Article
Biochemistry & Molecular Biology
Yuxing Xu, Jingxiong Zhang, Canrong Ma, Yunting Lei, Guojing Shen, Jianjun Jin, Deren A. R. Eaton, Jianqiang Wu
Summary: This study provides high-quality genomes for three parasitic plants and establishes a robust phylogenetic framework for Orobanchaceae. The study reveals that an ancient whole-genome duplication event may have played a role in the emergence of parasitism. Contrary to previous speculations, the emergence of holoparasitism is not associated with genome duplication. The study also identifies convergent gene loss between Orobanchaceae parasites and the dodder Cuscuta australis. Additionally, the expanded gene families in Orobanchaceae parasites are enriched in functions related to haustorium development, suggesting that recent gene family expansions have facilitated adaptation to different hosts.
Article
Plant Sciences
Zengzhi Si, Lianjun Wang, Zhixin Ji, Mingming Zhao, Kai Zhang, Yake Qiao
Summary: This study performed a comprehensive genome-wide comparative analysis of the MYB gene family in seven Ipomoea species and identified MYB genes in these species. The identified genes were classified into five types, with the MYB-related or R2R3-MYB type being the most abundant. Analysis of gene structure and protein motifs revealed similarities within the same phylogenetic group. Additionally, cis-regulatory elements related to stress responses were detected in the MYB promoters, and differential gene expression in response to stress treatments was observed.
FRONTIERS IN PLANT SCIENCE
(2023)
Review
Genetics & Heredity
Xi Zhang, David Roy Smith
Summary: This article provides a summary of research tools used for detecting gene duplicates, including metrics, computational approaches, and the latest developments in web tools and databases.
FRONTIERS IN GENETICS
(2022)
Article
Biotechnology & Applied Microbiology
Andres Cumsille, Nestor Serna-Cardona, Valentina Gonzalez, Fernanda Claverias, Agustina Undabarrena, Vania Molina, Francisco Salva-Serra, Edward R. B. Moore, Beatriz Camara
Summary: Exploring Brevibacterium strains from diverse ecosystems may lead to the discovery of new antibiotic-producing strains. The genome sequencing of Brevibacterium sp. H-BE7, isolated from marine sediments, revealed its potential to produce novel natural products. Pangenome analysis showed diverse biosynthetic gene clusters in different phylogenomic clades of Brevibacterium strains. Evaluating the antibacterial activity of strain H-BE7 identified the presence of bioactive compound 1-methoxyphenazine.
Article
Biochemistry & Molecular Biology
Qing Xiong, Angel Tsz-Yau Wan, Xiaoyu Liu, Cathy Sin-Hang Fung, Xiaojun Xiao, Nat Malainual, Jinpao Hou, Lingyi Wang, Mingqiang Wang, Kevin Yi Yang, Yubao Cui, Elaine Lai-Han Leung, Wenyan Nong, Soo-Kyung Shin, Shannon Wing-Ngor Au, Kyoung Yong Jeong, Fook-Tim Chew, Jerome Ho-Lam Hui, Ting-Fan Leung, Anchalee Tungtrongchitr, Nanshan Zhong, Zhigang Liu, Stephen Kwok-Wing Tsui
Summary: This study examines the evolutionary origin, diverse lifestyles, and quick adaptation of astigmatic mites in human household environments using six high-quality assembled and annotated genomes. The research reveals that astigmatic mites evolved from Prostigmata, notorious plant pests, and rapidly diversified from soil oribatid mites. The study also highlights the rapid expansion of gene families via tandem gene duplications in astigmatic mites, providing genetic resources for adaptation to changing household environments. Additionally, massive horizontal gene transfer events occurred during the evolution of astigmatic mites, enabling detoxification and digestive functions and offering potential drug targets for pest control.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Christian Roedelsperger, Annabel Ebbing, Devansh Raj Sharma, Misako Okumura, Ralf J. Sommer, Hendrik C. Korswagen
Summary: Comparing the spatially resolved transcriptomes of Caenorhabditis elegans and Pristionchus pacificus, researchers found that regional gene expression in adult worms is driven by recent duplication and emergence of novel genes, rather than strong conservation at the level of single genes. Novel genes are enriched in sperm-related regions, supporting the out of testis hypothesis. Numerous novel genes are also found to have known functions during meiosis, suggesting rapid evolution even in universal processes like meiosis. This study highlights the importance of novel genes in generating phenotypic diversity and characterizes gene origination in sperm-related regions.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Microbiology
Dahe Zhao, Shengjie Zhang, Sumit Kumar, Heng Zhou, Qiong Xue, Wurunze Sun, Jian Zhou, Hua Xiang
Summary: By studying two novel families within the Candidatus Nanohaloarchaeota phylum, we have gained insights into the evolutionary process of this phylum and its symbiotic relationship with Halobacteria. This research contributes to the understanding of symbiosis evolution in Candidatus Nanohaloarchaeota and provides a model for the evolution of other DPANN lineages.
