Genomic DNA was extracted from fresh leaves using a Plant DNA Isolation Kit (Tiangen, Beijing, China) and sequenced using the MiSeq PE150 platform (Illumina, San Diego, CA, United States), yielding 150 bp paired-end reads, at Novogene Co. (Tianjing, China). The cp genome was de novo assembled using NOVOPlasty (Dierckxsens et al., 2019 (link)) with default parameters. Genomes were annotated using the plastid genome annotator (PGA) tool (Qu et al., 2019 (link)), coupled with manually edited start and stop codons using Geneious (Kearse et al., 2012 (link)). A. mongholicus cp genome sequence (NCBI accession number: NC029828 ) was used as a reference. The annotation results were checked using the Dual Organellar GenoMe Annotator (DOGMA) (Wyman et al., 2004 (link)) and CpGAVAS2 (Shi et al., 2019 (link)). OGDRAW1 (version 1.3.1) (Greiner et al., 2019 (link)) was used to draw the gene map of the cp genomes.
Miseq pe150 platform
Manufactured by Illumina
Sourced in China
The MiSeq PE150 platform is a benchtop sequencing system designed for targeted resequencing, small genome sequencing, and amplicon-based studies. The system generates paired-end reads of up to 150 base pairs in length.
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Lab products found in correlation
2 protocols using miseq pe150 platform
1
De novo assembly and annotation of chloroplast genomes
2
Profiling Gut Microbiome Composition
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Fecal samples were profiled for bacterial taxa using 16S rDNA gene sequencing as previously reported.31 Briefly, microbial DNA was extracted from feces samples using the FastDNA SPIN Kit (MP Biomedicals, Santa Ana, CA) according to the manufacturer’s protocol. Amplification and sequencing of the V4 hypervariable region of the 16S rRNA gene was performed using the validated, region‐specific bacterial primers 515F and 806R. The PCR conditions consisted of an initial denaturation step of 95℃ for 3 minutes; 30 cycles of 98℃ for 1 minute, 98℃ for 10 seconds, 50℃ for 30 seconds, 72℃ for 30 seconds, followed by 72℃ for 5 minutes. Replicate amplicons were pooled and purified using the AxyPrep DNA purification Kit (AXYGEN, Inc, Union City, CA). Subsequently, paired‐end sequencing was performed using the Miseq PE150 platform (Illumina, San Diego, CA). Operational taxonomic units were picked at 97% sequence similarity using the Greengene bacterial database for taxonomy information. Microbial composition at each taxonomic level was defined using the summarize_taxa function in Quantitative Insights Into Microbial Ecology. The abundance of each taxon was calculated by dividing the sequences pertaining to a specific taxon by the total number of bacterial sequences for that sample.
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