scholarly journals Characterization of the leaf microbiome from whole-genome sequencing data of the 3000 rice genomes project.

2020 ◽  
Author(s):  
Veronica Roman-Reyna ◽  
Dale Pinili ◽  
Frances Nikki Borja ◽  
Ian Lorenzo Quibod ◽  
Simon C. Groen ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Crop Improvement ◽  
Rice Genome ◽  
Plant Genome ◽  
Whole Genome Sequencing Data ◽  
Sequencing Data ◽  
Rice Leaf ◽  
Relative Contribution ◽  
Bacterial Microbiome ◽  
Host Microbe Interactions

Abstract Background: The crop microbial communities are shaped by interactions between the host, microbes and the environment, however, their relative contribution is beginning to be understood. Here, we explore these interactions in the leaf bacterial community across 3,024 rice accessions. Findings: By using unmapped DNA sequencing reads as microbial reads, we characterized the structure of the rice bacterial microbiome. We identified central bacteria taxa that emerge as microbial “hubs” and may have an influence on the network of host-microbe interactions. We found regions in the rice genome that might control the assembly of these microbial hubs. To our knowledge this is one of the first studies that uses raw data from plant genome sequencing projects to characterize the leaf bacterial communities. Conclusion: We showed, that the structure of the rice leaf microbiome is modulated by multiple interactions among host, microbes, and environment. Our data provide insight into the factors influencing microbial assemblage in the rice leaf and also opens the door for future initiatives to modulate rice consortia for crop improvement efforts.

scholarly journals Characterization of the Leaf Microbiome from Whole-Genome Sequencing Data of the 3000 Rice Genomes Project

Rice ◽  
2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Veronica Roman-Reyna ◽  
Dale Pinili ◽  
Frances N. Borja ◽  
Ian L. Quibod ◽  
Simon C. Groen ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Crop Improvement ◽  
Rice Genome ◽  
Plant Genome ◽  
Whole Genome Sequencing Data ◽  
Sequencing Data ◽  
Rice Leaf ◽  
Relative Contribution ◽  
Bacterial Microbiome ◽  
Host Microbe Interactions

Abstract Background The crop microbial communities are shaped by interactions between the host, microbes and the environment, however, their relative contribution is beginning to be understood. Here, we explore these interactions in the leaf bacterial community across 3024 rice accessions. Findings By using unmapped DNA sequencing reads as microbial reads, we characterized the structure of the rice bacterial microbiome. We identified central bacteria taxa that emerge as microbial “hubs” and may have an influence on the network of host-microbe interactions. We found regions in the rice genome that might control the assembly of these microbial hubs. To our knowledge this is one of the first studies that uses raw data from plant genome sequencing projects to characterize the leaf bacterial communities. Conclusion We showed, that the structure of the rice leaf microbiome is modulated by multiple interactions among host, microbes, and environment. Our data provide insight into the factors influencing microbial assemblage in the rice leaf and also opens the door for future initiatives to modulate rice consortia for crop improvement efforts.

scholarly journals Characterization of the leaf microbiome from whole-genome sequencing data of the 3000 rice genomes project.

2020 ◽  
Author(s):  
Veronica Roman-Reyna ◽  
Dale Pinili ◽  
Frances Nikki Borja ◽  
Ian Lorenzo Quibod ◽  
Simon C. Groen ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Crop Improvement ◽  
Rice Genome ◽  
Plant Genome ◽  
Whole Genome Sequencing Data ◽  
Sequencing Data ◽  
Rice Leaf ◽  
Relative Contribution ◽  
Bacterial Microbiome ◽  
Host Microbe Interactions

Abstract Background: The crop microbial communities are shaped by interactions between the host, microbes and the environment, however, their relative contribution is beginning to be understood. Here, we explore these interactions in the leaf bacterial community across 3,024 rice accessions. Findings: By using unmapped DNA sequencing reads as microbial reads, we characterized the structure of the rice bacterial microbiome. We identified central bacteria taxa that emerge as microbial “hubs” and may have an influence on the network of host-microbe interactions. We found regions in the rice genome that might control the assembly of these microbial hubs. To our knowledge this is one of the first studies that uses raw data from plant genome sequencing projects to characterize the leaf bacterial communities. Conclusion: We showed, that the structure of the rice leaf microbiome is modulated by multiple interactions among host, microbes, and environment. Our data provide insight into the factors influencing microbial assemblage in the rice leaf and also opens the door for future initiatives to modulate rice consortia for crop improvement efforts.