Article
Genetics & Heredity
Yinggu Wu, Yuyang Lian, Sihua Peng, Aqiang Wang, Heming Yang, Jinlei Li, Shuyan Yang, Shihao Zhou
Summary: Zeugodacus cucurbitae, Bactrocera dorsalis, and Ceratitis capitata are important pests of fruit and vegetable crops, and their rapid reproduction rate and egg production make them difficult to control. This study investigates the key genes regulating reproduction in these three fruit fly species and finds that they have different specific genes enriched in immune system, cell growth and differentiation, and degradation and metabolism pathways. Z. cucurbitae may have a stronger immune system, B. dorsalis has a faster developmental and reproductive rate, and C. capitata has a higher detoxification capacity.
FRONTIERS IN GENETICS
(2022)
Review
Biochemistry & Molecular Biology
Xuan Zhou, Zhenhua Liu
Summary: Plants produce diverse natural chemicals that play adaptive roles throughout their life cycles. However, the complexity and size of plant genomes hinder the exploration of metabolic diversity. Advances in genome sequencing and pan-genomic data analysis have revealed gene clusters associated with important agronomic traits in plants, leading to the discovery of plant metabolic diversification. The future of investigating metabolic diversity in plants lies in the pan-genomics era.
PLANT COMMUNICATIONS
(2022)
Review
Physiology
Natalie Krahn, Dieter Soell, Oscar Vargas-Rodriguez
Summary: The evolution of aminoacyl-tRNA synthetase (aaRS) families is complex and has led to the emergence of unique characteristics and aaRS-like proteins. Recent studies have revealed widespread aaRS gene duplication and phylogenetic diversity, but only a fraction of these duplications have been characterized. Investigation of unexplored aaRS genomic duplications may uncover exciting biological processes, new drug targets, important bioactive molecules, and tools for synthetic biology applications.
FRONTIERS IN PHYSIOLOGY
(2022)
Article
Agriculture, Dairy & Animal Science
Bolin Ning, Jiaxin Huang, Haidong Xu, Yuqi Lou, Weishi Wang, Fang Mu, Xiaohong Yan, Hui Li, Ning Wang
Summary: The study explored the transcript isoforms of the chicken TGFBR2 gene, revealing the presence of 3 transcript isoforms and encoding 3 protein isoforms, along with an intragenic tandem duplication. Significant differential expression of the isoforms in tissue expression profiling among chickens selected for different abdominal fat content levels was observed.
Article
Genetics & Heredity
Qiaoying Pei, Nan Li, Qihang Yang, Tong Wu, Shuyan Feng, Xuehuan Feng, Zange Jing, Rong Zhou, Ke Gong, Tong Yu, Zhen Wang, Xiaoming Song
Summary: The ARF gene family in celery, coriander, and carrot consists of 89 genes, with coriander having a significantly greater number of paralogous genes compared to carrot and celery. The study revealed that ARF genes in the three Apiaceae species underwent significant positive selection in 34 branches of the phylogenetic tree. Whole-genome duplication played a crucial role in the expansion of the ARF gene family in these species.
FRONTIERS IN GENETICS
(2021)
Editorial Material
Multidisciplinary Sciences
Ambroise Wonkam
Summary: Despite being the epicentre of sickle-cell disease, Africa is underrepresented in genome-wide association studies.
