0
selected
-
1.
Through 40,000 years of human presence in Southern Europe: the Italian case study.
Aneli, S, Caldon, M, Saupe, T, Montinaro, F, Pagani, L
Human genetics. 2021;(10):1417-1431
-
-
Free full text
-
Abstract
The Italian Peninsula, a natural pier across the Mediterranean Sea, witnessed intricate population events since the very beginning of the human occupation in Europe. In the last few years, an increasing number of modern and ancient genomes from the area have been published by the international research community. This genomic perspective started unveiling the relevance of Italy to understand the post-Last Glacial Maximum (LGM) re-peopling of Europe, the earlier phase of the Neolithic westward migrations, and its linking role between Eastern and Western Mediterranean areas after the Iron Age. However, many open questions are still waiting for more data to be addressed in full. With this review, we summarize the current knowledge emerging from the available ancient Italian individuals and, by re-analysing them all at once, we try to shed light on the avenues future research in the area should cover. In particular, open questions concern (1) the fate of pre-Villabruna Europeans and to what extent their genomic components were absorbed by the post-LGM hunter-gatherers; (2) the role of Sicily and Sardinia before LGM; (3) to what degree the documented genetic structure within the Early Neolithic settlers can be described as two separate migrations; (4) what are the population events behind the marked presence of an Iranian Neolithic-like component in Bronze Age and Iron Age Italian and Southern European samples.
-
2.
How the pan-genome is changing crop genomics and improvement.
Della Coletta, R, Qiu, Y, Ou, S, Hufford, MB, Hirsch, CN
Genome biology. 2021;(1):3
Abstract
Crop genomics has seen dramatic advances in recent years due to improvements in sequencing technology, assembly methods, and computational resources. These advances have led to the development of new tools to facilitate crop improvement. The study of structural variation within species and the characterization of the pan-genome has revealed extensive genome content variation among individuals within a species that is paradigm shifting to crop genomics and improvement. Here, we review advances in crop genomics and how utilization of these tools is shifting in light of pan-genomes that are becoming available for many crop species.
-
3.
An overview of functional genomics and relevance of glycosyltransferases in exopolysaccharide production by lactic acid bacteria.
Soumya, MP, Nampoothiri, KM
International journal of biological macromolecules. 2021;:1014-1025
Abstract
There are many reports on exopolysaccharides of lactic acid bacteria (LAB EPS) such as isolation, production and applications. The LAB EPS have been proved to exhibit significantly improved texture and rheological properties in order to prevent syneresis of fermented foods. Furthermore, they are known to have many biological properties such as mouthwatering flavors, antioxidant activity, cholesterol lowering and antimicrobial activities. Considering their GRAS status, LAB EPS need to be explored for better titre and improved biological properties, where strain improvement by genetic engineering has a major role for making tailor-made EPS. The genetic overview of the EPS production by LAB is an auxiliary area of interest as the process and the biosynthetic pathway involves numerous genes and their proteins. Among them Glycosyltransferases (gtfs) are the key enzymes involved in EPS biosynthesis. Current knowledge of gtfs of LAB and its manipulation is limited. The present review spotlights the importance of glycosyltransferases and their specific role on the biosynthesis of LAB EPS and addresses the functionality and applicability of these enzymes and their products. It enfold the available literature including some patents in recent past to underline the fact that glycosyltransferases are un-reluctantly the key proteins involved in the EPS biosynthesis.
-
4.
Machine learning approaches for crop improvement: Leveraging phenotypic and genotypic big data.
Tong, H, Nikoloski, Z
Journal of plant physiology. 2021;:153354
Abstract
Highly efficient and accurate selection of elite genotypes can lead to dramatic shortening of the breeding cycle in major crops relevant for sustaining present demands for food, feed, and fuel. In contrast to classical approaches that emphasize the need for resource-intensive phenotyping at all stages of artificial selection, genomic selection dramatically reduces the need for phenotyping. Genomic selection relies on advances in machine learning and the availability of genotyping data to predict agronomically relevant phenotypic traits. Here we provide a systematic review of machine learning approaches applied for genomic selection of single and multiple traits in major crops in the past decade. We emphasize the need to gather data on intermediate phenotypes, e.g. metabolite, protein, and gene expression levels, along with developments of modeling techniques that can lead to further improvements of genomic selection. In addition, we provide a critical view of factors that affect genomic selection, with attention to transferability of models between different environments. Finally, we highlight the future aspects of integrating high-throughput molecular phenotypic data from omics technologies with biological networks for crop improvement.
-
5.
Genomics as a potential tool to unravel the rhizosphere microbiome interactions on plant health.
Priya, P, Aneesh, B, Harikrishnan, K
Journal of microbiological methods. 2021;:106215
Abstract
Intense agricultural practices to meet rising food demands have caused ecosystem perturbations. For sustainable crop production, biological agents are gaining attention, but exploring their functional potential on a multi-layered complex ecosystem like the rhizosphere is challenging. This review explains the significance of genomics as a culture-independent molecular tool to understand the diversity and functional significance of the rhizosphere microbiome for sustainable agriculture. It discusses the recent significant studies in the rhizosphere environment carried out using evolving techniques like metagenomics, metatranscriptomics, and metaproteomics, their challenges, constraints infield application, and prospective solutions. The recent advances in techniques such as nanotechnology for the development of bioformulations and visualization techniques contemplating environmental safety were also discussed. The need for development of metagenomic data sets of regionally important crops, their plant microbial interactions and agricultural practices for narrowing down significant data from huge databases have been suggested. The role of taxonomical and functional diversity of soil microbiota in understanding soil suppression and part played by the microbial metabolites in the process have been analyzed and discussed in the context of 'omics' approach. 'Omics' studies have revealed important information about microbial diversity, their responses to various biotic and abiotic stimuli, and the physiology of disease suppression. This can be translated to crop sustainability and combinational approaches with advancing visualization and analysis methodologies fix the existing knowledge gap to a huge extend. With improved data processing and standardization of the methods, details of plant-microbe interactions can be successfully decoded to develop sustainable agricultural practices.
