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Category Archives: next generation sequencing
I do not think it means what you think it means: "relic DNA" can obscure microbial diversity studies
Although microbes are small, they play an important part in both biogeochemical cycles in the ocean as well as on land. However, as they are not so easy to observe by eye, and in many cases can’t be cultured in … Continue reading →
Posted in community, community ecology, microbiology, next generation sequencing
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Tagged community structure, relic DNA, soil microbial diversity
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When the going gets hot the dinoflagellates (sometimes) get going, how viruses might affect coral symbionts
Corals represent more than meets the eye, they host intricate and interesting communities composed of dinoflagellates (also referred to as zooxanthellae), and a suite of microbes that include bacteria, archaea, fungi, protists, and viruses. One such dinoflagellate that often shares … Continue reading →
Posted in community ecology, microbiology, next generation sequencing, RNAseq, transcriptomics
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Tagged coral reef ecology, dinoflagellates, symbiodinium
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There are more microbes than meet the eye: exploring the genomic diversity in an aquifer
First: it’s Tuesday, November 8th, 2016 – before you even think about putting your feet up and reading this post, I hope you’ve managed to wrangle yourself one of those highly prized “I voted” stickers. Now, on to more microbial … Continue reading →
Posted in bioinformatics, community ecology, metagenomics, microbiology, next generation sequencing
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Tagged ecology, genomics, metagenomics
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1 Comment
Gene expression shows how a plant and its mutualists are better together
No living thing is an island, and many of the encounters between living things that happen every day are not antagonistic or even indifferent, but mutually beneficial. Two such mutualisms that could be among the most important on the planet … Continue reading →
Posted in microbiology, next generation sequencing, plants, RNAseq
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Tagged Medicago truncatula, mycorrhizae, rhizobia
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Building bridges across the chaos
In a new review, Eldon and co-authors (in press) attempt to build a bridge across the chaos of genetic patchiness in the sea. They i) describe the patterns characterized as chaotic genetic patchiness, ii) discuss the potential causes of these patterns and … Continue reading →
Is equilibrium out of reach or are there some sneaky bouts of sex?
Reproductive systems impact the evolution of genetic diversity at the population level. Yet, we don’t know a lot about organisms that are partially clonal, despite the large component of biodiversity that dabbles in asexual reproduction to varying degrees. Clonal dynamics are … Continue reading →
Posted in bioinformatics, evolution, genomics, natural history, next generation sequencing, theory
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Tagged clonality, Fis, models, population genomics
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1 Comment
The trouble with PCR duplicates
The sequencing center just sent your lane of Illumina data. You’re excited. Life is great. You begin to process the data. You align the data. You check for PCR duplicates. 50 percent. Half of your data is garbage. Everything is … Continue reading →
Posted in bioinformatics, genomics, methods, next generation sequencing
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Tagged genomics, methods, PCR duplicates, RADseq
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6 Comments
How do Missing Data Impact Phylogenetic Inference with UCEs?
Next-generation sequencing (NGS) has put gobs of sequence data in the hands of molecular biologists, and that data is measurably advancing our prospects for a fully resolved Tree of Life. Nearly simultaneously, however, we have realized that every NGS dataset … Continue reading →
Posted in next generation sequencing, phylogenetics
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Tagged missing data, ultraconserved elements
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2 Comments
Molecular Inversion Probes: phylogenomics without the excess?
The onset of the phylogenomic era has revolutionized molecular ecology and systematics, helping resolve relationships throughout the tree of life that have long eluded researchers working with only a handful of loci and morphological data. Phylogenetic studies of nonmodel organisms … Continue reading →
Posted in genomics, next generation sequencing, phylogenetics, phylogeography, population genetics, transcriptomics
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Tagged MIP, molecular inversion probes
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STITCH, in time, could save a lot of array design
A new algorithm for processing DNA sequence data, STITCH, could lower costs for studies of genetic variation within species by reconstructing, or “imputing”, the sequences of individual samples within a larger dataset. The ongoing proliferation of high-throughput (or, ugh, “next … Continue reading →
Posted in association genetics, bioinformatics, genomics, methods, next generation sequencing, software
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Tagged STITCH
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