The genomes of many yeast species or strain isolates have now been sequenced with an accelerating momentum that quickly relegates initial data to history, albeit that they are less than two decades old. Today, novel yeast genomes are entirely sequenced for a variety of reasons, often only to identify a few expected genes of specific interest, thus providing a wealth of data, heterogenous in quality and completion but informative about the origin and evolution of this heterogeneous collection of unicellular modern fungi. However, how many scientists fully appreciate the important conceptual and technological roles played by yeasts in the extraordinary development of today's genomics? Novel notions of general significance emerged from the very first eukaryote sequenced, Saccharomyces cerevisiae, and were successively refined and extended over time. Tools with general applications were originally developed with this yeast; and surprises emerged from the results. Here, I have tried to recollect the gradual building up of knowledge as yeast genomics developed, and then briefly summarize our present views about the basic nature of yeast genomes, based on the most recent data.
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http://dx.doi.org/10.1093/femsyr/fov047 | DOI Listing |
Front Plant Sci
December 2024
National Institute of Molecular Biology and Biotechnology, College of Science, University of the Philippines Diliman, Quezon City, Philippines.
Transfer RNAs (tRNAs) are noncoding RNAs involved in protein biosynthesis and have noncanonical roles in cellular metabolism, such as RNA silencing and the generation of transposable elements. Extensive tRNA gene duplications, modifications to mature tRNAs, and complex secondary and tertiary structures impede tRNA sequencing. As such, a comparative genomic analysis of complete tRNA sets is an alternative to understanding the evolutionary processes that gave rise to the extant tRNA sets.
View Article and Find Full Text PDFConnections between the mechanical properties of DNA and biological functions have been speculative due to the lack of methods to measure or predict DNA mechanics at scale. Recently, a proxy for DNA mechanics, cyclizability, was measured by loop-seq and enabled genome-scale investigation of DNA mechanics. Here, we use this dataset to build a computational model predicting bias-corrected intrinsic cyclizability, with near-perfect accuracy, solely based on DNA sequence.
View Article and Find Full Text PDFJ Agric Food Chem
January 2025
State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China.
Sugarcane has the most complex polyploid genome in the world, and sugar-related traits are one of the most important aims in sugarcane breeding. It is essential to construct a representative pan-transcriptome that contains all transcripts of a species for studies on genetic diversity, population expression, and omics analyses in sugarcane. In this study, we constructed the first comprehensive pan-transcriptome for sugarcane, and 8434 highly reliable open reading frames were found, which were not aligned with any published sugarcane genome.
View Article and Find Full Text PDFiScience
December 2024
Guangzhou Municipal Key Laboratory of Metabolic Diseases and Reproductive Health, The Affiliated Guangdong Second Provincial General Hospital of Jinan University, Guangzhou, China.
AT-rich sequence can cause structure variants such as translocations and its instability can be accelerated by replication stresses. When human 16p11.2 or 22q11.
View Article and Find Full Text PDFBMC Biol
January 2025
Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Synthetic Biology Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
Background: Alternative food sources are crucial for the survival and reproduction of moths during nectar scarcity. Noctuid moths make a better use of fermented food sources than moths from other families, while the underlying molecular and genetic basis remain unexplored. As the fermentation progresses, yeasts lysis and the accumulation of metabolic byproducts alter the composition and the volatile release of the sugary substrates.
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