Dynamics and complexity of genomes and transcriptomes underpin various aspects of plant growth, development, and responses to biotic and abiotic signals. Long read sequencing technologies, such as PacBio and Oxford Nanopore sequencing, have increased the length of a single contiguous read significantly from a few hundred to thousands or even millions of base pairs and thus overcame the limitation of second-generation sequencing. The increased read lengths have enabled the development of new analysis strategies and tools for plant genomics and transcriptomics. Long reads have been used to improve genome assembly in repetitive regions, to produce more complete and precise positioning of genomic loci, to assemble full-length transcripts, and identify DNA and RNA modifications. It enables detecting of alternative splicing, alternative polyadenylation, and alternative transcription initiation site which contribute to transcriptome diversity. However, the analysis of long-read data comes with new technical challenges, such as high error rates and limited coverage due to the high sequencing cost per base. There are also unique challenges in plant species, e.g. lack of genomic resources and high-quality annotations for many non-model plant species.
The aim of this Research Topic is to curate a collection of articles that will include: 1) studies where long-read sequencing has helped substantially to advance research in plant biology and agricultural research; 2) technical reports focusing on an in-depth understanding of the challenges of long-read sequence data analysis and 3) methods papers on the development of novel methods and tools that allows the more efficient and accurate characterization of plant genomes and transcriptomes.
In this Research Topic, we welcome submission on a broad spectrum, including topical reviews, original research that uses long-read sequencing to address a biological question, or methods and protocol development for sequencing, as well as computational tools and software for long-read sequence data analysis in the following areas:
• Genome assembly for model and non-model plant species
• Genotyping
• Gene annotation
• Alternative splicing
• Transcript and gene expressions analysis
• DNA and RNA modifications
By focusing on these aspects, this Research Topic will attempt to integrate various research in the field of usage long-read sequencing in plant biology to better understand the complexity of plants’ life processes. We encourage submission from various disciplines combining computational, physiological, functional genomics, and transcriptomics studies.
Please note that descriptive studies and those defining gene families or descriptive collection of transcripts, proteins, or metabolites, will not be considered for review unless they are expanded and provide mechanistic and/or physiological insights into the biological system or process being studied.
Dynamics and complexity of genomes and transcriptomes underpin various aspects of plant growth, development, and responses to biotic and abiotic signals. Long read sequencing technologies, such as PacBio and Oxford Nanopore sequencing, have increased the length of a single contiguous read significantly from a few hundred to thousands or even millions of base pairs and thus overcame the limitation of second-generation sequencing. The increased read lengths have enabled the development of new analysis strategies and tools for plant genomics and transcriptomics. Long reads have been used to improve genome assembly in repetitive regions, to produce more complete and precise positioning of genomic loci, to assemble full-length transcripts, and identify DNA and RNA modifications. It enables detecting of alternative splicing, alternative polyadenylation, and alternative transcription initiation site which contribute to transcriptome diversity. However, the analysis of long-read data comes with new technical challenges, such as high error rates and limited coverage due to the high sequencing cost per base. There are also unique challenges in plant species, e.g. lack of genomic resources and high-quality annotations for many non-model plant species.
The aim of this Research Topic is to curate a collection of articles that will include: 1) studies where long-read sequencing has helped substantially to advance research in plant biology and agricultural research; 2) technical reports focusing on an in-depth understanding of the challenges of long-read sequence data analysis and 3) methods papers on the development of novel methods and tools that allows the more efficient and accurate characterization of plant genomes and transcriptomes.
In this Research Topic, we welcome submission on a broad spectrum, including topical reviews, original research that uses long-read sequencing to address a biological question, or methods and protocol development for sequencing, as well as computational tools and software for long-read sequence data analysis in the following areas:
• Genome assembly for model and non-model plant species
• Genotyping
• Gene annotation
• Alternative splicing
• Transcript and gene expressions analysis
• DNA and RNA modifications
By focusing on these aspects, this Research Topic will attempt to integrate various research in the field of usage long-read sequencing in plant biology to better understand the complexity of plants’ life processes. We encourage submission from various disciplines combining computational, physiological, functional genomics, and transcriptomics studies.
Please note that descriptive studies and those defining gene families or descriptive collection of transcripts, proteins, or metabolites, will not be considered for review unless they are expanded and provide mechanistic and/or physiological insights into the biological system or process being studied.
