scholarly journals Development of Species-Specific Microsatellite Markers for Broomcorn Millet (Panicum miliaceum L.) via High-Throughput Sequencing

2017 ◽  
Vol 05 (04) ◽  
Author(s):  
Min Xuan Liu ◽  
Yue Xu ◽  
Tian Yu Yang ◽  
Zhi Jun Qiao ◽  
Rui Yun Wang ◽  
...  
Keyword(s):  
Microsatellite Markers ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Panicum Miliaceum ◽  
Broomcorn Millet ◽  
Species Specific

scholarly journals Development and Characterization of Novel Microsatellite Markers for a Dominant Parasitoid (Stethynium Empoasca) in Tea Plantations Using High-throughput Sequencing

2020 ◽  
Author(s):  
Jinyu Li ◽  
Longqing Shi ◽  
Jie Chen ◽  
Minsheng You ◽  
Shijun You
Keyword(s):  
Biological Control ◽  
Gene Flow ◽  
Genetic Differentiation ◽  
Microsatellite Markers ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Control Strategies ◽  
Null Alleles ◽  
Individual Gene ◽  
Tea Plantations

Abstract Background: Stethynium empoasca is an egg parasitoid of the predominant tea pest, and is regarded as the most promising candidate for both augmentative and conservative biological control in tea plantations. However, little is presently known about its biology, ecology, and genetics. Methods: Novel microsatellite markers were developed for S. empoasca from transcriptome sequences generated using high-throughput sequencing. The identified markers were then validated and characterized using 98 individuals from five geographically distinct populations through the tests of Hardy–Weinberg equilibrium and linkage disequilibrium as well as the analyses of genetic diversity, genetic differentiation, and gene flow.Results: A total of 54,520 microsatellites were identified from 117Mb clean sequences. By assessing with five geographical populations, a total of 18 loci were demonstrated to be polymorphic, stable, and repetitive. The genetic variation over the 18 loci varied with allele number ranging from 2 to 7, polymorphism information content from 0.234 to 0.634; and observed and expected heterozygosity from 0.166 to 0.686 and 0.276 to 0.753, respectively. Meanwhile, the 18 loci showed a low frequency of null alleles (0 – 0.107), and the inbreeding coefficient revealed a range from −0.143 to 0.173, with the exception of loci Ste36 (0.4076). Based on analysis of these 18 loci, the assessed populations showed low to moderate levels of genetic differentiation, in which individuals clearly grouped into two clusters. And the recent dispersal rates between the geographically distinct populations were identified to be much lower (0.011 – 0.250) than the individual gene exchange rates within a population (0.683 – 0.939).Conclusion: The identified 18 microsatellite markers could reveal a pattern of spatial structure and gene flow in S. empoasca populations according to geographic variability. This work provides an important basis for future studies on how these markers can be used in studies of the biology, genetics, and ecology of this important parasitoid. The findings can further provide important information for the development of biological control strategies in tea plantations. Additionally, our study reaffirms the importance and efficiency of high-throughput sequencing in microsatellite marker development for non-model species lacking reference genome information.

scholarly journals Development of Novel Microsatellite Markers for the BBCC Oryza Genome (Poaceae) Using High-Throughput Sequencing Technology

PLoS ONE ◽  
2014 ◽  
Vol 9 (3) ◽  
pp. e91826 ◽  
Author(s):  
Caihong Wang ◽  
Xiaojiao Liu ◽  
Suotang Peng ◽  
Qun Xu ◽  
Xiaoping Yuan ◽  
...  
Keyword(s):  
Microsatellite Markers ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Sequencing Technology

scholarly journals Variation in δD values of a single, species-specific molecular biomarker: a study of miliacin throughout a field of broomcorn millet (Panicum miliaceum L.)

2011 ◽  
Vol 25 (19) ◽  
pp. 2732-2740 ◽  
Author(s):  
Nicolas Bossard ◽  
Jérémy Jacob ◽  
Claude Le Milbeau ◽  
Elisabeth Lallier-Vergès ◽  
Valery J. Terwilliger ◽  
...  
Keyword(s):  
Single Species ◽  
Panicum Miliaceum ◽  
Molecular Biomarker ◽  
Broomcorn Millet ◽  
Species Specific

scholarly journals OGRE: Overlap Graph-based metagenomic Read clustEring

2020 ◽  
Author(s):  
Marleen Balvert ◽  
Xiao Luo ◽  
Ernestina Hauptfeld ◽  
Alexander Schönhuth ◽  
Bas E Dutilh
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Computation Time ◽  
Supplementary Information ◽  
Sequencing Data ◽  
High Throughput Sequencing Data ◽  
Computationally Intensive ◽  
Metagenome Sequencing ◽  
Species Specific ◽  
Cluster Purity