Article
Biology
Raphael T. F. Coimbra, Sven Winter, Arthur Muneza, Stephanie Fennessy, Moses Otiende, Domnic Mijele, Symon Masiaine, Jenna Stacy-Dawes, Julian Fennessy, Axel Janke
Summary: Through analyzing the genomes of wild giraffes, the study found evidence of historical gene flow between Nubian and reticulated giraffes. However, contemporary gene flow between these two lineages is minimal. The study also observed a decline in effective population sizes of Nubian and reticulated giraffes. Overall, the findings suggest that these three giraffe lineages have maintained their reproductive isolation.
Article
Biochemistry & Molecular Biology
Ji-Hye Oh, Sungyang Jo, Kye Won Park, Eun-Jae Lee, Seung Hyun Lee, Yun Su Hwang, Ha Ra Jeon, Yeonjin Ryu, Hee Jeong Yoon, Sung-Min Chun, Chong Jai Kim, Tae Won Kim, Chang Ohk Sung, Sehyun Chae, Sun Ju Chung
Summary: A whole-genome sequencing study of Korean individuals with Parkinson's disease (PD) has identified several new genetic risk factors, ranging from single nucleotide variations (SNVs) to larger DNA deletions. These findings provide a global, whole-genome view of PD and suggest that small genomic deletions in regulatory domains contribute to the risk of PD development.
EXPERIMENTAL AND MOLECULAR MEDICINE
(2023)
Article
Biology
Pedro Almeida, Estelle Proux-Wera, Allison Churcher, Lucile Soler, Jacques Dainat, Pascal Pucholt, Jessica Nordlund, Tom Martin, Ann-Christin Ronnberg-Wastljung, Bjorn Nystedt, Sofia Berlin, Judith E. Mank
Article
Rheumatology
Johanna K. Sandling, Pascal Pucholt, Lina Hultin Rosenberg, Fabiana H. G. Farias, Sergey Kozyrev, Maija-Leena Eloranta, Andrei Alexsson, Matteo Bianchi, Leonid Padyukov, Christine Bengtsson, Roland Jonsson, Roald Omdal, Benedicte A. Lie, Laura Massarenti, Rudi Steffensen, Marianne A. Jakobsen, Soren T. Lillevang, Karoline Lerang, Oyvind Molberg, Anne Voss, Anne Troldborg, Soren Jacobsen, Ann-Christine Syvanen, Andreas Jonsen, Iva Gunnarsson, Elisabet Svenungsson, Solbritt Rantapaa-Dahlqvist, Anders A. Bengtsson, Christopher Sjowall, Dag Leonard, Kerstin Lindblad-Toh, Lars Ronnblom
Summary: The study identified two main independent pathways involved in SLE susceptibility: T lymphocyte differentiation and innate immunity, characterized by HLA and interferon, respectively. Pathway PRS could define pathways in individual patients, who on average were positive for seven pathways. Pathway PRS-based clustering allowed stratification of patients into four groups with different risk score profiles.
ANNALS OF THE RHEUMATIC DISEASES
(2021)
Article
Microbiology
Andreas N. Schneider, John Sundh, Gorel Sundstrom, Kerstin Richau, Nicolas Delhomme, Manfred Grabherr, Vaughan Hurry, Nathaniel R. Street
Summary: The study compared fungal community information obtained from RNA-Seq and fungal ITS1 DNA amplicon sequencing, revealing both consistency and differences between the two methods in terms of taxonomic and functional insights. It also demonstrated the potential of transcriptomic data to provide biologically informative functional insights, advancing our understanding of the interaction and effect between host plants and their associated microbial communities.
Article
Biology
Chao Wang, Ola Wallerman, Maja-Louise Arendt, Elisabeth Sundstrom, Asa Karlsson, Jessika Nordin, Suvi Makelainen, Gerli Rosengren Pielberg, Jeanette Hanson, Asa Ohlsson, Sara Saellstrom, Henrik Ronnberg, Ingrid Ljungvall, Jens Haggstrom, Tomas F. Bergstrom, Ake Hedhammar, Jennifer R. S. Meadows, Kerstin Lindblad-Toh
Summary: The GSD_1.0 domestic dog reference genome shows a 55-fold increase in contiguity over CanFam3.1 and uncovers previously hidden functional elements. Sequencing of 27 dogs revealed millions of genetic variations, some of which could directly impact gene products.
