Correction: Structural variation underlies functional diversity at methyl salicylate loci in tomato
by Manoj Sapkota, Lara Pereira, Yanbing Wang, Lei Zhang, Yasin Topcu, Denise Tieman, Esther van der Knaap (Source: PLoS Genetics)
Source: PLoS Genetics - January 18, 2024 Category: Genetics & Stem Cells Authors: Manoj Sapkota Source Type: research
A major endogenous glycoside hydrolase mediating quercetin uptake in < i > Bombyx mori < /i >
by Ryusei Waizumi, Chikara Hirayama, Shuichiro Tomita, Tetsuya Iizuka, Seigo Kuwazaki, Akiya Jouraku, Takuya Tsubota, Kakeru Yokoi, Kimiko Yamamoto, Hideki Sezutsu
Quercetin is a common plant flavonoid which is involved in herbivore –plant interactions. Mulberry silkworms (domestic silkworm,Bombyx mori, and wild silkworm,Bombyx mandarina) take up quercetin from mulberry leaves and accumulate the metabolites in the cocoon, thereby improving its protective properties. Here we identified a glycoside hydrolase, named glycoside hydrolase family 1 group G 5 (GH1G5), which is expressed in the midgut and is involved in querceti...
Source: PLoS Genetics - January 17, 2024 Category: Genetics & Stem Cells Authors: Ryusei Waizumi Source Type: research
A conserved transcription factor controls gluconeogenesis via distinct targets in hypersaline-adapted archaea with diverse metabolic capabilities
by Rylee K. Hackley, Angie Vreugdenhil-Hayslette, Cynthia L. Darnell, Amy K. Schmid
Timely regulation of carbon metabolic pathways is essential for cellular processes and to prevent futile cycling of intracellular metabolites. InHalobacterium salinarum, a hypersaline adapted archaeon, a sugar-sensing TrmB family protein controls gluconeogenesis and other biosynthetic pathways. Notably,Hbt. salinarum does not utilize carbohydrates for energy, uncommon among Haloarchaea. We characterized a TrmB-family transcriptional regulator in a saccharolytic generalist,Haloarcula hispanica, to investigate whether the targets and functio...
Source: PLoS Genetics - January 16, 2024 Category: Genetics & Stem Cells Authors: Rylee K. Hackley Source Type: research
The genome of < i > Litomosoides sigmodontis < /i > illuminates the origins of Y chromosomes in filarial nematodes
by Lewis Stevens, Manuela Kieninger, Brian Chan, Jonathan M. D. Wood, Pablo Gonzalez de la Rosa, Judith Allen, Mark Blaxter
Heteromorphic sex chromosomes are usually thought to have originated from a pair of autosomes that acquired a sex-determining locus and subsequently stopped recombining, leading to degeneration of the sex-limited chromosome. The majority of nematodes species lack heteromorphic sex chromosomes and determine sex using an X-chromosome counting mechanism, with males being hemizygous for one or more X chromosomes (XX/X0). Some filarial nematode species, including important parasites of humans, have hetero...
Source: PLoS Genetics - January 16, 2024 Category: Genetics & Stem Cells Authors: Lewis Stevens Source Type: research
Phosphoregulation of the yeast Pma1 H < sup > + < /sup > -ATPase autoinhibitory domain involves the Ptk1/2 kinases and the Glc7 PP1 phosphatase and is under TORC1 control
In this study, we show that S911-T912 phosphorylation in Pma1 is mediated by the largely redundant Ptk1 and Ptk2 kinase paralogs. Dephosphorylation of S911-T912, as occurs under glucose starvation, is dependent on the Glc7 PP1 phosphatase. Furthermore, proper S911-T912 phosphorylation in Pma1 is required for optimal TORC1 activation upon H+ influx coupled amino-acid uptake. We finally show that TORC1 controls S911-T912 phosphorylation in a manner suggesting that activated TORC1 promotes feedback inhibition of Pma1. Our results shed important new light on phosphoregulation of the yeast Pma1 H+-ATPase and on its interconnect...
