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Table of Contents

January 2024

Cover

Domestic silkworms under ultraviolet irradiation
Issue Image

The domestic silkworm, Bombyx mori, and its wild ancestor, Bombyx mandarina, take up quercetin from mulberry leaves and accumulate its glycosides in their tissues. Quercetin glycosides in the hemolymph and silk glands exhibit obvious yellow fluorescence under ultraviolet irradiation. This fluorescence is characteristic of the two major forms of quercetin glycosides observed in the domestic silkworm tissues, quercetin-5-O-glucoside and quercetin-5,4´-di-O-glucoside. Quercetin glycosides in the mulberry leaves do not exhibit such fluorescence because they are present as a series of glycosides formed by glycosylation at the 3-O position. See Waizumi et al. Download January’s cover page.

Image Credit: Ryusei Waizumi

Reviews

A unifying model that explains the origins of human inverted copy number variants

Bonita J. Brewer, Maitreya J. Dunham, M. K. Raghuraman

PLOS Genetics: published January 4, 2024 | https://doi.org/10.1371/journal.pgen.1011091

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The era of the ARG: An introduction to ancestral recombination graphs and their significance in empirical evolutionary genomics

Alexander L. Lewanski, Michael C. Grundler, Gideon S. Bradburd

PLOS Genetics: published January 18, 2024 | https://doi.org/10.1371/journal.pgen.1011110

Research Articles

H3K27me3 is vital for fungal development and secondary metabolite gene silencing, and substitutes for the loss of H3K9me3 in the plant pathogen Fusarium proliferatum

Lena Studt-Reinhold, Anna K. Atanasoff-Kardjalieff, Harald Berger, Celine Petersen, Simone Bachleitner, Michael Sulyok, Alica Fischle, Hans-Ulrich Humpf, Svetlana Kalinina, Teis Esben Søndergaard

PLOS Genetics: published January 2, 2024 | https://doi.org/10.1371/journal.pgen.1011075

Template switching between the leading and lagging strands at replication forks generates inverted copy number variants through hairpin-capped extrachromosomal DNA

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

PLOS Genetics: published January 4, 2024 | https://doi.org/10.1371/journal.pgen.1010850

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The Cross-Regulation Between Set1, Clr4, and Lsd1/2 in Schizosaccharomyces pombe

Haoran Liu, Bahjat Fadi Marayati, David de la Cerda, Brendan Matthew Lemezis, Jieyu Gao, Qianqian Song, Minghan Chen, Ke Zhang Reid

PLOS Genetics: published January 5, 2024 | https://doi.org/10.1371/journal.pgen.1011107

SH2 domain protein E and ABL signaling regulate blood vessel size

Jennifer A. Schumacher, Zoë 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

PLOS Genetics: published January 8, 2024 | https://doi.org/10.1371/journal.pgen.1010851

Leveraging shared ancestral variation to detect local introgression

Lesly Lopez Fang, David Peede, Diego Ortega-Del Vecchyo, Emily Jane McTavish, Emilia Huerta-Sánchez

PLOS Genetics: published January 8, 2024 | https://doi.org/10.1371/journal.pgen.1010155

Growth-inhibiting effects of the unconventional plant APYRASE 7 of Arabidopsis thaliana influences the LRX/RALF/FER growth regulatory module

Shibu Gupta, Amandine Guérin, Aline Herger, Xiaoyu Hou, Myriam Schaufelberger, Romain Roulard, Anouck Diet, Stefan Roffler, Valérie Lefebvre, Thomas Wicker, Jérôme Pelloux, Christoph Ringli

PLOS Genetics: published January 8, 2024 | https://doi.org/10.1371/journal.pgen.1011087

Large scale sequence-based screen for recessive variants allows for identification and monitoring of rare deleterious variants in pigs

Anne Boshove, Martijn F. L. Derks, Claudia A. Sevillano, Marcos S. Lopes, Maren van Son, Egbert F. Knol, Bert Dibbits, Barbara Harlizius

PLOS Genetics: published January 10, 2024 | https://doi.org/10.1371/journal.pgen.1011034

