scholarly journals Population genomic analyses from low-coverage RAD-Seq data: a case study on the non-model cucurbit bottle gourd

2013 ◽  
Vol 77 (3) ◽  
pp. 430-442 ◽  
Author(s):  
Pei Xu ◽  
Shizhong Xu ◽  
Xiaohua Wu ◽  
Ye Tao ◽  
Baogen Wang ◽  
...  
Keyword(s):  
Bottle Gourd ◽  
Population Genomic ◽  
Genomic Analyses ◽  
Low Coverage

scholarly journals Comparative genomic and transcriptomic analyses of transposable elements in polychaetous annelids highlight LTR retrotransposon diversity and evolution

Mobile DNA ◽  
2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Jonathan Filée ◽  
Sarah Farhat ◽  
Dominique Higuet ◽  
Laure Teysset ◽  
Dominique Marie ◽  
...  
Keyword(s):  
Transposable Elements ◽  
High Throughput Sequencing ◽  
Comparative Genomic ◽  
Ltr Retrotransposon ◽  
Genomic Evolution ◽  
Genome Wide ◽  
Genomic Analyses ◽  
Different Types ◽  
Evolutionary Success ◽  
Low Coverage

Abstract Background With the expansion of high throughput sequencing, we now have access to a larger number of genome-wide studies analyzing the Transposable elements (TEs) composition in a wide variety of organisms. However, genomic analyses often remain too limited in number and diversity of species investigated to study in depth the dynamics and evolutionary success of the different types of TEs among metazoans. Therefore, we chose to investigate the use of transcriptomes to describe the diversity of TEs in phylogenetically related species by conducting the first comparative analysis of TEs in two groups of polychaetes and evaluate the diversity of TEs that might impact genomic evolution as a result of their mobility. Results We present a detailed analysis of TEs distribution in transcriptomes extracted from 15 polychaetes depending on the number of reads used during assembly, and also compare these results with additional TE scans on associated low-coverage genomes. We then characterized the clades defined by 1021 LTR-retrotransposon families identified in 26 species. Clade richness was highly dependent on the considered superfamily. Copia elements appear rare and are equally distributed in only three clades, GalEa, Hydra and CoMol. Among the eight BEL/Pao clades identified in annelids, two small clades within the Sailor lineage are new for science. We characterized 17 Gypsy clades of which only 4 are new; the C-clade largely dominates with a quarter of the families. Finally, all species also expressed for the majority two distinct transcripts encoding PIWI proteins, known to be involved in control of TEs mobilities. Conclusions This study shows that the use of transcriptomes assembled from 40 million reads was sufficient to access to the diversity and proportion of the transposable elements compared to those obtained by low coverage sequencing. Among LTR-retrotransposons Gypsy elements were unequivocally dominant but results suggest that the number of Gypsy clades, although high, may be more limited than previously thought in metazoans. For BEL/Pao elements, the organization of clades within the Sailor lineage appears more difficult to establish clearly. The Copia elements remain rare and result from the evolutionary consistent success of the same three clades.

scholarly journals The Popgen Pipeline Platform: A Software Platform for Facilitating Population Genomic Analyses

2019 ◽  
Author(s):  
Andrew Webb ◽  
Jared Knoblauch ◽  
Nitesh Sabankar ◽  
Apeksha Sukesh Kallur ◽  
Jody Hey ◽  
...  
Keyword(s):  
Open Source ◽  
Development Time ◽  
End Users ◽  
File Format ◽  
Software Platform ◽  
Format Conversion ◽  
Link Type ◽  
Population Genomic ◽  
Genomic Analyses ◽  
File Format Conversion

AbstractHere we present the Pop-Gen Pipeline Platform (PPP), a software platform with the goal of reducing the computational expertise required for conducting population genomic analyses. The PPP was designed as a collection of scripts that facilitate common population genomic workflows in a consistent and standardized Python environment. Functions were developed to encompass entire workflows, including: input preparation, file format conversion, various population genomic analyses, output generation, and visualization. By facilitating entire workflows, the PPP offers several benefits to prospective end users - it reduces the need of redundant in-house software and scripts that would require development time and may be error-prone, or incorrect. The platform has also been developed with reproducibility and extensibility of analyses in mind. The PPP is an open-source package that is available for download and use at https://ppp.readthedocs.io/en/latest/PPP_pages/install.html

scholarly journals Author Correction: Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch

2019 ◽  
Vol 51 (7) ◽  
pp. 1187-1189
Author(s):  
Jarkko Salojärvi ◽  
Olli-Pekka Smolander ◽  
Kaisa Nieminen ◽  
Sitaram Rajaraman ◽  
Omid Safronov ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Silver Birch ◽  
Adaptive Landscape ◽  
Population Genomic ◽  
Genomic Analyses

scholarly journals Population Genomic Analyses of Wild and Farmed Striped Catfish Pangasianodon Hypophthalmus in the Lower Mekong River

