Article
Multidisciplinary Sciences
Francesca Menghi, Edison T. Liu
Summary: Cancer functional genomics explores how genetic, epigenetic, and transcriptional changes impact cancer phenotypes, using next generation sequencing and systems biology to uncover novel cancer vulnerabilities beyond the traditional one gene-one phenotype paradigm.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Cheng Sun, Jiaxing Huang, Yun Wang, Xiaomeng Zhao, Long Su, Gregg W. C. Thomas, Mengya Zhao, Xingtan Zhang, Irwin Jungreis, Manolis Kellis, Saverio Vicario, Igor Sharakhov, Semen M. Bondarenko, Martin Hasselmann, Chang N. Kim, Benedict Paten, Luca Penso-Dolfin, Li Wang, Yuxiao Chang, Qiang Gao, Ling Ma, Lina Ma, Zhang Zhang, Hongbo Zhang, Huahao Zhang, Livio Ruzzante, Hugh M. Robertson, Yihui Zhu, Yanjie Liu, Huipeng Yang, Lele Ding, Quangui Wang, Dongna Ma, Weilin Xu, Cheng Liang, Michael W. Itgen, Lauren Mee, Gang Cao, Ze Zhang, Ben M. Sadd, Matthew W. Hahn, Sarah Schaack, Seth M. Barribeau, Paul H. Williams, Robert M. Waterhouse, Rachel Lockridge Mueller
Summary: Bumblebees are globally important pollinators facing threats such as pathogen transmission, habitat loss, pesticide usage, and global climate change. By de novo sequencing and assembling genomes of 17 species, researchers have identified genetic and genomic variations potentially linked to key ecological and behavioral traits. This study provides insights into the evolutionary processes of bumblebee genes and genomes across phylogeny and their adaptations for survival.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biology
Raul A. Gonzalez-Pech, Timothy G. Stephens, Yibi Chen, Amin R. Mohamed, Yuanyuan Cheng, Sarah Shah, Katherine E. Dougan, Michael D. A. Fortuin, Remi Lagorce, David W. Burt, Debashish Bhattacharya, Mark A. Ragan, Cheong Xin Chan
Summary: Genome sequences of Symbiodiniaceae are still scarce due to their large genome sizes and unique genome features. This study presented de novo genome assemblies of seven members of the genus Symbiodinium, revealing high sequence and structural divergence among different lineages, with some Symbiodinium isolates showing comparable divergence to distinct genera of Symbiodiniaceae.
Article
Plant Sciences
Tong Zhou, Ning Wang, Yuan Wang, Xian-Liang Zhang, Bao-Guo Li, Wei Li, Jun-Ji Su, Cai-Xiang Wang, Ai Zhang, Xiong-Feng Ma, Zhong-Hu Li
Summary: In this study, the evolutionary rate, domestication selection, and genetic relationships of cotton species were investigated using chloroplast genome sequences. The results showed that there is significant genetic differentiation between cultivated cotton accessions and semi-wild races, with the wild species experiencing greater selection pressure and the cultivated cotton genotypes undergoing artificial and domestication selection.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Multidisciplinary Sciences
Kazuki Ichikawa, Riki Kawahara, Takeshi Asano, Shinichi Morishita
Summary: This study uses a high-precision algorithm to determine complex TR structures from long accurate sequences, revealing the abundance and diversity of TRs. It finds that complex TRs are more common than single-unit TRs, and that they tend to consist of <10-bp units. Several known disease-associated TRs are found in loci with extended TRs, making them potential candidates for disease association.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Kayoko Yamamoto, Takashi Hamaji, Hiroko Kawai-Toyooka, Ryo Matsuzaki, Fumio Takahashi, Yoshiki Nishimura, Masanobu Kawachi, Hideki Noguchi, Yohei Minakuchi, James G. Umen, Atsushi Toyoda, Hisayoshi Nozaki
Summary: Transitions between separate sexes and other mating systems are common in eukaryotes, with the research on a haploid dioecious green algal species showing a breakdown of dioecy. The investigation into the sex-determining gene regions in different species revealed variations in the SDR and the involvement of homothallism in the breakdown of dioecy.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Plant Sciences
Sophia V. Yudina, Mikhail I. Schelkunov, Lars Nauheimer, Darren Crayn, Sahut Chantanaorrapint, Michal Hrones, Michal Sochor, Martin Dancak, Shek-Shing Mar, Hong Truong Luu, Maxim S. Nuraliev, Maria D. Logacheva
