In vitro, long-range sequence information for de novo genome assembly via transposase contiguity

Adey, Andrew; Kitzman, Jacob O.; Burton, Joshua N.; Daza, Riza M.; Kumar, Akash; Christiansen, Lena; Ronaghi, Mostafa; Amini, Sasan; Gunderson, Kevin L.; Steemers, Frank J.; Shendure, Jay

doi:10.1101/gr.178319.114

Cited by 158 publications

(143 citation statements)

References 39 publications

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“…We used BWA mem to align the 10X Genomics data to the filled gaps assembly using default settings. Then, we used fragScaff 38 for scaffolding. The options were as follows: A. shenzhenica (stages1 "-m 3000 -q 30"; stages2 "-C 2"; stages3 "-j 1.25 -u 2"), D. catenatum (stages1 "-m 3000 -q 30"; stages2 "-C 1"; stages3 "-j 2 -u 2") and P. equestris (stages1 "-m 3000 -q 30"; stages2 "-C 1"; stages3 "-j 2 -u 2") 39 .…”

Section: Methodsmentioning

confidence: 99%

The Apostasia genome and the evolution of orchids

Zhang¹,

Liu²,

et al. 2017

Nature

315

347

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Constituting approximately 10% of flowering plant species, orchids (Orchidaceae) display unique flower morphologies, possess an extraordinary diversity in lifestyle, and have successfully colonized almost every habitat on Earth 1-3 . Here we report the draft genome sequence of Apostasia shenzhenica 4 , a representative of one of two genera that form a sister lineage to the rest of the Orchidaceae, providing a reference for inferring the genome content and structure of the most recent common ancestor of all extant orchids and improving our understanding of their origins and evolution. In addition, we present transcriptome data for representatives of Vanilloideae, Cypripedioideae and Orchidoideae, and novel thirdgeneration genome data for two species of Epidendroideae, covering all five orchid subfamilies. A. shenzhenica shows clear evidence of a whole-genome duplication, which is shared by all orchids and occurred shortly before their divergence. Comparisons between A. shenzhenica and other orchids and angiosperms also permitted the reconstruction of an ancestral orchid gene toolkit. We identify new gene families, gene family expansions and contractions, and changes within MADS-box gene classes, which control a diverse suite of developmental processes, during orchid evolution. This study sheds new light on the genetic mechanisms underpinning key orchid innovations, including the development of the labellum and gynostemium, pollinia, and seeds without endosperm, as well as the evolution of epiphytism; reveals relationships between the Orchidaceae subfamilies; and helps clarify the evolutionary history of orchids within the angiosperms.

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Section: Methodsmentioning

confidence: 99%

The Apostasia genome and the evolution of orchids

Zhang¹,

Liu²,

et al. 2017

Nature

315

347

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“…Illumina's TruSeq Synthetic Long-Read technology, previously referred to as Moleculo, is based on fragmenting genomic DNA to approximately 10 kb fragments, their clonal amplification, shearing, and indexing with a unique barcode. Similarly, contiguity preserving transposase sequencing from Illumina provide in vitro means of generating libraries comprised of thousands of indexed pools, each containing thousands of sparsely sequenced long fragments, ranging from 5 kb up to 1 megabase [130]. The Chromium platform (10× Genomics) provides synthetic long reads by partitioning and barcoding the genome, followed by sequencing on any NGS platform.…”

Section: Emerging Technologies Facilitating Biomarker Discoverymentioning

confidence: 99%

Pharmacogenomic Biomarkers for Improved Drug Therapy—Recent Progress and Future Developments