2020 ◽  
Vol 8 (6) ◽  
pp. 471
Author(s):  
Nguyen Thanh Vu ◽  
Tran Thi Thuy Ha ◽  
Vo Thi Bich Thuy ◽  
Vu Thi Trang ◽  
Nguyen Hong Nguyen
Keyword(s):  
Genetic Diversity ◽  
Mekong River ◽  
Effective Population ◽  
Wild Stock ◽  
Pangasianodon Hypophthalmus ◽  
Population Genomic ◽  
Diversity Assessment ◽  
Genomic Analyses ◽  
In The Wild ◽  
Striped Catfish

The striped catfish Pangasianodon hypophthalmus is an important freshwater fish cultured in many countries where the collection of wild brooders is still widely practiced. Global farming development of this species makes use of significant natural resources that pose challenges for the genetic diversity of striped catfish. Hence, this study aims to conduct a systematic genetic diversity assessment of wild and farmed catfish stocks collected from four major pangasius-farming countries, using a new genotyping by sequencing platform known as DArT-seq technology. Our population genomic analyses using 7263 single-nucleotide polymorphisms (SNPs) after high-quality-control showed that there were two distinct populations of striped catfish in the lower Mekong river: (i) wild catfish from Thailand and (ii) catfish from Cambodia and Vietnam. The genetic diversity was greatest (0.363) in the wild stock from Thailand, but it was lower in farmed and wild stocks in other countries (0.049 to 0.088). The wild stocks were more genetically diverse than the farmed animals (0.103 vs. 0.064). The inbreeding coefficient ranged from 0.004 and 0.109, with the lowest value (−0.499) in the wild animals from Thailand. Molecular inference methods revealed high degree of historical effective population size (1043.9–1258.4), but there was considerable decline in the contemporary estimates in all populations (10.8 to 73.6). Our additional analyses calculating divergent times and migration patterns showed that the wild catfish from Thailand stand out as separate lineages, while those from Cambodia and Vietnam are genetically identical. Our results also indicated that the cultured stock in Bangladesh originated from the lower part of the Mekong river. These findings have significant practical implications in the context of genetic selection and conservation of striped catfish in the region. Collectively, they will contribute to the sustainable development of the striped catfish sector in these countries.

scholarly journals Mitochondrial Ecophysiology: Assessing the Evolutionary Forces That Shape Mitochondrial Variation

2019 ◽  
Vol 59 (4) ◽  
pp. 925-937 ◽  
Author(s):  
Jessica L McKenzie ◽  
Dillon J Chung ◽  
Timothy M Healy ◽  
Reid S Brennan ◽  
Heather J Bryant ◽  
...  
Keyword(s):  
Adaptive Evolution ◽  
Mitochondrial Function ◽  
Fundulus Heteroclitus ◽  
Secondary Contact ◽  
Mitochondrial Genomes ◽  
Evolutionary Forces ◽  
Population Genomic ◽  
Genomic Studies

Abstract The mitonuclear species concept hypothesizes that incompatibilities between interacting gene products of the nuclear and mitochondrial genomes are a major factor establishing and maintaining species boundaries. However, most of the data available to test this concept come from studies of genetic variation in mitochondrial DNA, and clines in the mitochondrial genome across contact zones can be produced by a variety of forces. Here, we show that using a combination of population genomic analyses of the nuclear and mitochondrial genomes and studies of mitochondrial function can provide insight into the relative roles of neutral processes, adaptive evolution, and mitonuclear incompatibility in establishing and maintaining mitochondrial clines, using Atlantic killifish (Fundulus heteroclitus) as a case study. There is strong evidence for a role of secondary contact following the last glaciation in shaping a steep mitochondrial cline across a contact zone between northern and southern subspecies of killifish, but there is also evidence for a role of adaptive evolution in driving differentiation between the subspecies in a variety of traits from the level of the whole organism to the level of mitochondrial function. In addition, studies are beginning to address the potential for mitonuclear incompatibilities in admixed populations. However, population genomic studies have failed to detect evidence for a strong and pervasive influence of mitonuclear incompatibilities, and we suggest that polygenic selection may be responsible for the complex patterns observed. This case study demonstrates that multiple forces can act together in shaping mitochondrial clines, and illustrates the challenge of disentangling their relative roles.

scholarly journals PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses in R

2014 ◽  
Vol 31 (7) ◽  
pp. 1929-1936 ◽  
Author(s):  
Bastian Pfeifer ◽  
Ulrich Wittelsbürger ◽  
Sebastian E. Ramos-Onsins ◽  
Martin J. Lercher
Keyword(s):  
Population Genomic ◽  
Genomic Analyses

scholarly journals Population genomic analyses reveal a history of range expansion and trait evolution across the native and invaded range of yellow starthistle (Centaurea solstitialis)

2017 ◽  
Vol 26 (4) ◽  
pp. 1131-1147 ◽  
Author(s):  
Brittany S. Barker ◽  
Krikor Andonian ◽  
Sarah M. Swope ◽  
Douglas G. Luster ◽  
Katrina M. Dlugosch
Keyword(s):  
Range Expansion ◽  
Centaurea Solstitialis ◽  
Yellow Starthistle ◽  
Trait Evolution ◽  
Population Genomic ◽  
Genomic Analyses ◽  
History Of
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