Abstract Motivation The microbes that live in an environment can be identified from the combined genomic material, also referred to as the metagenome. Sequencing a metagenome can result in large volumes of sequencing reads. A promising approach to reduce the size of metagenomic datasets is by clustering reads into groups based on their overlaps. Clustering reads are valuable to facilitate downstream analyses, including computationally intensive strain-aware assembly. As current read clustering approaches cannot handle the large datasets arising from high-throughput metagenome sequencing, a novel read clustering approach is needed. In this article, we propose OGRE, an Overlap Graph-based Read clustEring procedure for high-throughput sequencing data, with a focus on shotgun metagenomes. Results We show that for small datasets OGRE outperforms other read binners in terms of the number of species included in a cluster, also referred to as cluster purity, and the fraction of all reads that is placed in one of the clusters. Furthermore, OGRE is able to process metagenomic datasets that are too large for other read binners into clusters with high cluster purity. Conclusion OGRE is the only method that can successfully cluster reads in species-specific clusters for large metagenomic datasets without running into computation time- or memory issues. Availabilityand implementation Code is made available on Github (https://github.com/Marleen1/OGRE). Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Can DNA-based ecosystem assessments quantify species abundance? Testing primer bias and biomass - sequence relationships with an innovative metabarcoding protocol

2015 ◽  
Author(s):  
Vasco Elbrecht ◽  
Florian Leese
Keyword(s):  
High Throughput ◽  
Statistical Power ◽  
High Throughput Sequencing ◽  
Species Abundance ◽  
Reference Database ◽  
Dna Metabarcoding ◽  
Coi Barcoding ◽  
Species Abundances ◽  
Species Specific ◽  
Sequence Relationships

Metabarcoding is an emerging genetic tool to rapidly assess biodiversity in ecosystems. It involves high-throughput sequencing of a standard gene from an environmental sample and comparison to a reference database. However, no consensus has emerged regarding laboratory pipelines to screen species diversity and infer species abundances from environmental samples. In particular, the effect of primer bias and the detection limit for specimens with a low biomass has not been systematically examined, when processing samples in bulk. We developed and tested a DNA metabarcoding protocol that utilises the standard cytochrome c oxidase subunit I (COI) barcoding fragment to detect freshwater macroinvertebrate taxa. DNA was extracted in bulk, amplified in a single PCR step, and purified, and the libraries were directly sequenced in two independent MiSeq runs (300-bp paired-end reads). Specifically, we assessed the influence of specimen biomass on sequence read abundance by sequencing 31 specimens of a stonefly species with known haplotypes spanning three orders of magnitude in biomass (experiment I). Then, we tested the recovery of 52 different freshwater invertebrate taxa of similar biomass using the same standard barcoding primers (experiment II). Each experiment was replicated ten times to maximise statistical power. The results of both experiments were consistent across replicates. We found a distinct positive correlation between species biomass and resulting numbers of MiSeq reads. Furthermore, we reliably recovered 83% of the 52 taxa used to test primer bias. However, sequence abundance varied by four orders of magnitudes between taxa despite the use of similar amounts of biomass. Our metabarcoding approach yielded reliable results for high-throughput assessments. However, the results indicated that primer efficiency is highly species-specific, which would prevent straightforward assessments of species abundance and biomass in a sample. Thus, PCR-based metabarcoding assessments of biodiversity should rely on presence-absence metrics.

Successful development of microsatellite markers in a challenging species: the horizontal borer Austroplatypus incompertus (Coleoptera: Curculionidae)

2011 ◽  
Vol 101 (5) ◽  
pp. 551-555 ◽  
Author(s):  
S. Smith ◽  
T. Joss ◽  
A. Stow
Keyword(s):  
Microsatellite Markers ◽  
High Throughput ◽  
Evolutionary Biology ◽  
High Throughput Sequencing ◽  
Genomic Library ◽  
454 Sequencing ◽  
Cost Effective ◽  
Microsatellite Isolation ◽  
Potential Benefits ◽  
Neutral Markers

AbstractThe analysis of microsatellite loci has allowed significant advances in evolutionary biology and pest management. However, until very recently, the potential benefits have been compromised by the high costs of developing these neutral markers. High-throughput sequencing provides a solution to this problem. We describe the development of 13 microsatellite markers for the eusocial ambrosia beetle, Austroplatypus incompertus, a significant pest of forests in southeast Australia. The frequency of microsatellite repeats in the genome of A. incompertus was determined to be low, and previous attempts at microsatellite isolation using a traditional genomic library were problematic. Here, we utilised two protocols, microsatellite-enriched genomic library construction and high-throughput 454 sequencing and characterised 13 loci which were polymorphic among 32 individuals. Numbers of alleles per locus ranged from 2 to 17, and observed and expected heterozygosities from 0.344 to 0.767 and from 0.507 to 0.860, respectively. These microsatellites have the resolution required to analyse fine-scale colony and population genetic structure. Our work demonstrates the utility of next-generation 454 sequencing as a method for rapid and cost-effective acquisition of microsatellites where other techniques have failed, or for taxa where marker development has historically been both complicated and expensive.

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