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A resource for characterizing genome‐wide binding and putative target genes of transcription factors expressed during secondary growth and wood formation in Populus
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Lijun Liu Trevor Ramsay Matthew Zinkgraf David Sundell Nathaniel Robert Street Vladimir Filkov Andrew Groover 《The Plant journal : for cell and molecular biology》2015,82(5):887-898
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Transcriptional regulatory networks underlying gene expression changes in Huntington's disease
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![点击此处可从《Molecular systems biology》网站下载免费的PDF全文](/ch/ext_images/free.gif)
Jeffrey P Cantle Robert M Bragg Peter J Skene Sydney R Coffey Dani E Bergey Vanessa C Wheeler Marcy E MacDonald Nitin S Baliga Jim Rosinski Leroy E Hood Jeffrey B Carroll Nathan D Price 《Molecular systems biology》2018,14(3)
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Coline C. Jaworski Carson W. Allan Luciano M. Matzkin 《Molecular ecology resources》2020,20(5):1277-1293
The emergence of third‐generation sequencing (3GS; long‐reads) is bringing closer the goal of chromosome‐size fragments in de novo genome assemblies. This allows the exploration of new and broader questions on genome evolution for a number of nonmodel organisms. However, long‐read technologies result in higher sequencing error rates and therefore impose an elevated cost of sufficient coverage to achieve high enough quality. In this context, hybrid assemblies, combining short‐reads and long‐reads, provide an alternative efficient and cost‐effective approach to generate de novo, chromosome‐level genome assemblies. The array of available software programs for hybrid genome assembly, sequence correction and manipulation are constantly being expanded and improved. This makes it difficult for nonexperts to find efficient, fast and tractable computational solutions for genome assembly, especially in the case of nonmodel organisms lacking a reference genome or one from a closely related species. In this study, we review and test the most recent pipelines for hybrid assemblies, comparing the model organism Drosophila melanogaster to a nonmodel cactophilic Drosophila, D. mojavensis. We show that it is possible to achieve excellent contiguity on this nonmodel organism using the dbg2olc pipeline. 相似文献
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Substantial differences in bias between single‐digest and double‐digest RAD‐seq libraries: A case study
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The trade‐offs of using single‐digest vs. double‐digest restriction site‐associated DNA sequencing (RAD‐seq) protocols have been widely discussed. However, no direct empirical comparisons of the two methods have been conducted. Here, we sampled a single population of Gulf pipefish (Syngnathus scovelli) and genotyped 444 individuals using RAD‐seq. Sixty individuals were subjected to single‐digest RAD‐seq (sdRAD‐seq), and the remaining 384 individuals were genotyped using a double‐digest RAD‐seq (ddRAD‐seq) protocol. We analysed the resulting Illumina sequencing data and compared the two genotyping methods when reads were analysed either together or separately. Coverage statistics, observed heterozygosity, and allele frequencies differed significantly between the two protocols, as did the results of selection components analysis. We also performed an in silico digestion of the Gulf pipefish genome and modelled five major sources of bias: PCR duplicates, polymorphic restriction sites, shearing bias, asymmetric sampling (i.e., genotyping fewer individuals with sdRAD‐seq than with ddRAD‐seq) and higher major allele frequencies. This combination of approaches allowed us to determine that polymorphic restriction sites, an asymmetric sampling scheme, mean allele frequencies and to some extent PCR duplicates all contribute to different estimates of allele frequencies between samples genotyped using sdRAD‐seq versus ddRAD‐seq. Our finding that sdRAD‐seq and ddRAD‐seq can result in different allele frequencies has implications for comparisons across studies and techniques that endeavour to identify genomewide signatures of evolutionary processes in natural populations. 相似文献
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