Source: PLoS Genetics - January 16, 2024 Category: Genetics & Stem Cells Authors: Nadia Guarini Source Type: research
Searching across-cohort relatives in 54,092 GWAS samples via encrypted genotype regression
In this study, we developedencG-reg, a regression approach that can detect relatives of various degrees based on encrypted genomic data, which is immune of ethical constraints. The encryption properties ofencG-reg are based on the random matrix theory by masking the original genotypic matrix without sacrificing precision of individual-level genotype data. We established a connection between the dimension of a random matrix, which masked genotype matrices, and the required precision of a study for encrypted genotype data.encG-reg has false positive and false negative rates equivalent to sharing original individual level dat...
Source: PLoS Genetics - January 11, 2024 Category: Genetics & Stem Cells Authors: Qi-Xin Zhang Source Type: research
F-actin coordinates spindle morphology and function in < i > Drosophila < /i > meiosis
by Benjamin W. Wood, Xingzhu Shi, Timothy T. Weil
Meiosis is a highly conserved feature of sexual reproduction that ensures germ cells have the correct number of chromosomes prior to fertilization. A subset of microtubules, known as the spindle, are essential for accurate chromosome segregation during meiosis. Building evidence in mammalian systems has recently highlighted the unexpected requirement of the actin cytoskeleton in chromosome segregation; a network of spindle actin filaments appear to regulate many aspects of this process. Here we show thatDrosophila oocytes also have a spindle population of actin that appear...
Source: PLoS Genetics - January 11, 2024 Category: Genetics & Stem Cells Authors: Benjamin W. Wood Source Type: research
Large scale sequence-based screen for recessive variants allows for identification and monitoring of rare deleterious variants in pigs
In this study we report a large-scale sequence based genome-wide association study (GWAS) in pigs, with a total of 120,000 Large White and 80,000 Synthetic breed animals imputed to sequence using a reference population of approximately 1,100 whole genome sequenced pigs. We imputed over 20 million variants with high accuracies (R2>0.9) even for low frequency variants (1 –5% minor allele frequency). This sequence-based analysis revealed a total of 14 additive and 9 non-additive significant quantitative trait loci (QTLs) for growth rate and backfat thickness. With the non-additive (recessive) model, we identified a deleteri...
Source: PLoS Genetics - January 10, 2024 Category: Genetics & Stem Cells Authors: Anne Boshove Source Type: research
Peripheral thickening of the sarcomeres and pointed end elongation of the thin filaments are both promoted by SALS and its formin interaction partners
by D ávid Farkas, Szilárd Szikora, A. S. Jijumon, Tamás F. Polgár, Roland Patai, Mónika Ágnes Tóth, Beáta Bugyi, Tamás Gajdos, Péter Bíró, Tibor Novák, Miklós Erdélyi, József Mihály
During striated muscle development the first periodically repeated units appear in the premyofibrils, consisting of immature sarcomeres that must undergo a substantial growth both in length and width, to reach their final size. Here we report that, beyond its well established role in sarcomere elongation, the Sarcomere length short (SALS) protein is involved in Z-disc formation and peripheral growth of the sarcomeres. Our prot...
Source: PLoS Genetics - January 10, 2024 Category: Genetics & Stem Cells Authors: D ávid Farkas Source Type: research
Leveraging shared ancestral variation to detect local introgression
by Lesly Lopez Fang, David Peede, Diego Ortega-Del Vecchyo, Emily Jane McTavish, Emilia Huerta-Sanchez
Introgression is a common evolutionary phenomenon that results in shared genetic material across non-sister taxa. Existing statistical methods such as Patterson ’sD statistic can detect introgression by measuring an excess of shared derived alleles between populations. TheD statistic is effective to detect genome-wide patterns of introgression but can give spurious inferences of introgression when applied to local regions. We propose a new statistic,D+, that leverages both shared ancestral and derived alleles to infer ...