Summary: This study investigates a diversity of plastid genomes in closely related non-photosynthetic plants, illustrating how gradual gene loss shapes the miniaturized plastomes of these plants and revealing the process of reductive evolution in heterotrophic plants.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Qiang Li, Peng Wu, Lijiao Li, Huiyu Feng, Wenying Tu, Zhijie Bao, Chuan Xiong, Mingying Gui, Wenli Huang
Summary: The present study assembled and compared eleven novel complete mitogenomes of Boletus, revealing differences in gene arrangement and evolution rates among Boletus species. The study also found a close relationship between Boletus species and Paxillus in the phylogenetic tree of 72 Agaricomycetes.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Plant Sciences
Lingfei Li, Xiaoli Chen, Dongming Fang, Shanshan Dong, Xing Guo, Na Li, Lucia Campos-Dominguez, Wenguang Wang, Yang Liu, Xiaoan Lang, Yang Peng, Daike Tian, Daniel C. Thomas, Weixue Mu, Min Liu, Chenyu Wu, Ting Yang, Suzhou Zhang, Leilei Yang, Jianfen Yang, Zhong-Jian Liu, Liangsheng Zhang, Xingtan Zhang, Fei Chen, Yuannian Jiao, Yalong Guo, Mark Hughes, Wei Wang, Xiaofei Liu, Chunmei Zhong, Airong Li, Sunil Kumar Sahu, Huanming Yang, Ernest Wu, Joel Sharbrough, Michael Lisby, Xin Liu, Xun Xu, Douglas E. Soltis, Yves Van de Peer, Catherine Kidner, Shouzhou Zhang, Huan Liu
Summary: This study investigates the lineage evolution and shade adaptation of Begonia, one of the most species-rich angiosperm genera, using chromosome-scale genome assemblies for four species and additional genomic data. The results reveal a lineage-specific whole-genome duplication event and expansions of gene families related to shade adaptation.
Article
Biotechnology & Applied Microbiology
Yu-Tong Ji, Xiao-Juan Zhou, Qian Yang, Yuan-Biao Lu, Jun Wang, Jie-Xin Zou
Summary: A new species classification scheme of the freshwater crab genus Aparapotamon has been discovered, and mitochondrial genome characteristics and protein-coding genes associated with altitudinal adaptation have been identified. Geological movements of the Qinghai-Tibet Plateau and Hengduan Mountains significantly influenced speciation and differentiation of the genus.
Article
Biochemistry & Molecular Biology
Wenjie Mu, Kexin Li, Yongzhi Yang, Adina Breiman, Jiao Yang, Ying Wu, Mingjia Zhu, Shuai Wang, Pilar Catalan, Eviatar Nevo, Jianquan Liu
Summary: The study found that both homeologous exchanges and homeologous expression bias show consistency across multiple allopolyploidization events, and are closely related to the progenitor species genomes. In addition, the density of transposons is not associated with the initial establishment of subgenome dominance, but rather inherited from the progenitor genome. Drought response genes are highly induced in the subgenomes, contributing to the species' adaptation to arid habitats.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Microbiology
Owen Donohoe, Haiyan Zhang, Natacha Delrez, Yuan Gao, Nicolas M. Suarez, Andrew J. Davison, Alain Vanderplasschen
Summary: AngHV-1 shows slower evolutionary rate and less positive selection compared to other cypriniviruses, possibly due to differences in host species and epidemiological circumstances. There is significantly lower genetic diversity in core gene sequences within cyprinivirus species clades, suggesting more rigorous purifying selection post species clade divergence.
Article
Biology
Pengju Zhao, Lihong Gu, Yahui Gao, Zhangyuan Pan, Lei Liu, Xingzheng Li, Huaijun Zhou, Dongyou Yu, Xinyan Han, Lichun Qian, George E. Liu, Lingzhao Fang, Zhengguang Wang
Summary: This study found that transposable elements (TEs), particularly young short interspersed nuclear elements (SINEs), play important roles in genetic polymorphisms, chromatin architecture, gene regulatory networks, and genomic evolution in pigs. Silencing of young SINEs was observed through histone modifications, DNA methylation, and decreased accessibility, but some active young SINE transcripts showed tissue-specific expression. The presence of population-specific dimorphic SINEs suggested their involvement in local adaptation, and these SINEs were found to be associated with candidate genes related to complex traits in pigs.
