Publications by authors named "Zhengshan He"
Background: The era of high throughput sequencing offers new paths to identifying species boundaries that are complementary to traditional morphology-based delimitations. De novo species delimitation using traditional or DNA super-barcodes serve as efficient approaches to recognizing putative species (molecular operational taxonomic units, MOTUs). Tea plants (Camellia sect.
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- - The study focuses on the CAM (crassulacean acid metabolism) photosynthesis in epiphytic plants, particularly exploring the genome of Cymbidium mannii, a type of orchid that utilizes this photosynthetic strategy for adaptation in diverse environments.
- - A detailed genome analysis revealed a 2.88-Gb size with 27,192 genes, highlighting the significant role of repetitive elements and retrotransposon expansions in the plant's genomic evolution.
- - Utilizing advanced techniques like transcriptomics and proteomics, the research discovered oscillating metabolite patterns linked to circadian rhythms, which play a key role in the regulation of CAM photosynthesis, showcasing insights into how plants optimize carbon fixation.
Posttranscriptional modifications, including intron splicing and RNA editing, are common processes during regulation of gene expression in plant organelle genomes. However, the intermediate products of intron-splicing, and the interplay between intron-splicing and RNA-editing were not well studied. Most organelle transcriptome analyses were based on the Illumina short reads which were unable to capture the full spectrum of transcript intermediates within an organelle.
View Article and Find Full Text PDFBackground: Robust phylogenies for species with giant genomes and closely related taxa can build evolutionary frameworks for investigating the origin and evolution of these genomic gigantisms. Paris japonica (Melanthiaceae) has the largest genome that has been confirmed in eukaryotes to date; however, its phylogenetic position remains unresolved. As a result, the evolutionary history of the genomic gigantisms in P.
View Article and Find Full Text PDFComplete plastid genome (plastome) sequences and nuclear ribosomal DNA (nrDNA) regions have been proposed as candidates for the next generation of DNA barcodes for plant species discrimination. However, the efficacy of this approach still lacks comprehensive evaluation. We carried out a case study in the economically important but phylogenetically and taxonomically difficult genus Panax (Araliaceae).
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- The study highlights the challenge of accessing historical DNA from herbarium specimens due to degradation, but new next-generation sequencing (NGS) techniques have made it easier to extract genetic material from these samples.
- Researchers successfully sequenced DNA from 25 herbarium specimens, some up to 80 years old, achieving meaningful results with minimal DNA and sample destruction.
- The findings demonstrate that routine sequencing of plastid genomes from herbarium specimens is not only possible but also more cost-effective compared to traditional methods like Sanger sequencing.