Source: PLoS Genetics - January 8, 2024 Category: Genetics & Stem Cells Authors: Lesly Lopez Fang Source Type: research
SH2 domain protein E and ABL signaling regulate blood vessel size
by Jennifer A. Schumacher, Zo ë A. Wright, Diandra Rufin Florat, Surendra K. Anand, Manish Dasyani, Surya Prakash Rao Batta, Valentina Laverde, Kaitlin Ferrari, Laurita Klimkaite, Nina O. Bredemeier, Suman Gurung, Gretchen M. Koller, Kalia N. Aguera, Griffin P. Chadwick, Riley D. Johnson, George E. Davis, Saulius Sumanas
Blood vessels in different vascular beds vary in size, which is essential for their function and fluid flow along the vascular network. Molecular mechanisms involved in the formation of a vascular lumen of appropriate size, or tubulogenesis, are still only partially understood.Src homology 2 domain conta...
Source: PLoS Genetics - January 8, 2024 Category: Genetics & Stem Cells Authors: Jennifer A. Schumacher Source Type: research
Growth-inhibiting effects of the unconventional plant APYRASE 7 of < i > Arabidopsis thaliana < /i > influences the LRX/RALF/FER growth regulatory module
by Shibu Gupta, Amandine Gu érin, Aline Herger, Xiaoyu Hou, Myriam Schaufelberger, Romain Roulard, Anouck Diet, Stefan Roffler, Valérie Lefebvre, Thomas Wicker, Jérôme Pelloux, Christoph Ringli
Plant cell growth involves coordination of numerous processes and signaling cascades among the different cellular compartments to concomitantly enlarge the protoplast and the surrounding cell wall. The cell wall integrity-sensing process involves the extracellular LRX (LRR-Extensin) proteins that bind RALF (Rapid ALkalinization Factor) peptide hormones and, in vegetative tissues, interact with the transmembrane receptor kinase ...
Source: PLoS Genetics - January 8, 2024 Category: Genetics & Stem Cells Authors: Shibu Gupta Source Type: research
The Cross-Regulation Between Set1, Clr4, and Lsd1/2 in < i > Schizosaccharomyces pombe < /i >
by Haoran Liu, Bahjat Fadi Marayati, David de la Cerda, Brendan Matthew Lemezis, Jieyu Gao, Qianqian Song, Minghan Chen, Ke Zhang Reid
Eukaryotic chromatin is organized into either silenced heterochromatin or relaxed euchromatin regions, which controls the accessibility of transcriptional machinery and thus regulates gene expression. In fission yeast,Schizosaccharomyces pombe, Set1 is the sole H3K4 methyltransferase and is mainly enriched at the promoters of actively transcribed genes. In contrast, Clr4 methyltransferase initiates H3K9 methylation, which has long been regarded as a hallmark of heterochromatic silencing. L...
Source: PLoS Genetics - January 5, 2024 Category: Genetics & Stem Cells Authors: Haoran Liu Source Type: research
Template switching between the leading and lagging strands at replication forks generates inverted copy number variants through hairpin-capped extrachromosomal DNA
by Rebecca Martin, Claudia Y. Espinoza, Christopher R. L. Large, Joshua Rosswork, Cole Van Bruinisse, Aaron W. Miller, Joseph C. Sanchez, Madison Miller, Samantha Paskvan, Gina M. Alvino, Maitreya J. Dunham, M. K. Raghuraman, Bonita J. Brewer
Inherited and germ-linede novo copy number variants (CNVs) are increasingly found to be correlated with human developmental and cancerous phenotypes. Several models for template switching during replication have been proposed to explain the generation of these gross chromosomal rearrangements. We proposed a model of template switching (ODIRA —origin dependent inverted repeat amplif...
Source: PLoS Genetics - January 4, 2024 Category: Genetics & Stem Cells Authors: Rebecca Martin Source Type: research
A unifying model that explains the origins of human inverted copy number variants
by Bonita J. Brewer, Maitreya J. Dunham, M. K. Raghuraman
With the release of the telomere-to-telomere human genome sequence and the availability of both long-read sequencing and optical genome mapping techniques, the identification of copy number variants (CNVs) and other structural variants is providing new insights into human genetic disease. Different mechanisms have been proposed to account for the novel junctions in these complex architectures, including aberrant forms of DNA replication, non-allelic homologous recombination, and various pathways that repair DNA breaks. Here, we have focused on a set of structural v...
Source: PLoS Genetics - January 4, 2024 Category: Genetics & Stem Cells Authors: Bonita J. Brewer Source Type: research
