Applications of High Throughput Sequencing Technologies in Forest and Other Species

Dear Colleagues,

Long-read sequencing technologies including PacBio and Oxford Nanopore sequencing provide unprecedented opportunities for forestry to overcome the disadvantage of short reads, especially for gymnosperm genome. At genome-wide level, PacBio or Nanopore has far superior contiguity for forestry genome assembly due to the long reads. At transcriptome level, both PacBio and Oxford Nanopore Technologies sequence single molecules can detect post-transcriptional regulation, including complex alternative splicing (AS), full-length splice variants, fusion transcripts, and alternative polyadenylation (APA) events, which contribute to transcriptome diversity. In addition, direct RNA-Seq based on an Oxford Nanopore Technologies sequence provides valuable information about RNA modifications, which are lost during PCR amplification in other methods.

However, the analysis of PacBio and Oxford Nanopore long-read data comes with new technical challenges, such as lack of genomic reference and high-quality gene annotations for non-model forestry species, such as gymnosperm. Both new experimental and bioinformatics method are needed to fully utilize the advantage of long-read sequencing for forestry genomics and transcriptomics research. In this SI, we welcome submission on reviews or original research that uses high throughput sequencing technology to address biological question in forestry and other species, or bioinformatics methods/computational tools or database for sequence data analysis in plant genomics and transcriptomics areas.

Prof. Dr. Lianfeng Gu
Guest Editor

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