Analyzing Modern Biomolecules: The Revolution of Nucleic-Acid Sequencing – Review

Abstract

Recent developments have revolutionized the study of biomolecules. Among them are molecular markers, amplification and sequencing of nucleic acids. The latter is classified into three generations. The first allows to sequence small DNA fragments. The second one increases throughput, reducing turnaround and pricing, and is therefore more convenient to sequence full genomes and transcriptomes. The third generation is currently pushing technology to its limits, being able to sequence single molecules, without previous amplification, which was previously impossible. Besides, this represents a new revolution, allowing researchers to directly sequence RNA without previous retrotranscription. These technologies are having a significant impact on different areas, such as medicine, agronomy, ecology and biotechnology. Additionally, the study of biomolecules is revealing interesting evolutionary information. That includes deciphering what makes us human, including phenomena like non-coding RNA expansion. All this is redefining the concept of gene and transcript. Basic analyses and applications are now facilitated with new genome editing tools, such as CRISPR. All these developments, in general, and nucleic-acid sequencing, in particular, are opening a new exciting era of biomolecule analyses and applications, including personalized medicine, and diagnosis and prevention of diseases for humans and other animals.

Next-Generation Sequencing Applications for the Study of Fungal Pathogens

“…Next-generation sequencing (NGS), which is also named high-throughput sequencing (HTS) [ 1 ], provides new ways of detecting microorganisms beyond microbial culture-based methods. NGS was groundbreaking and introduced a reversible stop-codon determination and achieved sequencing by synthesis as a PCR- and GeneChip-based DNA sequencing technique.…”

Application Progress of High-Throughput Sequencing in Ocular Diseases

“…High-throughput sequencing (HTS), also referred to as next-generation sequencing (NGS) [ 7 ], can directly sequence nucleic acids in clinical samples without the traditional culture technology, whose results can then be compared with databases for disease traceability, detection, typing, and drug resistance assessment [ 8 ]. The first-generation sequencing technology enables the sequencing of small-molecule DNA fragments; however, the advancement to the second-generation sequencing with improved throughput simplifies the procedure and reduces the cost [ 7 ]. The first NGS technology was born in 2000, which opened up new arenas for mammalian genomics research, and sequencing technology has now progressed to the third generation [ 9 ].…”

“…The first NGS technology was born in 2000, which opened up new arenas for mammalian genomics research, and sequencing technology has now progressed to the third generation [ 9 ]. In addition to the advantages of the previous two generations, third-generation sequencing technology can directly sequence single molecules, such as RNA, without reverse transcription [ 7 ]. Commercial NGS technologies are currently used by companies such as Illumina, Oxford, and Pacific Biosciences and involve methods such as 16S rDNA, metagenomic, and single-molecule real-time (SMRT) sequencing.…”

The Botrytis cinerea Gene Expression Browser

“…Researchers thus employ specialized short read alignments tools such as STAR (Dobin et al, 2012), TopHat2 (Kim et al, 2013), Hisat2 (Kim et al, 2015), or Kallisto (Bray et al, 2016), among others, to quantify each read (Liao et al, 2019; Anders et al, 2014) to ultimately apply a suitable differential expression detection algorithm (Love et al, 2014; Chen et al, 2016). Readers can consult several reviews to address many critical considerations at each step (Stark et al, 2019; Dorado et al, 2021; Hrdlickova et al, 2017; Bayega et al, 2018). Ironically, after all these massive scientific and computational efforts to make RNA-Seq data biologically accurate, meaningful, and accessible to most biologists, RAW sequence files are deposited back into public databases such as NCBI’s Sequence Read Archive (SRA) (Leinonen et al, 2011).…”