COMMUNICATIONS BIOLOGY
(2021)
Article
Rheumatology
A. Mathioudaki, J. Nordin, A. Kastbom, P. Soderkvist, P. Eriksson, J. Cedergren, K. Lindblad-Toh, J. R. S. Meadows
Summary: This study aimed to characterize known ankylosing spondylitis (AS) susceptibility variants in a homogeneous Swedish data set and successfully replicated major histocompatibility complex (MHC) and non-MHC loci associated with AS in the Swedish population. The study showed a different replication pattern compared to discovery data sets, possibly due to differences in population demographics.
SCANDINAVIAN JOURNAL OF RHEUMATOLOGY
(2022)
Article
Genetics & Heredity
Xuyue Yang, Tanja Slotte, Jacques Dainat, Peter A. Hamback
Summary: This study reported the genome assemblies and annotations of three closely related Galerucella species with varying genome sizes and scaffold numbers. A large number of protein-coding genes were identified, contributing to future population genomics studies.
G3-GENES GENOMES GENETICS
(2021)
Article
Rheumatology
Matteo Bianchi, Sergey V. Kozyrev, Antonella Notarnicola, Lina Hultin Rosenberg, Asa Karlsson, Pascal Pucholt, Simon Rothwell, Andrei Alexsson, Johanna K. Sandling, Helena Andersson, Robert G. Cooper, Leonid Padyukov, Anna Tjarnlund, Maryam Dastmalchi, Jennifer R. S. Meadows, Louise Pyndt Diederichsen, Oyvind Molberg, Hector Chinoy, Janine Lamb, Lars Ronnblom, Kerstin Lindblad-Toh, Ingrid E. Lundberg
Summary: By conducting targeted DNA sequencing of immune-related genes in IIM patients and healthy controls, this study identified IFI35 as a potential genetic risk locus for IIMs, highlighting a genetic signature of type I IFN pathway activation. Genetic associations with AGER and PSMB8 in the major histocompatibility complex locus were detected in the antisynthetase syndrome subgroup, suggesting a less marked genetic signature of the type I IFN pathway. Enrichment analyses revealed a burden of synonymous and noncoding rare variants in IIM patients, indicating increased disease predisposition associated with these classes of rare variants.
ARTHRITIS & RHEUMATOLOGY
(2022)
Article
Genetics & Heredity
Jessika Nordin, Mats Pettersson, Lina Hultin Rosenberg, Argyri Mathioudaki, Asa Karlsson, Eva Muren, Karolina Tandre, Lars Ronnblom, Alf Kastbom, Jan Cedergren, Per Eriksson, Peter Soderkvist, Kerstin Lindblad-Toh, Jennifer R. S. Meadows
Summary: This study investigated the role of MHC in ankylosing spondylitis through typing 17 genes, identifying 25 HLA protein-coding variants associated with the disease. Novel protective associations were found in a HLA-B*27 positive population, and unique risk variants were identified in different sexes, highlighting the impact of population composition on disease associations.
FRONTIERS IN GENETICS
(2021)
Letter
Plant Sciences
Ren-Gang Zhang, Guang-Yuan Li, Xiao-Ling Wang, Jacques Dainat, Zhao-Xuan Wang, Shujun Ou, Yongpeng Ma
HORTICULTURE RESEARCH
(2022)
Article
Multidisciplinary Sciences
Simon R. Law, Alonso R. Serrano, Yohann Daguerre, John Sundh, Andreas N. Schneider, Zsofia R. Stangl, David Castro, Manfred Grabherr, Torgny Nasholm, Nathaniel R. Street, Vaughan Hurry
Summary: Carbon storage and cycling in boreal forests, which are the largest terrestrial carbon store, are influenced by the complex interactions between trees and soil microorganisms. This study developed a metatranscriptomic approach to examine the impact of nutrient enrichment on Norway spruce fine roots and the fungal community structure and function. The findings demonstrate the important role of host-microbe dynamics in mediating the carbon storage potential of boreal soils under changing nutrient conditions.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Chemistry, Analytical
Christian Greve, Hobey Tam, Manfred Grabherr, Aditya Ramesh, Bart Scheerder, Juha M. Hijmans
Summary: This study developed a novel machine learning algorithm and tested its validity for automated gait partitioning of laboratory-based and sensor-based gait data, showing low mean errors. By combining reinforcement learning with deep neural networks, significant reduction in the size of training datasets was achieved, providing high flexibility for end-users.