-
6.
Integration of comprehensive data and biotechnological tools for industrial applications of Kluyveromyces marxianus.
Nurcholis, M, Lertwattanasakul, N, Rodrussamee, N, Kosaka, T, Murata, M, Yamada, M
Applied microbiology and biotechnology. 2020;(2):475-488
Abstract
Among the so-called non-conventional yeasts, Kluyveromyces marxianus has extremely potent traits that are suitable for industrial applications. Indeed, it has been used for the production of various enzymes, chemicals, and macromolecules in addition to utilization of cell biomass as nutritional materials, feed and probiotics. The yeast is expected to be an efficient ethanol producer with advantages over Saccharomyces cerevisiae in terms of high growth rate, thermotolerance and a wide sugar assimilation spectrum. Results of comprehensive analyses of its genome and transcriptome may accelerate studies for applications of the yeast and may further increase its potential by combination with recent biotechnological tools including the CRISPR/Cas9 system. We thus review published studies by merging with information obtained from comprehensive data including genomic and transcriptomic data, which would be useful for future applications of K. marxianus.
-
7.
Highlights on Genomics Applications for Lysosomal Storage Diseases.
La Cognata, V, Guarnaccia, M, Polizzi, A, Ruggieri, M, Cavallaro, S
Cells. 2020;(8)
Abstract
Lysosomal storage diseases (LSDs) are a heterogeneous group of rare multisystem genetic disorders occurring mostly in infancy and childhood, characterized by a gradual accumulation of non-degraded substrates inside the lysosome. Although the cellular pathogenesis of LSDs is complex and still not fully understood, the approval of disease-specific therapies and the rapid emergence of novel diagnostic methods led to the implementation of extensive national newborn screening (NBS) programs in several countries. In the near future, this will help the development of standardized workflows aimed to more timely diagnose these conditions. Hereby, we report an overview of LSD diagnostic process and treatment strategies, provide an update on the worldwide NBS programs, and discuss the opportunities and challenges arising from genomics applications in screening, diagnosis, and research.
-
8.
Hyperbolic rules of the cooperative organization of eukaryotic and prokaryotic genomes.
Petoukhov, SV
Bio Systems. 2020;:104273
-
-
Free full text
-
Abstract
The author's method of oligomer sums for analysis of oligomer compositions of eukaryotic and prokaryotic genomes is described. The use of this method revealed the existence of general rules for the cooperative oligomeric organization of a wide list of genomes. These rules are called hyperbolic because they are associated with hyperbolic sequences including the harmonic progression 1, 1/2, 1/3, .., 1/n. These rules are demonstrated by examples of quantitative analysis of many genomes from the human genome to the genomes of archaea and bacteria. The hyperbolic (harmonic) rules, speaking about the existence of algebraic invariants in full genomic sequences, are considered as candidates for the role of universal rules for the cooperative organization of genomes. The results concerns additionally the problem of the origin of life. The described phenomenological results were obtained as consequences of the previously published author's quantum-information model of long DNA sequences. The oligomer sums method was also applied to the analysis of long genes and viruses including the COVID-19 virus; this revealed, in characteristics of many of them, the phenomenon of such rhythmically repeating deviations from model hyperbolic sequences, which are associated with DNA triplets. In addition, an application of the oligomer sums method is shown to the analysis of amino acid sequences in long proteins like the protein Titin. The topics of the algebraic harmony in living bodies and of the quantum-information approach in biology are discussed.
-
9.
The Past, Present, and Future of Maize Improvement: Domestication, Genomics, and Functional Genomic Routes toward Crop Enhancement.
Liu, J, Fernie, AR, Yan, J
Plant communications. 2020;(1):100010
Abstract
After being domesticated from teosinte, cultivated maize (Zea mays ssp. mays) spread worldwide and now is one of the most important staple crops. Due to its tremendous phenotypic and genotypic diversity, maize also becomes to be one of the most widely used model plant species for fundamental research, with many important discoveries reported by maize researchers. Here, we provide an overview of the history of maize domestication and key genes controlling major domestication-related traits, review the currently available resources for functional genomics studies in maize, and discuss the functions of most of the maize genes that have been positionally cloned and can be used for crop improvement. Finally, we provide some perspectives on future directions regarding functional genomics research and the breeding of maize and other crops.
-
10.
Plant phenomics: High-throughput technology for accelerating genomics.
Pasala, R, Pandey, BB
Journal of biosciences. 2020
Abstract
Plant phenomics is a high-throughput path-breaking area that meets all the requirements for the collection of accurate, rapid and multi-faceted phenotypic data. Plant phenomics is an approach to envisage complex traits that are appropriate for selection, and provides relevant information as to why particular genotype can stand out in particular environmental conditions. The technique of plant phenotyping can be operated in various dimensions, from the gene to the whole-plant level under a specific environment, and management practices. Through this review, we discuss the recent advances in plant phenomics, highlighting different field and confined high-throughput technologies for utilization in forward and reverse genetics. These plant phenomics technique are very relevant in stress identification, study physiological processes, rapid and efficient screening, dissection and confirmation for understanding the genetic basis of different traits, genes and aspects. Highthroughput phenomics technologies are essential to avoid human error and to reduce time consumption while phenotyping large germplasm populations, or for confirmation of gene or trait functional analysis.