Genetic Diversity of Kalopanax septemlobus (Thunb.) Koidz. at the Northern Edge of the Range according to Chloroplast DNA Sequencing Data

Abstract Background Cancer arises from an evolutionary process where somatic mutations give rise to clonal expansions. Reconstructing this evolutionary process is useful for treatment decision-making as well as understanding evolutionary patterns across patients and cancer types. In particular, classifying a tumor’s evolutionary process as either linear or branched and understanding what cancer types and which patients have each of these trajectories could provide useful insights for both clinicians and researchers. While comprehensive cancer phylogeny inference from single-cell DNA sequencing data is challenging due to limitations with current sequencing technology and the complexity of the resulting problem, current data might provide sufficient signal to accurately classify a tumor’s evolutionary history as either linear or branched. Results We introduce the Linear Perfect Phylogeny Flipping (LPPF) problem as a means of testing two alternative hypotheses for the pattern of evolution, which we prove to be NP-hard. We develop Phyolin, which uses constraint programming to solve the LPPF problem. Through both in silico experiments and real data application, we demonstrate the performance of our method, outperforming a competing machine learning approach. Conclusion Phyolin is an accurate, easy to use and fast method for classifying an evolutionary trajectory as linear or branched given a tumor’s single-cell DNA sequencing data.

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Whole genome sequencing reveals high differentiation, low levels of genetic diversity and short runs of homozygosity among Swedish wels catfish

Heredity ◽

10.1038/s41437-021-00438-5 ◽

2021 ◽

Author(s):

Axel Jensen ◽

Mette Lillie ◽

Kristofer Bergström ◽

Per Larsson ◽

Jacob Höglund

Keyword(s):

Genetic Diversity ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Whole Genome Sequencing Data ◽

Peripheral Populations ◽

Whole Genome ◽

Runs Of Homozygosity ◽

Sequencing Data ◽

Isolated Populations ◽

Native Populations

AbstractThe use of genetic markers in the context of conservation is largely being outcompeted by whole-genome data. Comparative studies between the two are sparse, and the knowledge about potential effects of this methodology shift is limited. Here, we used whole-genome sequencing data to assess the genetic status of peripheral populations of the wels catfish (Silurus glanis), and discuss the results in light of a recent microsatellite study of the same populations. The Swedish populations of the wels catfish have suffered from severe declines during the last centuries and persists in only a few isolated water systems. Fragmented populations generally are at greater risk of extinction, for example due to loss of genetic diversity, and may thus require conservation actions. We sequenced individuals from the three remaining native populations (Båven, Emån, and Möckeln) and one reintroduced population of admixed origin (Helge å), and found that genetic diversity was highest in Emån but low overall, with strong differentiation among the populations. No signature of recent inbreeding was found, but a considerable number of short runs of homozygosity were present in all populations, likely linked to historically small population sizes and bottleneck events. Genetic substructure within any of the native populations was at best weak. Individuals from the admixed population Helge å shared most genetic ancestry with the Båven population (72%). Our results are largely in agreement with the microsatellite study, and stresses the need to protect these isolated populations at the northern edge of the distribution of the species.

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Phylogeography of Prunus armeniaca L. revealed by chloroplast DNA and nuclear ribosomal sequences

Scientific Reports ◽

10.1038/s41598-021-93050-w ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Wen-Wen Li ◽

Li-Qiang Liu ◽

Qiu-Ping Zhang ◽

Wei-Quan Zhou ◽

Guo-Quan Fan ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Chloroplast Dna ◽

Population Expansion ◽

Prunus Armeniaca ◽

River Valley ◽

Nuclear Ribosomal Dna ◽

Glacial Refugium ◽

Ili River Valley ◽

Wild Apricot

AbstractTo clarify the phytogeography of Prunus armeniaca L., two chloroplast DNA fragments (trnL-trnF and ycf1) and the nuclear ribosomal DNA internal transcribed spacer (ITS) were employed to assess genetic variation across 12 P. armeniaca populations. The results of cpDNA and ITS sequence data analysis showed a high the level of genetic diversity (cpDNA: HT = 0.499; ITS: HT = 0.876) and a low level of genetic differentiation (cpDNA: FST = 0.1628; ITS: FST = 0.0297) in P. armeniaca. Analysis of molecular variance (AMOVA) revealed that most of the genetic variation in P. armeniaca occurred among individuals within populations. The value of interpopulation differentiation (NST) was significantly higher than the number of substitution types (GST), indicating genealogical structure in P. armeniaca. P. armeniaca shared genotypes with related species and may be associated with them through continuous and extensive gene flow. The haplotypes/genotypes of cultivated apricot populations in Xinjiang, North China, and foreign apricot populations were mixed with large numbers of haplotypes/genotypes of wild apricot populations from the Ili River Valley. The wild apricot populations in the Ili River Valley contained the ancestral haplotypes/genotypes with the highest genetic diversity and were located in an area considered a potential glacial refugium for P. armeniaca. Since population expansion occurred 16.53 kyr ago, the area has provided a suitable climate for the population and protected the genetic diversity of P. armeniaca.