Article
Biochemistry & Molecular Biology
Juanita Gutierrez-Valencia, Marco Fracassetti, Emma L. Berdan, Ignas Bunikis, Lucile Soler, Jacques Dainat, Verena E. Kutschera, Aleksandra Losvik, Aurelie Desamore, P. William Hughes, Alireza Foroozani, Benjamin Laenen, Edouard Pesquet, Mohamed Abdelaziz, Olga Vinnere Pettersson, Bjorn Nystedt, Adrian C. Brennan, Juan Arroyo, Tanja Slotte
Summary: This study characterized the genetic architecture and evolution of the distyly supergene in Linum, showing that hemizygosity and thrum-specific expression of S-linked genes are major features. Structural variation plays a key role in recombination suppression, and S-linked genes are under purifying selection. These findings provide insights into the origin and maintenance of floral polymorphism.
Article
Multidisciplinary Sciences
Argyri Mathioudaki, Viktor Ljungstrom, Malin Melin, Maja Louise Arendt, Jessika Nordin, Asa Karlsson, Eva Muren, Pushpa Saksena, Jennifer R. S. Meadows, Voichita D. Marinescu, Tobias Sjoblom, Kerstin Lindblad-Toh
SCIENTIFIC REPORTS
(2020)
Article
Multidisciplinary Sciences
Diane P. Genereux, Aitor Serres, Joel Armstrong, Jeremy Johnson, Voichita D. Marinescu, Eva Muren, David Juan, Gill Bejerano, Nicholas R. Casewell, Leona G. Chemnick, Joana Damas, Federica Di Palma, Mark Diekhans, Ian T. Fiddes, Manuel Garber, Vadim N. Gladyshev, Linda Goodman, Wilfried Haerty, Marlys L. Houck, Robert Hubley, Teemu Kivioja, Klaus-Peter Koepfli, Lukas F. K. Kuderna, Eric S. Lander, Jennifer R. S. Meadows, William J. Murphy, Will Nash, Hyun Ji Noh, Martin Nweeia, Andreas R. Pfenning, Katherine S. Pollard, David A. Ray, Beth Shapiro, Arian F. A. Smit, Mark S. Springer, Cynthia C. Steiner, Ross Swofford, Jussi Taipale, Emma C. Teeling, Jason Turner-Maier, Jessica Alfoldi, Bruce Birren, Oliver A. Ryder, Harris A. Lewin, Benedict Paten, Tomas Marques-Bonet, Kerstin Lindblad-Toh, Elinor K. Karlsson
Article
Rheumatology
Gudny Ella Thorlacius, Lina Hultin-Rosenberg, Johanna K. Sandling, Matteo Bianchi, Juliana Imgenberg-Kreuz, Pascal Pucholt, Elke Theander, Marika Kvarnstrom, Helena Forsblad-d'Elia, Sara Magnusson Bucher, Katrine B. Norheim, Svein Joar Auglaend Johnsen, Daniel Hammenfors, Kathrine Skarstein, Malin V. Jonsson, Eva Baecklund, Lara A. Aqrawi, Janicke Liaaen Jensen, Oyvind Palm, Andrew P. Morris, Jennifer R. S. Meadows, Solbritt Rantapaa-Dahlqvist, Thomas Mandl, Per Eriksson, Lars Lind, Roald Omdal, Roland Jonsson, Kerstin Lindblad-Toh, Lars Ronnblom, Marie Wahren-Herlenius, Gunnel Nordmark
Summary: The clinical presentation of primary Sjogren's syndrome (pSS) varies widely. A multicentre study identified two patient subgroups based on the presence of SSA/SSB antibodies and genetic markers in the HLA region, with strong association signals found in HLA-DQA1 locus for the antibody-positive subgroup. Replication confirmed the association with MHC class I and II variants, indicating distinct clinical manifestations in pSS subgroups.