Using next generation sequencing of alpine plants to improve fecal metabarcoding diet analysis for Dall’s sheep

Abstract Objectives Dall’s sheep (Ovis dalli dalli) are important herbivores in the mountainous ecosystems of northwestern North America, and recent declines in some populations have sparked concern. Our aim was to improve capabilities for fecal metabarcoding diet analysis of Dall’s sheep and other herbivores by contributing new sequence data for arctic and alpine plants. This expanded reference library will provide critical reference sequence data that will facilitate metabarcoding diet analysis of Dall’s sheep and thus improve understanding of plant-animal interactions in a region undergoing rapid climate change. Data description We provide sequences for the chloroplast rbcL gene of 16 arctic-alpine vascular plant species that are known to comprise the diet of Dall’s sheep. These sequences contribute to a growing reference library that can be used in diet studies of arctic herbivores.

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Rapid, raw-read reference and identification (R4IDs): A flexible platform for rapid generic species ID using long-read sequencing technology

10.1101/281048 ◽

2018 ◽

Cited By ~ 2

Author(s):

Joe Parker ◽

Andrew Helmstetter ◽

James Crowe ◽

John Iacona ◽

Dion Devey ◽

...

Keyword(s):

Dna Sequencing ◽

Species Identification ◽

Sequence Data ◽

Vascular Plant ◽

Reference Sequence ◽

Read Length ◽

Reference Database ◽

Sequencing Technology ◽

Long Read ◽

Suitable Reference

AbstractThe versatility of the current DNA sequencing platforms and the development of portable, nanopore sequencers means that it has never been easier to collect genetic data for unknown sample ID. DNA barcoding and meta-barcoding have become increasingly popular and barcode databases continue to grow at an impressive rate. However, the number of canonical genome assemblies (reference or draft) that are publically available is relatively tiny, hindering the more widespread use of genome scale DNA sequencing technology for accurate species identification and discovery. Here, we show that rapid raw-read reference datasets, or R4IDs for short, generated in a matter of hours on the Oxford Nanopore MinION, can bridge this gap and accelerate the generation of useable reference sequence data. By exploiting the long read length of this technology, shotgun genomic sequencing of a small portion of an organism’s genome can act as a suitable reference database despite the low sequencing coverage. These R4IDs can then be used for accurate species identification with minimal amounts of re-sequencing effort (1000s of reads). We demonstrated the capabilities of this approach with six vascular plant species for which we created R4IDs in the laboratory and then re-sequenced, live at the Kew Science Festival 2016. We further validated our method using simulations to determine the broader applicability of the approach. Our data analysis pipeline has been made available as a Dockerised workflow for simple, scalable deployment for a range of uses.

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Superovulation in Dall's sheep (Ovis dalli dalli)

Theriogenology ◽

10.1016/0093-691x(90)90625-4 ◽

1990 ◽

Vol 33 (1) ◽

pp. 201 ◽

Cited By ~ 2

Author(s):

B.C. Buckrell ◽

C.J. Gartley ◽

K.G. Mehren ◽

K.L. Goodrowe

Keyword(s):

Ovis Dalli ◽

Dall’S Sheep

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Critical snow density threshold for Dall’s sheep (Ovis dalli dalli)

Canadian Journal of Zoology ◽

10.1139/cjz-2017-0259 ◽

2018 ◽

Vol 96 (10) ◽

pp. 1170-1177 ◽

Cited By ~ 2

Author(s):

Kelly J. Sivy ◽

Anne W. Nolin ◽

Christopher L. Cosgrove ◽

Laura R. Prugh

Keyword(s):

Snow Depth ◽

Animal Movement ◽

Population Declines ◽

Snow Density ◽

Energetic Costs ◽

Snow Properties ◽

Ovis Dalli ◽

Snow Conditions ◽

Dall’S Sheep ◽

Density Threshold

Snow cover can significantly impact animal movement and energetics, yet few studies have investigated the link between physical properties of snow and energetic costs. Quantification of thresholds in snow properties that influence animal movement are needed to help address this knowledge gap. Recent population declines of Dall’s sheep (Ovis dalli dalli Nelson, 1884) could be due in part to changing snow conditions. We examined the effect of snow density, snow depth, and snow hardness on sinking depths of Dall’s sheep tracks encountered in Wrangell–St. Elias National Park and Preserve, Alaska. Snow depth was a poor predictor of sinking depths of sheep tracks (R2 = 0.02, p = 0.38), as was mean weighted hardness (R2 = 0.09, p = 0.07). Across competing models, top layer snow density (0–10 cm) and sheep age class were the best predictors of track sink depths (R2 = 0.58). Track sink depth decreased with increasing snow density, and the snowpack supported the mass of a sheep above a density threshold of 329 ± 18 kg/m3 (mean ± SE). This threshold could aid interpretation of winter movement and energetic costs by animals, thus improving our ability to predict consequences of changing snowpack conditions on wildlife.