Peripheral thickening of the sarcomeres and pointed end elongation of the thin filaments are both promoted by SALS and its formin interaction partners

Dávid 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

PLOS Genetics: published January 10, 2024 | https://doi.org/10.1371/journal.pgen.1011117

F-actin coordinates spindle morphology and function in Drosophila meiosis

Benjamin W. Wood, Xingzhu Shi, Timothy T. Weil

PLOS Genetics: published January 11, 2024 | https://doi.org/10.1371/journal.pgen.1011111

Phosphoregulation of the yeast Pma1 H+-ATPase autoinhibitory domain involves the Ptk1/2 kinases and the Glc7 PP1 phosphatase and is under TORC1 control

Nadia Guarini, Elie Saliba, Bruno André

PLOS Genetics: published January 16, 2024 | https://doi.org/10.1371/journal.pgen.1011121

A conserved transcription factor controls gluconeogenesis via distinct targets in hypersaline-adapted archaea with diverse metabolic capabilities

Rylee K. Hackley, Angie Vreugdenhil-Hayslette, Cynthia L. Darnell, Amy K. Schmid

PLOS Genetics: published January 16, 2024 | https://doi.org/10.1371/journal.pgen.1011115

The genome of Litomosoides sigmodontis illuminates the origins of Y chromosomes in filarial nematodes

Lewis Stevens, Manuela Kieninger, Brian Chan, Jonathan M. D. Wood, Pablo Gonzalez de la Rosa, Judith Allen, Mark Blaxter

PLOS Genetics: published January 16, 2024 | https://doi.org/10.1371/journal.pgen.1011116

A major endogenous glycoside hydrolase mediating quercetin uptake in Bombyx mori

Ryusei Waizumi, Chikara Hirayama, Shuichiro Tomita, Tetsuya Iizuka, Seigo Kuwazaki, Akiya Jouraku, Takuya Tsubota, Kakeru Yokoi, Kimiko Yamamoto, Hideki Sezutsu

PLOS Genetics: published January 17, 2024 | https://doi.org/10.1371/journal.pgen.1011118

Failure to mate enhances investment in behaviors that may promote mating reward and impairs the ability to cope with stressors via a subpopulation of Neuropeptide F receptor neurons

Julia Ryvkin, Liora Omesi, Yong-Kyu Kim, Mali Levi, Hadar Pozeilov, Lital Barak-Buchris, Bella Agranovich, Ifat Abramovich, Eyal Gottlieb, Avi Jacob, Dick R. Nässel, Ulrike Heberlein, Galit Shohat-Ophir

PLOS Genetics: published January 18, 2024 | https://doi.org/10.1371/journal.pgen.1011054

Species-wide survey of the expressivity and complexity spectrum of traits in yeast

Andreas Tsouris, Téo Fournier, Anne Friedrich, Jing Hou, Maitreya J. Dunham, Joseph Schacherer

PLOS Genetics: published January 18, 2024 | https://doi.org/10.1371/journal.pgen.1011119

Genome-wide analyses reveal the contribution of somatic variants to the immune landscape of multiple cancer types

Wenjian Bi, Zhiyu Xu, Feng Liu, Zhi Xie, Hao Liu, Xiaotian Zhu, Wenge Zhong, Peipei Zhang, Xing Tang

PLOS Genetics: published January 19, 2024 | https://doi.org/10.1371/journal.pgen.1011134

Genetic drift promotes and recombination hinders speciation on holey fitness landscapes

Ata Kalirad, Christina L. Burch, Ricardo B. R. Azevedo

PLOS Genetics: published January 22, 2024 | https://doi.org/10.1371/journal.pgen.1011126

Mycobacterium tuberculosis response to cholesterol is integrated with environmental pH and potassium levels via a lipid metabolism regulator

Yue Chen, Nathan J. MacGilvary, Shumin Tan

PLOS Genetics: published January 24, 2024 | https://doi.org/10.1371/journal.pgen.1011143

