Peering into peer-review at <i>GigaScience</i>

Edmunds, Scott

doi:10.1186/2047-217x-2-1

Cited by 67 publications

(67 citation statements)

References 5 publications

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“…Genome assemblies for Boa constrictor (boa), Python bivittatus (Burmese python), and Ophiophagus hannah (king cobra) have recently become available (Bradnam et al, 2013; Castoe et al, 2013; Vonk et al, 2013). We reasoned that the evolution of limb loss in snakes might lead to substantial sequence divergence or complete loss of genomic regions that function exclusively in the limbs, such as limb-specific cis -regulatory elements.…”

Section: Resultsmentioning

confidence: 99%

Shared Enhancer Activity in the Limbs and Phallus and Functional Divergence of a Limb-Genital cis-Regulatory Element in Snakes

et al. 2015

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Summary The amniote phallus and limbs differ dramatically in their morphologies but share patterns of signaling and gene expression in early development. Thus far, the extent to which genital and limb transcriptional networks also share cis-regulatory elements has remained unexplored. We show that many limb enhancers are retained in snake genomes, suggesting that these elements may function in non-limb tissues. Consistent with this, our analysis of cis-regulatory activity in mice and Anolis lizards reveals that patterns of enhancer activity in embryonic limbs and genitalia overlap heavily. In mice, deletion of HLEB, an enhancer of Tbx4, produces defects in hindlimbs and genitalia, establishing the importance of this limb-genital enhancer for development of these different appendages. Further analyses demonstrate the HLEB of snakes has lost hindlimb enhancer function while retaining genital activity. Our findings identify roles for Tbx4 in genital development and highlight deep similarities in cis-regulatory activity between limbs and genitalia.

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Section: Resultsmentioning

confidence: 99%

Shared Enhancer Activity in the Limbs and Phallus and Functional Divergence of a Limb-Genital cis-Regulatory Element in Snakes

et al. 2015

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“…However, assembly errors are common, and, even with the same input data, alternative assembly algorithms and assembly parameters can result in different assemblies (Earl et al 2011). Multiple methods should be implemented in parallel and compared to achieve the best assembly (Earl et al 2011; Bradnam et al 2013). In addition, reference genomes based on short-read technologies can be greatly improved by including some data from longer-read platforms to generate a hybrid genome assembly (English et al 2012; Koren et al 2012).…”

Section: The Missing Genome: Current Genotyping and Sequencing Approamentioning

confidence: 99%

Finding the Genomic Basis of Local Adaptation: Pitfalls, Practical Solutions, and Future Directions

Hoban

Kelley

Lotterhos

et al. 2016

The American Naturalist

732

876

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Uncovering the genetic and evolutionary basis of local adaptation is a major focus of evolutionary biology. The recent development of cost-effective methods for obtaining high-quality genome-scale data makes it possible to identify some of the loci responsible for adaptive differences among populations. Two basic approaches for identifying putatively locally adaptive loci have been developed and are broadly used: one that identifies loci with unusually high genetic differentiation among populations (differentiation outlier methods) and one that searches for correlations between local population allele frequencies and local environments (genetic-environment association methods). Here, we review the promises and challenges of these genome scan methods, including correcting for the confounding influence of a species’ demographic history, biases caused by missing aspects of the genome, matching scales of environmental data with population structure, and other statistical considerations. In each case, we make suggestions for best practices for maximizing the accuracy and efficiency of genome scans to detect the underlying genetic basis of local adaptation. With attention to their current limitations, genome scan methods can be an important tool in finding the genetic basis of adaptive evolutionary change.

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“…For an estimation of alpha diversity, the data set was rarefied to the same level (67), and the observed OTU richness, Chao 1 (68), and ACE (69) richness estimators, and Shannon (70) diversity indices were calculated and further plotted using the phyloseq package (71). The bacterial community structure (beta diversity) of each treatment and sampling time was evaluated using the weighted UniFrac distances (72) and visualized as principal-coordinate analysis (PCoA) plots using EMPeror (73). The fungal community structure was assessed using Bray-Curtis distances and PCoA plots.…”

mentioning

confidence: 99%

Condensed Tannins Affect Bacterial and Fungal Microbiomes and Mycotoxin Production during Ensiling and upon Aerobic Exposure

Peng

Jin

Niu

et al. 2018

Appl Environ Microbiol

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Purple prairie clover (PPC; Vent.) containing 84.5 g/kg DM of condensed tannin (CT) was ensiled without (Control) or with polyethylene glycol (PEG) for 76 days, followed by 14 days of aerobic exposure. Changes in fermentation characteristics were determined and bacterial and fungal communities were assessed using metagenomic sequencing. Addition of PEG that deactivated CT at ensiling increased ( < 0.05∼0.001) soluble N, non-protein N, lactic acid, total volatile fatty acids, ammonia N, deoxynivalenol (DON) and ochratoxin A (OTA), but decreased ( < 0.001) pH and water soluble carbohydrates. Concentration of DON and OTA increased ( < 0.001) for both silages with the extent of increase being greater for Control than for PEG treated silage during aerobic exposure. The PEG treated silage exhibited higher ( < 0.01∼0.001) copy numbers of total bacteria, , yeasts and fungi than Control. Addition of PEG decreased ( < 0.01) bacterial diversity during both ensiling and aerobic exposure, whereas it increased ( < 0.05) fungal diversity during aerobic exposure. Addition of PEG at ensiling increased ( < 0.05) abundances of and, but decreased ( < 0.01) abundances of and Filamentous fungi were found in the microbiome at ensiling and after aerobic exposure, whereas the were the dominate bacteria after aerobic exposure. In conclusion, CT decreased protein degradation and improved aerobic stability of silage. These desirable outcomes likely reflect the ability of PPC CT to inhibit those microorganisms involved in lowering silage quality and in the production of mycotoxins. The present study reports the effects of condensed tannins on the complex microbial communities involved in ensiling and aerobic exposure of purple prairie clover. This study documents the ability of condensed tannins to lower mycotoxin production and associated microbiome. Taxonomic bacterial community profiles were dominated by the after fermentation, with a notable increase in as a result of aerobic exposure. It is interesting to observe that condensed tannins decreased bacterial diversity during both ensiling and aerobic exposure but increased fungal diversity during aerobic exposure only. The present study indicates that the effects of condensed tannins on microbial communities lead to a reduced lactic acid and total volatile fatty acids production, proteolysis and mycotoxin concentration in the terminal silage and an improved aerobic stability. Condensed tannins could be used as additive to control unfavorable microbial development and maybe enhanced feed safety.

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Peering into peer-review at GigaScience

Cited by 67 publications

References 5 publications

Shared Enhancer Activity in the Limbs and Phallus and Functional Divergence of a Limb-Genital cis-Regulatory Element in Snakes

Shared Enhancer Activity in the Limbs and Phallus and Functional Divergence of a Limb-Genital cis-Regulatory Element in Snakes

Finding the Genomic Basis of Local Adaptation: Pitfalls, Practical Solutions, and Future Directions

Condensed Tannins Affect Bacterial and Fungal Microbiomes and Mycotoxin Production during Ensiling and upon Aerobic Exposure

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