Lauschke

Milani

Ingelman‐Sundberg

2017

AAPS J

120

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Abstract.Much of the inter-individual variability in drug efficacy and risk of adverse reactions is due to polymorphisms in genes encoding proteins involved in drug pharmacokinetics and pharmacodynamics or immunological responses. Pharmacogenetic research has identified a multitude of gene-drug response associations, which have resulted in genetically guided treatment and dosing decisions to yield a higher success rate of pharmacological treatment. The rapid technological developments for genetic analyses reveal that the number of genetic variants with importance for drug action is much higher than previously thought and that a true personalized prediction of drug response requires attention to millions of rare mutations. Here, we review the evolutionary background of genetic polymorphisms in drugmetabolizing enzymes, provide some important examples of current use of pharmacogenomic biomarkers, and give an update of germline and somatic genome biomarkers that are in use in drug development and clinical practice. We also discuss the current technology development with emphasis on complex genetic loci, review current initiatives for validation of pharmacogenomic biomarkers, and present scenarios for the future taking rare genetic variants into account for a true personalized genetically guided drug prescription. We conclude that pharmacogenomic information for patient stratification is of value to tailor optimized treatment regimens particularly in oncology. However, the routine use of pharmacogenomic biomarkers in clinical practice in other therapeutic areas is currently sparse and the prospects of its future implementation are being scrutinized by different international consortia.

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“…To assess the performance of nucleosome depletion with our single cell combinatorial indexing workflow, we chose to first focus on the euploid lymphoblastoid cell line GM12878, as it is in abundant supply and has been deeply profiled by a number of studies 13,14,18 . In order to test different Lithium diiodosalycylate concentrations and flow sorting conditions for the LAND method of nucleosome depletion, we generated seven SCI-seq libraries, six of which were successful with the seventh failing due to poor FANS gating on the second (post-transposition) sort.…”

Section: Sci-seq With Nucleosome Depletionmentioning

confidence: 99%

“…The nuclei remain intact during this process, thus utilizing the nuclear scaffold itself as an individual reaction compartment that contains an indexed sequencing library representative of regions of open chromatin. Furthermore, the transposase complex remains tightly bound after adaptor incorporation 13,14 , which prevents individual library molecules from diffusing out of the nucleus. The set of 96 wells are then pooled and then 15-25 of these randomly indexed nuclei are deposited by a second round of FANS into each well of one or more new 96-well plates.…”

Section: Introductionmentioning

confidence: 99%

“…Recently, we established a method to simultaneously produce thousands of individually barcoded libraries of linked sequence reads using a combinatorial indexing strategy with transposase-based library construction 12 and applied the technology to haplotype resolution 13 as well as contig scaffolding for de novo genome assembly 14 . The combinatorial indexing concept, which involves two tiers of library indexing (transposase stage and PCR stage) was integrated with the widely utilized assay for transposase accessible chromatin (ATAC-seq) 15 , to simultaneously produce profiles of active regulatory elements in thousands of single cells 16 (scATAC-seq, Fig.…”

Section: Introductionmentioning

confidence: 99%

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Construction of thousands of single cell genome sequencing libraries using combinatorial indexing

Vitak

Torkenczy

Rosenkrantz

et al. 2016

Preprint

Self Cite

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Single cell genome sequencing has proven to be a valuable tool for the detection of somatic variation, particularly in the context of tumor evolution and neuronal heterogeneity. Current technologies suffer from high per-cell library construction costs which restrict the number of cells that can be assessed, thus imposing limitations on the ability to quantitatively measure genomic heterogeneity within a tissue. Here, we present Single cell Combinatorial Indexed Sequencing (SCI-seq) as a means of simultaneously generating thousands of low-pass single cell libraries for the purpose of somatic copy number variant detection. In total, we constructed libraries for 16,698 single cells from a combination of cultured cell lines, frontal cortex tissue from Macaca mulatta, and two human adenocarcinomas. This novel technology provides the opportunity for low-cost, deep characterization of somatic copy number variation in single cells, providing a foundational knowledge across both healthy and diseased tissues.peer-reviewed)

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In vitro, long-range sequence information for de novo genome assembly via transposase contiguity

Cited by 158 publications

References 39 publications

The Apostasia genome and the evolution of orchids

The Apostasia genome and the evolution of orchids

Pharmacogenomic Biomarkers for Improved Drug Therapy—Recent Progress and Future Developments

Construction of thousands of single cell genome sequencing libraries using combinatorial indexing

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