Traditional herbal medicines, basically plant- and fungi-based remedies, have been used for more than 5,000 years. Among those years, tens of thousands of species have been screened for their potential utility as medicines. However, serveral critical factors such as genetic background, agricultural traits and the medical quality of most traditional herbs are poorly understood which slow down the progression on the research. To accelarate the herbal research and to elucidate those factors, “herbal genomics”, as a new discipline, has emerged by sequencing, assembling, and annotating herbal genomes, and by analyzing herbal genes’ function.
Nowadays, sequencing the whole genome to generate chromosomal assemblies is no longer a big deal. Nevertheless, resolving repeat elements is still one of the most important issues for the contiguity of primary assemblies. Long-read technologies from Pacific Biosciences and Oxford Nanopore, which could generate single reads with hundreds of thousands of bases long, provide a great possibility to tackle repeat sequence problems by spanning and resolving most repeat elements. In addition, data generated by Hi-C and related methods using proximity ligation can be applied to stitch sequence contigs into chromosomes. Progressions on assembly and annotation algorithms ensure better results by using less computing power and less time.
As an effective platform, herbal genomics would give an opportunity to investigate the chemical and biological analyses of complicated herbal products that may contain more than one active component to help understand the quality of traditional medicines and for molecular herb identification. Inspirations of workflow and data processing could be drawn from genome sequencing project such as the Darwin Tree of Life Project (DToL), the Earth Biogenome Project (EBP) and Biobank, etc.
Booming of research on traditional herbal medicines requires a close collaboration between diverse communities of researchers by collating specimen metadata and tracking information through identification, DNA barcoding, extraction, sequencing, assembly, curation, annotation, and submission.
This Research Topic aims to give a comprehensive insight into challenges and progressions in Herbal genomics mainly based on long-read sequencing technologies. Collecting and identifying specimens for sequencing is one of the major tasks. Informatic methods and data processing of new herbal genome such as genome assembly, curation, data repositories, and automated workflows that permit high-throughput with reliable quality in every stage would be respectable.
In this Research Topic, we welcome submissions of various article types, including original research papers, reviews, mini-reviews, methods, perspectives, etc., on the following subtopics but not limited to:
1) Herbal genome sample collections and barcoding;
2) Herbal genome assemblies;
3) Assembly pipelines and genome curation;
4) Herbal omics data repositories establishment;
5) Iso-seq genomes: full-length cDNA;
6) DNA methylation in herbs: mechanisms and tools for targeted manipulation.
Traditional herbal medicines, basically plant- and fungi-based remedies, have been used for more than 5,000 years. Among those years, tens of thousands of species have been screened for their potential utility as medicines. However, serveral critical factors such as genetic background, agricultural traits and the medical quality of most traditional herbs are poorly understood which slow down the progression on the research. To accelarate the herbal research and to elucidate those factors, “herbal genomics”, as a new discipline, has emerged by sequencing, assembling, and annotating herbal genomes, and by analyzing herbal genes’ function.
Nowadays, sequencing the whole genome to generate chromosomal assemblies is no longer a big deal. Nevertheless, resolving repeat elements is still one of the most important issues for the contiguity of primary assemblies. Long-read technologies from Pacific Biosciences and Oxford Nanopore, which could generate single reads with hundreds of thousands of bases long, provide a great possibility to tackle repeat sequence problems by spanning and resolving most repeat elements. In addition, data generated by Hi-C and related methods using proximity ligation can be applied to stitch sequence contigs into chromosomes. Progressions on assembly and annotation algorithms ensure better results by using less computing power and less time.
As an effective platform, herbal genomics would give an opportunity to investigate the chemical and biological analyses of complicated herbal products that may contain more than one active component to help understand the quality of traditional medicines and for molecular herb identification. Inspirations of workflow and data processing could be drawn from genome sequencing project such as the Darwin Tree of Life Project (DToL), the Earth Biogenome Project (EBP) and Biobank, etc.
Booming of research on traditional herbal medicines requires a close collaboration between diverse communities of researchers by collating specimen metadata and tracking information through identification, DNA barcoding, extraction, sequencing, assembly, curation, annotation, and submission.
This Research Topic aims to give a comprehensive insight into challenges and progressions in Herbal genomics mainly based on long-read sequencing technologies. Collecting and identifying specimens for sequencing is one of the major tasks. Informatic methods and data processing of new herbal genome such as genome assembly, curation, data repositories, and automated workflows that permit high-throughput with reliable quality in every stage would be respectable.
In this Research Topic, we welcome submissions of various article types, including original research papers, reviews, mini-reviews, methods, perspectives, etc., on the following subtopics but not limited to:
1) Herbal genome sample collections and barcoding;
2) Herbal genome assemblies;
3) Assembly pipelines and genome curation;
4) Herbal omics data repositories establishment;
5) Iso-seq genomes: full-length cDNA;
6) DNA methylation in herbs: mechanisms and tools for targeted manipulation.
