scholarly journals Holocene chloroplast genetic variation of shrubs ( Alnus alnobetula , Betula nana , Salix sp.) at the siberian tundra‐taiga ecotone inferred from modern chloroplast genome assembly and sedimentary ancient DNA analyses

2021 ◽  
Author(s):  
Stefano Meucci ◽  
Luise Schulte ◽  
Heike H. Zimmermann ◽  
Kathleen R. Stoof‐Leichsenring ◽  
Laura Epp ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Chloroplast Genome ◽  
Ancient Dna ◽  
Genome Assembly ◽  
Betula Nana ◽  
Dna Analyses

scholarly journals Slaves as burial gifts in Viking Age Norway? Evidence from stable isotope and ancient DNA analyses

2014 ◽  
Vol 41 ◽  
pp. 533-540 ◽  
Author(s):  
Elise Naumann ◽  
Maja Krzewińska ◽  
Anders Götherström ◽  
Gunilla Eriksson
Keyword(s):  
Stable Isotope ◽  
Ancient Dna ◽  
Viking Age ◽  
Dna Analyses

scholarly journals GraphAligner: rapid and versatile sequence-to-graph alignment

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Mikko Rautiainen ◽  
Tobias Marschall
Keyword(s):  
Genetic Variation ◽  
Error Correction ◽  
Genome Assembly ◽  
State Of The Art ◽  
Source Code ◽  
The State ◽  
Graph Alignment ◽  
Link Type ◽  
Long Reads

Abstract Genome graphs can represent genetic variation and sequence uncertainty. Aligning sequences to genome graphs is key to many applications, including error correction, genome assembly, and genotyping of variants in a pangenome graph. Yet, so far, this step is often prohibitively slow. We present GraphAligner, a tool for aligning long reads to genome graphs. Compared to the state-of-the-art tools, GraphAligner is 13x faster and uses 3x less memory. When employing GraphAligner for error correction, we find it to be more than twice as accurate and over 12x faster than extant tools.Availability: Package manager: https://anaconda.org/bioconda/graphalignerand source code: https://github.com/maickrau/GraphAligner

scholarly journals Multi-scale ancient DNA analyses confirm the western origin of Michelsberg farmers and document probable practices of human sacrifice

PLoS ONE ◽  
2017 ◽  
Vol 12 (7) ◽  
pp. e0179742 ◽  
Author(s):  
Alice Beau ◽  
Maïté Rivollat ◽  
Hélène Réveillas ◽  
Marie-Hélène Pemonge ◽  
Fanny Mendisco ◽  
...  
Keyword(s):  
Ancient Dna ◽  
Human Sacrifice ◽  
Multi Scale ◽  
Dna Analyses

scholarly journals Population dynamics and genetic changes of Picea abies in the South Carpathians revealed by pollen and ancient DNA analyses

2011 ◽  
Vol 11 (1) ◽  
Author(s):  
Enikő K Magyari ◽  
Ágnes Major ◽  
Miklós Bálint ◽  
Judit Nédli ◽  
Mihály Braun ◽  
...  
Keyword(s):  
Population Dynamics ◽  
Picea Abies ◽  
Ancient Dna ◽  
The South ◽  
Genetic Changes ◽  
Dna Analyses

scholarly journals Aquila: diploid personal genome assembly and comprehensive variant detection based on linked reads

2019 ◽  
Author(s):  
Xin Zhou ◽  
Lu Zhang ◽  
Ziming Weng ◽  
David L. Dill ◽  
Arend Sidow
Keyword(s):  
Genetic Variation ◽  
Genome Sequence ◽  
Genome Assembly ◽  
Sequence Data ◽  
Association Studies ◽  
Cost Effective ◽  
Whole Genome Sequence ◽  
Personal Genome ◽  
Whole Genome ◽  
Nucleotide Polymorphisms

AbstractVariant discovery in personal, whole genome sequence data is critical for uncovering the genetic contributions to health and disease. We introduce a new approach, Aquila, that uses linked-read data for generating a high quality diploid genome assembly, from which it then comprehensively detects and phases personal genetic variation. Assemblies cover >95% of the human reference genome, with over 98% in a diploid state. Thus, the assemblies support detection and accurate genotyping of the most prevalent types of human genetic variation, including single nucleotide polymorphisms (SNPs), small insertions and deletions (small indels), and structural variants (SVs), in all but the most difficult regions. All heterozygous variants are phased in blocks that can approach arm-level length. The final output of Aquila is a diploid and phased personal genome sequence, and a phased VCF file that also contains homozygous and a few unphased heterozygous variants. Aquila represents a cost-effective evolution of whole-genome reconstruction that can be applied to cohorts for variation discovery or association studies, or to single individuals with rare phenotypes that could be caused by SVs or compound heterozygosity.

scholarly journals Archaeological mitogenomes illuminate the historical ecology of sea otters ( Enhydra lutris ) and the viability of reintroduction

2020 ◽  
Vol 287 (1940) ◽  
pp. 20202343
Author(s):  
Hannah P. Wellman ◽  
Rita M. Austin ◽  
Nihan D. Dagtas ◽  
Madonna L. Moss ◽  
Torben C. Rick ◽  
...  
Keyword(s):  
British Columbia ◽  
Ancient Dna ◽  
Historical Ecology ◽  
Mitochondrial Genomes ◽  
Sea Otter ◽  
Enhydra Lutris ◽  
Dental Calculus ◽  
Sea Otters ◽  
Dna Analyses ◽  
Modern Context

Genetic analyses are an important contribution to wildlife reintroductions, particularly in the modern context of extirpations and ecological destruction. To address the complex historical ecology of the sea otter ( Enhydra lutris ) and its failed 1970s reintroduction to coastal Oregon, we compared mitochondrial genomes of pre-extirpation Oregon sea otters to extant and historical populations across the range. We sequenced, to our knowledge, the first complete ancient mitogenomes from archaeological Oregon sea otter dentine and historical sea otter dental calculus. Archaeological Oregon sea otters ( n = 20) represent 10 haplotypes, which cluster with haplotypes from Alaska, Washington and British Columbia, and exhibit a clear division from California haplotypes. Our results suggest that extant northern populations are appropriate for future reintroduction efforts. This project demonstrates the feasibility of mitogenome capture and sequencing from non-human dental calculus and the diverse applications of ancient DNA analyses to pressing ecological and conservation topics and the management of at-risk/extirpated species.

scholarly journals Assessment of intraspecific genetic variation between three morphotypes of Cissus quadrangularis using CCMP markers

2015 ◽  
Vol 24 (2) ◽  
pp. 205-212
Author(s):  
Ritesh Kaur ◽  
CP Malik
Keyword(s):  
Genetic Variation ◽  
Sequence Analysis ◽  
Chloroplast Genome ◽  
Intraspecific Variation ◽  
Microsatellite Primers ◽  
Genome Sequences ◽  
Chloroplast Microsatellite ◽  
Cissus Quadrangularis ◽  
High Degree ◽  
Degree Of Similarity

The objective of the current study was to assess and establish intraspecific variation between three morphotypes of Cissus quadrangularis using ten Consensus Chloroplast Microsatellite Primers. Significant level of genetic variation was detected between the three morphotypes. Sequence analysis of the CCMP PCR fragment showed the high degree of similarity to the chloroplast genome sequences of other Vitaceae members indicating that these regions are highly conserved.Plant Tissue Cult. & Biotech. 24(2): 205-212, 2014 (December)

Sign in / Sign up

Export Citation Format

Share Document