COMMUNICATIONS BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Yong-Bi Fu
Summary: The study analyzed the cp genomes of five Aegilops and 11 Triticum species and subspecies, revealing similarities in genome structure and gene arrangement among the species. The analysis also detected a large number of SNPs and SSRs, with the highest nucleotide diversity in a specific genomic region and weak selection pressure on cp coding genes. Phylogenetic analyses confirmed three deep lineages representing diploid species within the Triticum-Aegilops complex, with the maternal divergence estimated to have occurred around 8200-11,200 years ago. These findings provide valuable insights for further genomic studies and understanding the maternal divergence of the complex.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
David Peris, Emily J. Ubbelohde, Meihua Christina Kuang, Jacek Kominek, Quinn K. Langdon, Marie Adams, Justin A. Koshalek, Amanda Beth Hulfachor, Dana A. Opulente, David J. Hall, Katie Hyma, Justin C. Fay, Jean-Baptiste Leducq, Guillaume Charron, Christian R. Landry, Diego Libkind, Carla Goncalves, Paula Goncalves, Jose Paulo Sampaio, Qi-Ming Wang, Feng-Yan Bai, Russel L. Wrobel, Chris Todd Hittinger
Summary: The authors describe the geographical distribution, hosts, substrates, and phylogenetic relationships for 1,794 Saccharomyces strains. Through analyzing complete genome sequences of 163 strains and phenotyping 128 phylogenetically diverse strains, they provide insights into how gene flow and selection have affected traits in the evolution of this genus. These findings elevate the importance of Saccharomyces as a model for understanding biodiversity and evolution in microbial eukaryotes.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Elzbieta Wolny, Aleksandra Skalska, Agnieszka Braszewska, Luis A. J. Mur, Robert Hasterok
Summary: Salt stress affects germination and root growth in Brachypodium, influencing the expression of cell wall expansion-regulating proteins, induction of cell cycle genes, and alterations in genomic and epigenetic mechanisms such as histone acetylation and DNA methylation. These findings suggest a complex molecular response to salt stress in plants, indicating potential avenues for further functional genomics research.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Agronomy
F. J. Canales, G. Montilla-Bascon, W. A. Bekele, C. J. Howarth, T. Langdon, N. Rispail, N. A. Tinker, E. Prats
Summary: Genomic analysis of Mediterranean oats reveals high genetic diversity and adaptation loci; an interactive map resource combining genetic and phenotypic data was created; distinct genetic differences and adaptation loci were identified in red and white oat types from the Mediterranean region.
THEORETICAL AND APPLIED GENETICS
(2021)
Article
Cell Biology
Aleksandra Skalska, Elzbieta Wolny, Manfred Beckmann, John H. Doonan, Robert Hasterok, Luis A. J. Mur
Summary: This study conducted a comparative metabolomic analysis of embryos and endosperms from three annual Brachypodium species and found that the metabolomic impact of allotetraploidization could be observed as overlapping changes in seed germination process within 4 hours after imbibition. The formation of BdBs maintained much of the Bs metabolome during early stages of germination, suggesting an important role of elevated sugar metabolism in germination.
Article
Cell Biology
Aleksandra Skalska, Manfred Beckmann, Fiona Corke, Gulsemin Savas Tuna, Metin Tuna, John H. Doonan, Robert Hasterok, Luis A. J. Mur
Summary: Through studying the Turkish Brachypodium collection, it was found that genomic and methylomic variation differentiated into two subpopulations, coastal and central. By comparing the metabolomes of the two subpopulations, it was observed that the central subpopulation exhibited a metabolomic shift in response to drought, while the coastal subpopulation did not show significant changes.