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Putatively adaptive genetic variation in the giant California sea cucumber ( Parastichopus californicus ) as revealed by environmental association analysis of restriction‐site associated DNA sequencing data

Molecular Ecology ◽

10.1111/mec.14942 ◽

2018 ◽

Vol 27 (24) ◽

pp. 5035-5048 ◽

Cited By ~ 13

Author(s):

Amanda Xuereb ◽

Christopher M. Kimber ◽

Janelle M. R. Curtis ◽

Louis Bernatchez ◽

Marie‐Josée Fortin

Keyword(s):

Genetic Variation ◽

Dna Sequencing ◽

Association Analysis ◽

Sea Cucumber ◽

Restriction Site ◽

Sequencing Data ◽

Adaptive Genetic Variation ◽

Environmental Association

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Genetic diversity in endangered Notopterygium forbesii Boissieu based on intraspecies sequence variation of chloroplast DNA and implications for conservation

Biochemical Systematics and Ecology ◽

10.1016/j.bse.2010.09.012 ◽

2010 ◽

Vol 38 (5) ◽

pp. 911-916 ◽

Cited By ~ 11

Author(s):

Guoying Zhou ◽

Lucun Yang ◽

Chunli Li ◽

Wenhua Xu ◽

Guichen Chen

Keyword(s):

Genetic Diversity ◽

Chloroplast Dna ◽

Sequence Variation

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Design and performance of a bovine 200 k SNP chip developed for endangered German Black Pied cattle (DSN)

BMC Genomics ◽

10.1186/s12864-021-08237-2 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Guilherme B. Neumann ◽

Paula Korkuć ◽

Danny Arends ◽

Manuel J. Wolf ◽

Katharina May ◽

...

Keyword(s):

Genetic Diversity ◽

Association Studies ◽

Bos Indicus ◽

Diversity Management ◽

Whole Genome Sequencing Data ◽

General Interest ◽

Whole Genome ◽

Sequencing Data ◽

Snp Chip ◽

Selection Of

Abstract Background German Black Pied cattle (DSN) are an endangered dual-purpose breed which was largely replaced by Holstein cattle due to their lower milk yield. DSN cattle are kept as a genetic reserve with a current herd size of around 2500 animals. The ability to track sequence variants specific to DSN could help to support the conservation of DSN’s genetic diversity and to provide avenues for genetic improvement. Results Whole-genome sequencing data of 304 DSN cattle were used to design a customized DSN200k SNP chip harboring 182,154 variants (173,569 SNPs and 8585 indels) based on ten selection categories. We included variants of interest to DSN such as DSN unique variants and variants from previous association studies in DSN, but also variants of general interest such as variants with predicted consequences of high, moderate, or low impact on the transcripts and SNPs from the Illumina BovineSNP50 BeadChip. Further, the selection of variants based on haplotype blocks ensured that the whole-genome was uniformly covered with an average variant distance of 14.4 kb on autosomes. Using 300 DSN and 162 animals from other cattle breeds including Holstein, endangered local cattle populations, and also a Bos indicus breed, performance of the SNP chip was evaluated. Altogether, 171,978 (94.31%) of the variants were successfully called in at least one of the analyzed breeds. In DSN, the number of successfully called variants was 166,563 (91.44%) while 156,684 (86.02%) were segregating at a minor allele frequency > 1%. The concordance rate between technical replicates was 99.83 ± 0.19%. Conclusion The DSN200k SNP chip was proved useful for DSN and other Bos taurus as well as one Bos indicus breed. It is suitable for genetic diversity management and marker-assisted selection of DSN animals. Moreover, variants that were segregating in other breeds can be used for the design of breed-specific customized SNP chips. This will be of great value in the application of conservation programs for endangered local populations in the future.

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Splicing Express: a software suite for alternative splicing analysis using next-generation sequencing data

PeerJ ◽

10.7717/peerj.1419 ◽

2015 ◽

Vol 3 ◽

pp. e1419 ◽

Cited By ~ 6

Author(s):

Jose E. Kroll ◽

Jihoon Kim ◽

Lucila Ohno-Machado ◽

Sandro J. de Souza

Keyword(s):

Alternative Splicing ◽

Dna Sequencing ◽

Next Generation Sequencing Data ◽

Next Generation ◽

Sequencing Data ◽

Software Suite ◽

Next Generation Dna Sequencing ◽

Sequencing Technologies ◽

Body Map ◽

Sequencing Platforms

Motivation.Alternative splicing events (ASEs) are prevalent in the transcriptome of eukaryotic species and are known to influence many biological phenomena. The identification and quantification of these events are crucial for a better understanding of biological processes. Next-generation DNA sequencing technologies have allowed deep characterization of transcriptomes and made it possible to address these issues. ASEs analysis, however, represents a challenging task especially when many different samples need to be compared. Some popular tools for the analysis of ASEs are known to report thousands of events without annotations and/or graphical representations. A new tool for the identification and visualization of ASEs is here described, which can be used by biologists without a solid bioinformatics background.Results.A software suite namedSplicing Expresswas created to perform ASEs analysis from transcriptome sequencing data derived from next-generation DNA sequencing platforms. Its major goal is to serve the needs of biomedical researchers who do not have bioinformatics skills.Splicing Expressperforms automatic annotation of transcriptome data (GTF files) using gene coordinates available from the UCSC genome browser and allows the analysis of data from all available species. The identification of ASEs is done by a known algorithm previously implemented in another tool namedSplooce. As a final result,Splicing Expresscreates a set of HTML files composed of graphics and tables designed to describe the expression profile of ASEs among all analyzed samples. By using RNA-Seq data from the Illumina Human Body Map and the Rat Body Map, we show thatSplicing Expressis able to perform all tasks in a straightforward way, identifying well-known specific events.Availability and Implementation.Splicing Expressis written in Perl and is suitable to run only in UNIX-like systems. More details can be found at:http://www.bioinformatics-brazil.org/splicingexpress.

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