souza

Vaquerizas

Zerlotini

et al. 2018

Preprint

View full text Add to dashboard Cite

show abstract

“…Our study and [23] demonstrated that it is possible to consider NGS datasets as source of metagenomics information. We could envisage that routine mining of NGS data against viral genome sequences might become a common method to discover novel viral infections and novel viruses in the future.…”

Section: Discussionmentioning

confidence: 72%

A viral metagenomic approach on a non-metagenomic experiment: Mining next generation sequencing datasets from pig DNA identified several porcine parvoviruses for a retrospective evaluation of viral infections

et al. 2017

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Shot-gun next generation sequencing (NGS) on whole DNA extracted from specimens collected from mammals often produces reads that are not mapped (i.e. unmapped reads) on the host reference genome and that are usually discarded as by-products of the experiments. In this study, we mined Ion Torrent reads obtained by sequencing DNA isolated from archived blood samples collected from 100 performance tested Italian Large White pigs. Two reduced representation libraries were prepared from two DNA pools constructed each from 50 equimolar DNA samples. Bioinformatic analyses were carried out to mine unmapped reads on the reference pig genome that were obtained from the two NGS datasets. In silico analyses included read mapping and sequence assembly approaches for a viral metagenomic analysis using the NCBI Viral Genome Resource. Our approach identified sequences matching several viruses of the Parvoviridae family: porcine parvovirus 2 (PPV2), PPV4, PPV5 and PPV6 and porcine bocavirus 1-H18 isolate (PBoV1-H18). The presence of these viruses was confirmed by PCR and Sanger sequencing of individual DNA samples. PPV2, PPV4, PPV5, PPV6 and PBoV1-H18 were all identified in samples collected in 1998–2007, 1998–2000, 1997–2000, 1998–2004 and 2003, respectively. For most of these viruses (PPV4, PPV5, PPV6 and PBoV1-H18) previous studies reported their first occurrence much later (from 5 to more than 10 years) than our identification period and in different geographic areas. Our study provided a retrospective evaluation of apparently asymptomatic parvovirus infected pigs providing information that could be important to define occurrence and prevalence of different parvoviruses in South Europe. This study demonstrated the potential of mining NGS datasets non-originally derived by metagenomics experiments for viral metagenomics analyses in a livestock species.

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“…through ; Whitacre et al . ) were mapped without discarding the discordantly mapped reads using as reference sequences both the previously described BACs and UMD 3.1.1. Concordantly and discordantly mapped reads within the region of interest were filtered using samtools (Li et al .…”

Section: Methodsmentioning

confidence: 99%

Characterization of a deletion in the Hsp70 cluster in the bovine reference genome

et al. 2017

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The 70 kilodalton heat shock proteins (Hsp70) are highly conserved molecular chaperones which have a crucial role in the stress response of the cell. In mammals, the Hsp70 proteins are encoded by a cluster of three genes: HSPA1A, HSPA1B and HSPA1L. In bovines, this cluster is located on chromosome 23 downstream of the major histocompatibility complex (BoLA). We detected inconsistencies in the location of markers on the Hsp70 genes reported in the literature that pointed to a potential deletion in the bovine reference genome UMD 3.1.1. An in silico analysis of the bovine genomic region of the Hsp70 cluster, using available information from public databases, confirmed the existence of a deletion of 11.1-kb spanning the HSPA1B gene and the intergenic region between HSPA1B and HSPA1A. Although we originally considered this an assembly error, it is most likely a particular condition of L1 Dominette 01449, the cow sequenced in the Bovine Genome Project. Moreover, we suggest a new classification of bovine Hsp70 sequences reported in NCBI and a reassignment of the location of SNPs from dbSNP that map to the deletion on BTA23. We also compared the location of selected transcription factor binding sites on the promoters of HSPA1A and HSPA1B. The results generated in the present work could be helpful to refine the reference genome of an important livestock species and also to understand the role and the regulation of the bovine Hsp70 genes.

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What’s in your next-generation sequence data? An exploration of unmapped DNA and RNA sequence reads from the bovine reference individual

Cited by 33 publications

References 37 publications

A comprehensive manually-curated Compendium of Bovine Transcription Factors

A comprehensive manually-curated Compendium of Bovine Transcription Factors

A viral metagenomic approach on a non-metagenomic experiment: Mining next generation sequencing datasets from pig DNA identified several porcine parvoviruses for a retrospective evaluation of viral infections

Characterization of a deletion in the Hsp70 cluster in the bovine reference genome

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