Overcoming the Challenges of Complex Plant Genomes

Plant genomes exhibit a remarkable range in size, stretching from incredibly compact genomes¹ to some of the largest known eukaryotic genomes². Significant progress has been made in understanding plant genomics since the first plant genome (Arabidopsis thaliana) was sequenced over 20 years ago³. Since that date, advances in sequencing technologies and analytical tools have expanded our knowledge, facilitating crop development, conservation efforts, and our understanding of...

Within the extensive array of instruments that Thermo Fisher Scientific offers, their Ion Torrent Next-Generation Sequencing systems remain important technologies for genomic research. Introduced in 2010 with the Ion PGM System (Personal Genome Machine), these sequencers have been continually evolving and facilitating new scientific insights.

After over a decade in the sequencing market, Jose Luis Costa, Global Director of Scientific Affairs at Thermo Fisher Scientific,...

Established in 2004, Pacific Biosciences (PacBio) set out to create innovative tools that would elevate our understanding of genomics. Over the years, they have grown into global leaders in the field, known for their revolutionary HiFi sequencing—a high-accuracy, long-read sequencing solution.

Their journey began with the PacBio RS, their first commercial release, which employed their Single Molecule, Real-Time (SMRT) sequencing technology. This marked the beginning...

After celebrating its 18^th birthday, the team at Complete Genomics is more committed than ever to providing the sequencing community with affordable sequencing solutions. It comes as no surprise as their Co-founder and Chief Scientific Officer Dr. Radoje (Rade) Drmanac has a long history of paving the way for the advancement of genomics. From working on the Human Genome Project to his various genomic startups, Drmanac has always had the goal of improving genomics research and technologi...

Established in 1998, Illumina began its journey into the field of genomics with the launch of its BeadArray technology for high-throughput genotyping of single nucleotide polymorphisms (SNPs). Through the key acquisition of sequencing company Solexa and the persistent development of their instruments, Illumina transformed itself into an international leader in sequencing technologies.

Illumina currently maintains a large majority of the sequencing market,...

Epigenetics research has played a valuable role in understanding different components of various diseases and disorders, and utilizing the proper tools and methods is vital. “The method of choice to analyze epigenetic modifications and their role in diseases is dependent on the epigenetics platform to be investigated,” explained Said Goueli, Senior Research Fellow at Promega. As reviewed in our recent articles, there are many important methods for epigenetic profiling. Using many...

In the first segment of our review of epigenetic sequencing methods, we covered methylation detection, chromatin accessibility, and protein-DNA interactions. This final part of our review will break outside of the standard analysis and cover some influential multidimensional methods.

Spatial Epigenomics
“Epigenetic assays, whether conducted at the single-cell or bulk level, have played a crucial role in unraveling the underlying mechanisms of diseases and...

Developments in sequencing technologies and methodologies have transformed the field of epigenetics, giving researchers a better way to understand the complex world of gene regulation and heritable modifications. This article explores some of the diverse sequencing methods employed in the study of epigenetics, ranging from classic techniques to cutting-edge innovations while providing a brief overview of their processes, applications, and advances.

Methylation Detect...

After covering QC and alignment tools in the first segment and variant analysis and genome assembly in the second segment, we’re wrapping up with a discussion about tools for differential gene expression analysis and data visualization. In this article, we include recommendations from the following experts: Dr. Mark Ziemann, Senior Lecturer in Biotechnology and Bioinformatics, Deakin University; Dr. Medhat Mahmoud Postdoctoral Research Fellow at Baylor College of Medicine;...

Continuing from our previous article, we share variant analysis and genome assembly tools recommended by our experts Dr. Medhat Mahmoud, Postdoctoral Research Fellow at Baylor College of Medicine, and Dr. Ming "Tommy" Tang, Director of Computational Biology at Immunitas and author of From Cell Line to Command Line.

Variant detection and analysis tools
Mahmoud classifies variant detection work into two main groups: short variants (<50...