Bioinformatics for agriculture in the Next-Generation sequencing era

Abstract

Abstract:The key role of bioinformatics is acquiring striking importance in the era of outstanding advances in omics technologies for its fundamental support in describing the multifaceted aspects of biological functionalities. The manifold omics efforts flourishing worldwide are also contributing fundamental novelties in many aspects of agricultural sciences and, as a consequence, bioinformatics is acquiring a crucial role also in these research fields. Indeed, the transformation of natural environment for improvement of goods from animal, plants, and microbial worlds for human nutrition and health requires the comprehension of the molecular mechanisms influencing the structure and the function of the individuals, the populations, and the communities. The expanding knowledge about the molecules and the mechanisms associated with specific phenotypic traits and specific responses to biotic or abiotic stresses, complemented with the predictive power of bioinformatics, has an impact on agriculture practices and favors innovative methods in diagnostics, monitoring, and traceability, improving human benefits at lower costs, thus supporting sustainability. We here describe main bioinformatics approaches in the era of Next-Generation Sequencing for its impact in genomics, transcriptomics, and metagenomics efforts, describing their role in agriculture sciences. We aim to introduce common aspects, open questions and perspectives in this cutting-edge field of research.

BIOS-ParallelBlast: Paralelización optimizada de alineamiento de secuencias sobre Xeon Phi

“…La bioinformática es la aplicación de la estadística y las ciencias computacionales en el campo de la biología, donde el principal objetivo es mejorar el entendimiento de los procesos biológicos (Gobalan y John, 2016). La bioinformática ha aportado en muchos roles de la ciencia, por ejemplo, en el cambio climático y el problema del crecimiento de la población (Batley y Edwards, 2016), en la agricultura (Esposito et al, 2016), en la medicina, en el entendimiento de enfermedades congénitas, entre otras.…”

Bioinformatics and Computational Tools for Next-Generation Sequencing Analysis in Clinical Genetics

“…This information is very useful also to understand human health. It is clear that NGS brought a panoply of benefits and solutions for medicine and to other areas, such as agriculture that helped to increase the quality and productivity [34,[150][151][152]. However, it has also brought new challenges.…”

Bioinformatics Resources for Plant Abiotic Stress Responses: State of the Art and Opportunities in the Fast Evolving -Omics Era

“…The possibility of sequencing billions of fragments of DNA sequences in parallel, exploiting cheap and fast high-throughput technologies in place of the well-established Sanger technique, incredibly changed the scenario, making genome sequencing feasible and accessible even to not experienced laboratories [72]. This favored the spreading of several genome-sequencing efforts [73] moving from the sequencing of a limited number or reference model species [74][75][76][77][78][79] to the release of a multitude of draft genome sequences from different species and genotypes [80][81][82][83][84][85][86], often associated to preliminary gene annotations [87,88] of a variety of plant species and genotypes. These efforts provided reference collections, expanding the number of available resources for the same species or for representatives of under investigated clades [36,37,[89][90][91][92][93][94].…”

“…Although novel strategies are being introduced to face the big data challenge in bioinformatics [73,[119][120][121][122][123], the information quality assessment and the spread of well-established references requires longer-term efforts and validations to favor their dissemination to the scientific communities and fruitful subsequent exploitations. This is essential since reliable and stable references are also fundamental in order to appropriately exploit the resources in associated efforts, such as those from transcriptomics, epigenomics, proteomics and metabolomics [58,88].…”