Integration of expression QTLs with fine mapping via SuSiE

Xiangyu Zhang, Wei Jiang, Hongyu Zhao

PLOS Genetics: published January 25, 2024 | https://doi.org/10.1371/journal.pgen.1010929

Emergence and spread of the barley net blotch pathogen coincided with crop domestication and cultivation history

Demetris Taliadoros, Alice Feurtey, Nathan Wyatt, Benoit Barrès, Pierre Gladieux, Timothy L. Friesen, Eva H. Stukenbrock

PLOS Genetics: published January 29, 2024 | https://doi.org/10.1371/journal.pgen.1010884

Precise coordination between nutrient transporters ensures fertility in the malaria mosquito Anopheles gambiae

Iryna Stryapunina, Maurice A. Itoe, Queenie Trinh, Charles Vidoudez, Esrah Du, Lydia Mendoza, Oleksandr Hulai, Jamie Kauffman, John Carew, W. Robert Shaw, Flaminia Catteruccia

PLOS Genetics: published January 29, 2024 | https://doi.org/10.1371/journal.pgen.1011145

A connection between the ribosome and two S. pombe tRNA modification mutants subject to rapid tRNA decay

Thareendra De Zoysa, Alayna C. Hauke, Nivedita R. Iyer, Erin Marcus, Sarah M. Ostrowski, Franziska Stegemann, Dmitri N. Ermolenko, Justin C. Fay, Eric M. Phizicky

PLOS Genetics: published January 31, 2024 | https://doi.org/10.1371/journal.pgen.1011146

Transposon dynamics in the emerging oilseed crop Thlaspi arvense

Adrián Contreras-Garrido, Dario Galanti, Andrea Movilli, Claude Becker, Oliver Bossdorf, Hajk-Georg Drost, Detlef Weigel

PLOS Genetics: published January 31, 2024 | https://doi.org/10.1371/journal.pgen.1011141

Corrections

Correction: The Role of the Mammalian DNA End-processing Enzyme Polynucleotide Kinase 3’-Phosphatase in Spinocerebellar Ataxia Type 3 Pathogenesis

Arpita Chatterjee, Saikat Saha, Anirban Chakraborty, Anabela Silva-Fernandes, Santi M. Mandal, Andreia Neves-Carvalho, Yongping Liu, Raj K. Pandita, Muralidhar L. Hegde, Pavana M. Hegde, Istvan Boldogh, Tetsuo Ashizawa, Arnulf H. Koeppen, Tej K. Pandita, Patricia Maciel, Partha S. Sarkar, Tapas K. Hazra

PLOS Genetics: published January 18, 2024 | https://doi.org/10.1371/journal.pgen.1011124

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  1. The Role of the Mammalian DNA End-processing Enzyme Polynucleotide Kinase 3’-Phosphatase in Spinocerebellar Ataxia Type 3 Pathogenesis

Correction: Structural variation underlies functional diversity at methyl salicylate loci in tomato

Manoj Sapkota, Lara Pereira, Yanbing Wang, Lei Zhang, Yasin Topcu, Denise Tieman, Esther van der Knaap

PLOS Genetics: published January 18, 2024 | https://doi.org/10.1371/journal.pgen.1011125

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  1. Structural variation underlies functional diversity at methyl salicylate loci in tomato

Methods

Searching across-cohort relatives in 54,092 GWAS samples via encrypted genotype regression

Qi-Xin Zhang, Tianzi Liu, Xinxin Guo, Jianxin Zhen, Meng-yuan Yang, Saber Khederzadeh, Fang Zhou, Xiaotong Han, Qiwen Zheng, Peilin Jia, Xiaohu Ding, Mingguang He, Xin Zou, Jia-Kai Liao, Hongxin Zhang, Ji He, Xiaofeng Zhu, Daru Lu, Hongyan Chen, Changqing Zeng, Fan Liu, Hou-Feng Zheng, Siyang Liu, Hai-Ming Xu, Guo-Bo Chen

PLOS Genetics: published January 11, 2024 | https://doi.org/10.1371/journal.pgen.1011037

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  1. Correction: Searching across-cohort relatives in 54,092 GWAS samples via encrypted genotype regression