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

2018 ◽  
Vol 27 (24) ◽  
pp. 5035-5048 ◽  
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

scholarly journals A genetic legacy of introgression confounds phylogeny and biogeography in oaks

2017 ◽  
Vol 284 (1854) ◽  
pp. 20170300 ◽  
Author(s):  
John D. McVay ◽  
Andrew L. Hipp ◽  
Paul S. Manos
Keyword(s):  
Dna Sequencing ◽  
Restriction Site ◽  
Genetic Exchange ◽  
Sequencing Data ◽  
Biogeographic History ◽  
Phylogenetic Estimation ◽  
Phylogenomic Analyses

Oaks ( Quercus L.) have long been suspected to hybridize in nature, and widespread genetic exchange between morphologically defined species is well documented in two- to six-species systems, but the phylogenetic consequences of hybridization in oaks have never been demonstrated in a phylogenetically diverse sample. Here, we present phylogenomic analyses of a ca 30 Myr clade that strongly support morphologically defined species and the resolution of novel clades of white oaks; however, historical hybridization across clade boundaries is detectable and, undiagnosed, would obscure the imprint of biogeographic history in the phylogeny. Phylogenetic estimation from restriction-site-associated DNA sequencing data for 156 individuals representing 81 species supports two successive intercontinental disjunctions of white oaks: an early vicariance between the Eurasian and American white oaks, and a second, independent radiation represented by two relictual species. A suite of subsampled and partitioned analyses, however, supports a more recent divergence of the Eurasian white oaks from within the American white oaks and suggests that historic introgression between the Eurasian white oaks and a now-relictual lineage biases concatenated phylogenetic estimates. We demonstrate how divergence and reticulation both influence our understanding of the timing and nature of diversification and global colonization in these ecologically and economically important taxa.

scholarly journals Development of Insertion and Deletion Markers for Bottle Gourd Based on Restriction Site-associated DNA Sequencing Data

2017 ◽  
Vol 3 (1) ◽  
pp. 13-16 ◽  
Author(s):  
Xinyi WU ◽  
Pei XU ◽  
Xiaohua WU ◽  
Baogen WANG ◽  
Zhongfu LU ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
Restriction Site ◽  
Bottle Gourd ◽  
Sequencing Data ◽  
Insertion And Deletion

Phylogeography of the East Asian grassland plant, Viola orientalis (Violaceae), inferred from plastid and nuclear restriction site-associated DNA sequencing data

2021 ◽  
Vol 134 (6) ◽  
pp. 1181-1198
Author(s):  
Haruna Sata ◽  
Midori Shimizu ◽  
Takaya Iwasaki ◽  
Hajime Ikeda ◽  
Akiko Soejima ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
Restriction Site ◽  
East Asian ◽  
Sequencing Data

scholarly journals RADSex: a computational workflow to study sex determination using Restriction Site-Associated DNA Sequencing data

2020 ◽  
Author(s):  
Romain Feron ◽  
Qiaowei Pan ◽  
Ming Wen ◽  
Boudjema Imarazene ◽  
Elodie Jouanno ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
Sex Determination ◽  
Restriction Site ◽  
Sex Chromosome ◽  
R Package ◽  
Chromosome Polymorphism ◽  
Sequencing Data ◽  
Model Species ◽  
Determination System ◽  
Sex Determination System

ABSTRACTThe study of sex determination and sex chromosome organisation in non-model species has long been technically challenging, but new sequencing methodologies are now enabling precise and high-throughput identification of sex-specific genomic sequences. In particular, Restriction Site-Associated DNA Sequencing (RAD-Seq) is being extensively applied to explore sex determination systems in many plant and animal species. However, software designed to specifically search for sex-biased markers using RAD-Seq data is lacking. Here, we present RADSex, a computational analysis workflow designed to study the genetic basis of sex determination using RAD-Seq data. RADSex is simple to use, requires few computational resources, makes no prior assumptions about type of sex-determination system or structure of the sex locus, and offers convenient visualization through a dedicated R package. To demonstrate the functionality of RADSex, we re-analyzed a published dataset of Japanese medaka, Oryzias latipes, where we uncovered a previously unknown Y chromosome polymorphism. We then used RADSex to analyze new RAD-Seq datasets from 15 fish species spanning multiple systematic orders. We identified the sex determination system and sex-specific markers in six of these species, five of which had no known sex-markers prior to this study. We show that RADSex greatly facilitates the study of sex determination systems in non-model species and outperforms the commonly used RAD-Seq analysis software STACKS. RADSex in speed, resource usage, ease of application, and visualization options. Furthermore, our analysis of new datasets from 15 species provides new insights on sex determination in fish.

scholarly journals Wild to domesticates: genomes of edible diploid bananas hold traces of several undefined genepools

2021 ◽  
Author(s):  
Julie Sardos ◽  
Catherine Breton ◽  
Xavier Perrier ◽  
Ines Van Den Houwe ◽  
Janet Paofa ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
East Asia ◽  
Papua New Guinea ◽  
Restriction Site ◽  
New Guinea ◽  
The Philippines ◽  
Source Population ◽  
South East Asia ◽  
Sequencing Data ◽  
North Borneo

AbstractThis study is an unprecedent exploration of the diversity of 226 diploid bananas genotyped with restriction-site-associated DNA sequencing data (RADseq) to clarify the processes that led to the creation of edible diploid AA bananas. This wide set included 72 seedy bananas, mostly M. acuminata from different genepools, and 154 edible, i.e. parthenocarpic and sterile, AA accessions obtained from genebanks and recent collecting missions. We highlighted the geographic organisation of the diversity of edible AAs and confirmed the admixed nature of many and further conducted introgressions tests within AAs from South East Asia and New Guinea. Lastly, taking advantage of the presence of an important number of M. acuminata ssp. banksii (22) and of AA from Papua New Guinea (76) in the set, we investigated the patterns of differentiation between wild and cultivated bananas seemingly belonging to the same genepool. We discovered a few cultivated AAs that may be of pure origins both in South-East Asia and in New Guinea. We also detected two undefined parental genepools in South East Asia for which regions of origin could be Thailand and a region between north Borneo and the Philippines, respectively. Finally, we suggest the existence of a third genepool in New Guinea island that might be a source population for both edible AAs and the local M. acuminata ssp. banksii.

scholarly journals Distinguishing linear and branched evolution given single-cell DNA sequencing data of tumors

2021 ◽  
Vol 16 (1) ◽  
Author(s):  
Leah L. Weber ◽  
Mohammed El-Kebir
Keyword(s):  
Dna Sequencing ◽  
Single Cell ◽  
Evolutionary Process ◽  
Treatment Decision ◽  
Real Data ◽  
Current Data ◽  
Fast Method ◽  
Sequencing Data ◽  
Evolutionary Trajectory ◽  
Cancer Types

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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