scholarly journals Characterization of the leaf microbiome from whole-genome sequencing data of the 3000 rice genomes project

2020 ◽  
Author(s):  
Veronica Roman-Reyna ◽  
Dale Pinili ◽  
Frances Nikki Borja ◽  
Ian Lorenzo Quibod ◽  
Simon C. Groen ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Crop Improvement ◽  
Rice Genome ◽  
Plant Genome ◽  
Whole Genome Sequencing Data ◽  
Sequencing Data ◽  
Rice Leaf ◽  
Relative Contribution ◽  
Bacterial Microbiome ◽  
Host Microbe Interactions

Abstract Background: The crop microbial communities are shaped by interactions between the host, microbes and the environment, however, their relative contribution is beginning to be understood. Here, we explore these interactions in the leaf bacterial community across 3,024 rice accessions.Findings: By using unmapped DNA sequencing reads as microbial reads, we characterized the structure of the rice bacterial microbiome. We identified central bacteria taxa that emerge as microbial “hubs” and may have an influence on the network of host-microbe interactions. We found regions in the rice genome that might control the assembly of these microbial hubs. To our knowledge this is one of the first studies that uses raw data from plant genome sequencing projects to characterize the leaf bacterial communities. Conclusion: We showed, that the structure of the rice leaf microbiome is modulated by multiple interactions among host, microbes, and environment. Our data provide insight into the factors influencing microbial assemblage in the rice leaf and also opens the door for future initiatives to modulate rice consortia for crop improvement efforts.

scholarly journals T-lex3: an accurate tool to genotype and estimate population frequencies of transposable elements using the latest short-read whole genome sequencing data

2019 ◽  
Author(s):  
María Bogaerts-Márquez ◽  
Maite G Barrón ◽  
Anna-Sophie Fiston-Lavier ◽  
Pol Vendrell-Mir ◽  
Raúl Castanera ◽  
...  
Keyword(s):  
Transposable Elements ◽  
High Throughput Sequencing ◽  
Rice Genome ◽  
Significant Proportion ◽  
Plant Genome ◽  
Supplementary Information ◽  
Whole Genome Sequencing Data ◽  
Sequencing Data ◽  
Short Read ◽  
Minimum Number

Abstract Motivation Transposable elements (TEs) constitute a significant proportion of the majority of genomes sequenced to date. TEs are responsible for a considerable fraction of the genetic variation within and among species. Accurate genotyping of TEs in genomes is therefore crucial for a complete identification of the genetic differences among individuals, populations and species. Results In this work, we present a new version of T-lex, a computational pipeline that accurately genotypes and estimates the population frequencies of reference TE insertions using short-read high-throughput sequencing data. In this new version, we have re-designed the T-lex algorithm to integrate the BWA-MEM short-read aligner, which is one of the most accurate short-read mappers and can be launched on longer short-reads (e.g. reads >150 bp). We have added new filtering steps to increase the accuracy of the genotyping, and new parameters that allow the user to control both the minimum and maximum number of reads, and the minimum number of strains to genotype a TE insertion. We also showed for the first time that T-lex3 provides accurate TE calls in a plant genome. Availability and implementation To test the accuracy of T-lex3, we called 1630 individual TE insertions in Drosophila melanogaster, 1600 individual TE insertions in humans, and 3067 individual TE insertions in the rice genome. We showed that this new version of T-lex is a broadly applicable and accurate tool for genotyping and estimating TE frequencies in organisms with different genome sizes and different TE contents. T-lex3 is available at Github: https://github.com/GonzalezLab/T-lex3. Supplementary information Supplementary data are available at Bioinformatics online.

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

Heredity ◽  
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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