Fresh leaves of U. mianzhuensis were collected from Central Forest Tree Nursery in Sichuan, China and stored in silica gel prior. The voucher specimen (Deng11468) was deposited in the Herbarium of Henan Agricultural University. For this species, 50 mg dried leaves were ground and high-quality genomic DNAs were extracted using a Plant Genomic DNA Extraction Kit (Tiangen, Beijing, China), and then were subsequently sent to Novogene (http://www.novogene.com , China) for short insert (350 bp) library construction and next-generation sequencing by Illumina Hiseq 4000 genome analyzer platform (Illumina, San Diego, CA) by Novogene, Beijing, China. Raw reads from the paired-end for quality were filtered with the NGSQC ToolKit by removing adapter sequences and low-quality reads with Q value B20 [52 (link)]. Then the clean data were assembled by NOVOPlasty 2.6.3 [53 (link)]and annotated by GeSeq [54 (link)], and the results were manually checked and verified in Geneious v.9.1 according to Ulmus parvifolia (MT165940) [55 (link)]. The visualization of the cp genome map was performed in OGDRAW [56 (link)].
Hiseq 4000 genome analyzer platform
Manufactured by Illumina
The HiSeq 4000 is a high-throughput genome analyzer platform produced by Illumina. It is designed to perform large-scale sequencing of DNA samples. The core function of the HiSeq 4000 is to generate high-quality sequencing data by leveraging Illumina's SBS (Sequencing by Synthesis) technology.
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Lab products found in correlation
2 protocols using hiseq 4000 genome analyzer platform
1
Chloroplast Genome Sequencing of Ulmus mianzhuensis
2
Genomic DNA Extraction and Sequencing
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Leaf material for DNA extraction was dried using silica gel (Chase & Hills, 1991 (link)). Genomic DNA was extracted using a modified CTAB protocol (Chen et al., 2014 (link)) and assessed by agarose gel electrophoresis. The total gDNA sample was sent to Majorbio (http://www.majorbio.com/ , China) for library construction and next-generation sequencing. Short-insert (350 bp) paired-end read libraries preparation and 2 × 150 bp sequencing were performed on an Illumina (HiSeq4000) genome analyzer platform. Approximately 2 Gb of raw data for the new species was filtered using the FASTX-Toolkit to obtain high-quality clean data by removing adaptors and low-quality reads (http://hannonlab.cshl.edu/fastx_toolkit/download.html ).
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