Article
Biochemistry & Molecular Biology
Artur Pinski, Alexander Betekhtin, Jolanta Kwasniewska, Lukasz Chajec, Elzbieta Wolny, Robert Hasterok
Summary: Inhibiting prolyl-4-hydroxylases with 3,4-DHP results in vacuolar-type cell death in roots, highlighting the important role of HRGPs in root hair development and root growth.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Plant Sciences
Elisa Bellucci, Orlando Mario Aguilar, Saleh Alseekh, Kirstin Bett, Creola Brezeanu, Douglas Cook, Lucia de la Rosa, Massimo Delledonne, Denise F. Dostatny, Juan J. Ferreira, Valerie Geffroy, Sofia Ghitarrini, Magdalena Kroc, Shiv Kumar Agrawal, Giuseppina Logozzo, Mario Marino, Tristan Mary-Huard, Phil McClean, Vladimir Meglic, Tamara Messer, Frederic Muel, Laura Nanni, Kerstin Neumann, Filippo Servalli, Silvia Strajeru, Rajeev K. Varshney, Marta W. Vasconcelos, Massimo Zaccardelli, Aleksei Zavarzin, Elena Bitocchi, Emanuele Frontoni, Alisdair R. Fernie, Tania Gioia, Andreas Graner, Luis Guasch, Lena Prochnow, Markus Oppermann, Karolina Susek, Maud Tenaillon, Roberto Papa
Summary: Food legumes play a crucial role in addressing various challenges in agriculture and society, contributing to climate change mitigation, agrobiodiversity conservation, sustainable agriculture, food security, and human health. Utilizing intelligent collections and genetic resource characterization can promote the conservation and utilization of food legumes, benefiting the healthy food system and sustainable agriculture.
Article
Agronomy
A. A. Gnutikov, N. N. Nosov, I. G. Loskutov, E. M. Machs, E. Blinova, N. S. Probatova, T. Langdon, A. Rodionov
Summary: The study clarified the origin of diploid C-genome oat Avena bruhnsiana from Azerbaijan, its relationship with A. ventricosa and A. clauda, as well as revealed the rDNA sources of A. bruhnsiana and its relationship with other species.
Editorial Material
Biochemistry & Molecular Biology
Robert Hasterok, Alexander Betekhtin
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Christoph Stritt, Elena L. Gimmi, Michele Wyler, Abdelmonaim H. Bakali, Aleksandra Skalska, Robert Hasterok, Luis A. J. Mur, Nicola Pecchioni, Anne C. Roulin
Summary: Wild plant populations of Brachypodium distachyon exhibit extensive genetic subdivision, influenced by the interplay of high selfing and seed dispersal rates. The species' evolution is characterized by the independent expansion of three lineages during the Upper Pleistocene, with selfing and dispersal maintaining high genotypic diversity at regional scales.
Article
Plant Sciences
Ruben Sancho, Luis A. Inda, Antonio Diaz-Perez, David L. Des Marais, Sean Gordon, John P. Vogel, Joanna Lusinska, Robert Hasterok, Bruno Contreras-Moreira, Pilar Catalan
Summary: We designed a subgenome detection pipeline (PhyloSD) that can identify the progenitor subgenomes of six grass Brachypodium allopolyploids and infer their hypothetical evolutionary scenarios for their origins.
Article
Plant Sciences
Natalia Borowska-Zuchowska, Ewa Robaszkiewicz, Serhii Mykhailyk, Joanna Wartini, Artur Pinski, Ales Kovarik, Robert Hasterok
Summary: Nucleolar dominance (ND) is an epigenetic phenomenon that describes the selective inactivation of 35S rDNA loci from one progenitor in hybrids or allopolyploids. This study found that the stability of ND in different genotypes of Brachypodium hybridum may vary, with genotype-specific loss possibly occurring after fertilization during development. This suggests that B. hybridum is an attractive model for studying ND in grasses.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Food Science & Technology
Catherine J. Howarth, Pilar M. J. Martinez-Martin, Alexander A. Cowan, Irene M. Griffiths, Ruth Sanderson, Susan J. Lister, Tim Langdon, Sarah Clarke, Nick Fradgley, Athole H. Marshall
Summary: The study revealed significant differences in physical grain quality, composition, and yield across different environments, with grain yield closely related to grain number and milling quality related to grain size attributes. Genotype-by-environment interaction played a considerable role in determining grain quality traits, with some varieties showing higher sensitivity to environmental conditions. Environmental factors, such as temperature and rainfall during specific stages of crop development, were found to be correlated with grain yield and quality attributes.
Review
Plant Sciences
Robert Hasterok, Pilar Catalan, Samuel P. Hazen, Anne C. Roulin, John P. Vogel, Kai Wang, Luis A. J. Mur
Summary: It has been 20 years since Brachypodium distachyon was suggested as a model grass species, and the research has now expanded to the entire genus. Extensive genome sequencing and cytomolecular studies have provided important resources for understanding population diversity and various aspects of plant biology. Brachypodium is not only relevant to the biofuel industry, but also serves as an intriguing model plant for studying climate change and combinatorial stress.
TRENDS IN PLANT SCIENCE
(2022)