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A new Plasmodium vivax reference sequence with improved assembly of the subtelomeres reveals an abundance of pir genes

Wellcome Open Research ◽

10.12688/wellcomeopenres.9876.1 ◽

2016 ◽

Vol 1 ◽

pp. 4 ◽

Cited By ~ 56

Author(s):

Sarah Auburn ◽

Ulrike Böhme ◽

Sascha Steinbiss ◽

Hidayat Trimarsanto ◽

Jessica Hostetler ◽

...

Keyword(s):

South America ◽

Plasmodium Vivax ◽

Sequence Data ◽

Ex Vivo ◽

Vital Role ◽

Asia Pacific ◽

Reference Sequence ◽

Manual Curation ◽

Illumina Sequence

Plasmodium vivax is now the predominant cause of malaria in the Asia-Pacific, South America and Horn of Africa. Laboratory studies of this species are constrained by the inability to maintain the parasite in continuous ex vivo culture, but genomic approaches provide an alternative and complementary avenue to investigate the parasite’s biology and epidemiology. To date, molecular studies of P. vivax have relied on the Salvador-I reference genome sequence, derived from a monkey-adapted strain from South America. However, the Salvador-I reference remains highly fragmented with over 2500 unassembled scaffolds. Using high-depth Illumina sequence data, we assembled and annotated a new reference sequence, PvP01, sourced directly from a patient from Papua Indonesia. Draft assemblies of isolates from China (PvC01) and Thailand (PvT01) were also prepared for comparative purposes. The quality of the PvP01 assembly is improved greatly over Salvador-I, with fragmentation reduced to 226 scaffolds. Detailed manual curation has ensured highly comprehensive annotation, with functions attributed to 58% core genes in PvP01 versus 38% in Salvador-I. The assemblies of PvP01, PvC01 and PvT01 are larger than that of Salvador-I (28-30 versus 27 Mb), owing to improved assembly of the subtelomeres. An extensive repertoire of over 1200 Plasmodium interspersed repeat (pir) genes were identified in PvP01 compared to 346 in Salvador-I, suggesting a vital role in parasite survival or development. The manually curated PvP01 reference and PvC01 and PvT01 draft assemblies are important new resources to study vivax malaria. PvP01 is maintained at GeneDB and ongoing curation will ensure continual improvements in assembly and annotation quality.

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An iterative and automated computational pipeline for untargeted strain-level identification using MS/MS spectra from pathogenic samples

10.1101/812313 ◽

2019 ◽

Author(s):

Mathias Kuhring ◽

Joerg Doellinger ◽

Andreas Nitsche ◽

Thilo Muth ◽

Bernhard Y. Renard

Keyword(s):

Statistical Power ◽

Sequence Data ◽

A Priori ◽

Search Space ◽

Strain Level ◽

Reference Sequence ◽

Viral Origin ◽

Identification Of Species ◽

Taxonomic Assignments

AbstractUntargeted accurate strain-level classification of a priori unidentified organisms using tandem mass spectrometry is a challenging task. Reference databases often lack taxonomic depth, limiting peptide assignments to the species level. However, the extension with detailed strain information increases runtime and decreases statistical power. In addition, larger databases contain a higher number of similar proteomes.We present TaxIt, an iterative workflow to address the increasing search space required for MS/MS-based strain-level classification of samples with unknown taxonomic origin. TaxIt first applies reference sequence data for initial identification of species candidates, followed by automated acquisition of relevant strain sequences for low level classification. Furthermore, proteome similarities resulting in ambiguous taxonomic assignments are addressed with an abundance weighting strategy to improve candidate confidence.We apply our iterative workflow on several samples of bacterial and viral origin. In comparison to non-iterative approaches using unique peptides or advanced abundance correction, TaxIt identifies microbial strains correctly in all examples presented (with one tie), thereby demonstrating the potential for untargeted and deeper taxonomic classification. TaxIt makes extensive use of public, unrestricted and continuously growing sequence resources such as the NCBI databases and is available under open-source license at https://gitlab.com/rki_bioinformatics.

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Factors controlling lambing period of Dall's sheep

Canadian Journal of Zoology ◽

10.1139/z80-144 ◽

1980 ◽

Vol 58 (6) ◽

pp. 1027-1031 ◽

Cited By ~ 27

Author(s):

Fred L. Bunnell

Keyword(s):

Body Size ◽

Ovis Dalli ◽

Study Population ◽

Energetic Constraints ◽

Dall’S Sheep

Distribution of birth dates within the study population of Ovis dalli dalli reveal two distinct oestrous cycles with a further 15% of all births resulting from a third cycle. The onset of breeding appears governed by photoperiod. Lambs born early and late in the lambing period suffer higher mortality. Energetic constraints limit both onset and duration of lambing. Onset is delayed beyond the period critical to thermoregulation by lambs and until forage is adequate; duration is limited by the need of lambs to attain adequate body size by winter.

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Full-length transcriptome sequences of Agropyron cristatum facilitate the prediction of putative genes for thousand-grain weight in a wheat-A. cristatum translocation line

BMC Genomics ◽

10.1186/s12864-019-6416-4 ◽

2019 ◽

Vol 20 (1) ◽

Cited By ~ 1

Author(s):

Shenghui Zhou ◽

Jinpeng Zhang ◽

Haiming Han ◽

Jing Zhang ◽

Huihui Ma ◽

...

Keyword(s):

Single Molecule ◽

Sequence Data ◽

Full Length ◽

Grain Weight ◽

Agropyron Cristatum ◽

Reference Sequence ◽

Translocation Line ◽

Thousand Grain Weight ◽

Sequencing Platform ◽

Transcriptome Sequences

Abstract Background Agropyron cristatum (L.) Gaertn. (2n = 4x = 28; genomes PPPP) is a wild relative of common wheat (Triticum aestivum L.) and provides many desirable genetic resources for wheat improvement. However, there is still a lack of reference genome and transcriptome information for A. cristatum, which severely impedes functional and molecular breeding studies. Results Single-molecule long-read sequencing technology from Pacific Biosciences (PacBio) was used to sequence full-length cDNA from a mixture of leaves, roots, stems and caryopses and constructed the first full-length transcriptome dataset of A. cristatum, which comprised 44,372 transcripts. As expected, the PacBio transcripts were generally longer and more complete than the transcripts assembled via the Illumina sequencing platform in previous studies. By analyzing RNA-Seq data, we identified tissue-enriched transcripts and assessed their GO term enrichment; the results indicated that tissue-enriched transcripts were enriched for particular molecular functions that varied by tissue. We identified 3398 novel and 1352 A. cristatum-specific transcripts compared with the wheat gene model set. To better apply this A. cristatum transcriptome, the A. cristatum transcripts were integrated with the wheat genome as a reference sequence to try to identify candidate A. cristatum transcripts associated with thousand-grain weight in a wheat-A. cristatum translocation line, Pubing 3035. Conclusions Full-length transcriptome sequences were used in our study. The present study not only provides comprehensive transcriptomic insights and information for A. cristatum but also proposes a new method for exploring the functional genes of wheat relatives under a wheat genetic background. The sequence data have been deposited in the NCBI under BioProject accession number PRJNA534411.

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DNA barcodes for insect pest identification: a test case with tussock moths (Lepidoptera: Lymantriidae)

Canadian Journal of Forest Research ◽

10.1139/x05-276 ◽

2006 ◽

Vol 36 (2) ◽

pp. 337-350 ◽

Cited By ~ 106

Author(s):

Shelley L Ball ◽

Karen F Armstrong

Keyword(s):

Cytochrome C ◽

Cytochrome C Oxidase ◽

Sequence Data ◽

Mitochondrial Gene ◽

Insect Pest ◽

Reference Sequence ◽

Identification System ◽

Pest Species ◽

Dna Barcodes ◽

Data Set

Reliable and rapid identification of exotic pest species is critical to biosecurity. However, identification of morphologically indistinct specimens, such as immature life stages, that are frequently intercepted at borders is often impossible. Several DNA-based methods have been used for species identification; however, a more universal and anticipatory identification system is needed. Consequently, we tested the ability of DNA "barcodes" to identify species of tussock moths (Lymantriidae), a family containing several important pest species. We sequenced a 617 base pair fragment of the mitochondrial gene cytochrome c oxidase 1 for 20 lymantriid species. We used these, together with other Noctuoidea species sequences from GenBank and the Barcoding of Life Database to create a "profile" or reference sequence data set. We then tested the ability of this profile to provide correct species identifications for 93 additional lymantriid specimens from a data set of mock unknowns. Of the unknowns, 100% were correctly identified by the cytochrome c oxidase 1 profile. Mean interspecific sequence (Kimura 2-parameter) divergence was an order of magnitude greater (14%) than mean intraspecific divergence (<1%). Four species showed deeper genetic divergences among populations. We conclude that DNA barcodes provide a highly accurate means of identifying lymantriid species and show considerable promise as a universal approach to DNA-based identification of pest insects.

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