Article
Agriculture, Multidisciplinary
Huang Yi-le, Zhang Ling-kui, Zhang Kang, Chen Shu-min, Hu Jian-bin, Cheng Feng
Summary: Whole genome duplication (WGD) and tandem duplication (TD) are important mechanisms in plant genome evolution. This study found that Vitis vinifera, which did not undergo a whole genome triplication event, retained more tandem duplicated gene (TDG) clusters compared to Solanaceae species that experienced the event. There was also a bias in the functional categories of genes retained through WGD and TD, with WGD retaining dose-sensitive genes and TD retaining stress resistance genes. The study also provided evidence of gene fusion events in TDG clusters, which contribute to functional innovation.
JOURNAL OF INTEGRATIVE AGRICULTURE
(2022)
Article
Developmental Biology
Constantina Theofanopoulou
Summary: Through analyzing the evolutionary history of the oxytocin/vasotocin receptor family, the study found that there may have been a whole genome duplication event in the common ancestor of lampreys and gnathostomes, followed by segmental duplications in both lineages, or alternatively, two rounds of whole genome duplication with the first in the gnathostome-lamprey ancestor and the second in the jawed vertebrate ancestor. The study suggests that a single round of whole genome duplication scenario is more consistent with the syntax and evolution of chromosomes containing OTR-VTRs, while not excluding the possibility of two rounds of whole genome duplication.
DEVELOPMENTAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Jie Huang, Weibin Xu, Junwen Zhai, Yi Hu, Jing Guo, Caifei Zhang, Yiyong Zhao, Lin Zhang, Christopher Martine, Hong Ma, Chien-Hsun Huang
Summary: This study generated transcriptomes/genomes for 180 Solanaceae species and constructed a highly resolved phylogenetic tree. The study revealed a specific whole-genome triplication event in the evolutionary history of Solanaceae, which may have contributed to the development of fleshy fruits.
PLANT COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Pravrutha Raman, Mary C. Rominger, Janet M. Young, Antoine Molaro, Toshio Tsukiyama, Harmit S. Malik
Summary: Histones and their posttranslational modifications play diverse chromatin functions in eukaryotes. This study reveals the presence of five H2B variants widely present in mammalian genomes, with two new variants identified. These variants are broadly retained in mammals and expressed in germline cells. The findings suggest that H2B variants likely have important roles in mammalian germline cells through unconventional chromatin packaging or nonchromatin functions.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Genetics & Heredity
Guan Liu, Dongye Zhang, Tingting Zhao, Huanhuan Yang, Jingbin Jiang, Jingfu Li, He Zhang, Xiangyang Xu
Summary: This study investigates the expansion of the WRKY gene family in tomato and its wild relatives through evolutionary analysis of whole genome triplication (WGT) and tandem duplication (TD) events, providing insight into the response mechanisms to biotic stress in plants.
FRONTIERS IN GENETICS
(2022)
Article
Biochemistry & Molecular Biology
Magdalena Bohutinska, Mark Alston, Patrick Monnahan, Terezie Mandakova, Sian Bray, Pirita Paajanen, Filip Kolar, Levi Yant
Summary: Two plant species exhibit different genomic responses to whole genome duplication, suggesting the presence of multiple evolutionary trajectories when adapting to the challenges of whole genome duplication.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Genetics & Heredity
Xi Wang, Yu Xiao, Zi-Han He, Ling-Ling Li, Yan-Wen Lv, Xin-Sheng Hu
Summary: Toona ciliata and Toona sinensis, two important timber species in China, show genetic and evolutionary divergences that are potentially associated with their reproductive systems and ecological adaptation.
Article
Multidisciplinary Sciences
Donald Davesne, Matt Friedman, Armin D. Schmitt, Vincent Fernandez, Giorgio Carnevale, Per E. Ahlberg, Sophie Sanchez, Roger B. J. Benson
Summary: Teleost fishes, which make up half of all vertebrate species, underwent a whole-genome duplication early in their evolutionary history, likely contributing to their exceptional radiation. By analyzing bone cell volumes, researchers have concluded that this duplication occurred in the stem lineage of teleosts, with all known extinct stem-group teleosts possessing duplicated genomes. This early event allowed for significant postduplication reorganization before the emergence of the teleost crown group, indicating a potentially indirect link between WGD and evolutionary success.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biotechnology & Applied Microbiology
Chunliu Zuo, Lan Zhang, Xinyue Yan, Xinyue Guo, Qing Zhang, Songyang Li, Yanling Li, Wen Xu, Xiaoming Song, Jinpeng Wang, Min Yuan
Summary: This study identified nine BZR1 genes in celery and demonstrated their important roles in plant development. The findings provide a foundation for further research on agronomic traits and environmental adaptation of celery.
Article
Biochemistry & Molecular Biology
Kevin J. Peterson, Alan Beavan, Peter J. Chabot, Mark A. McPeek, Davide Pisani, Bastian Fromm, Oleg Simakov
Summary: WGDs do not result in the creation of miRNA novelty, nor do WGDs correlate to increases in complexity. Instead, it is the number of miRNA seed sequences in the genome itself that not only better correlate to instances in complexification, but also mechanistically explain why complexity increases when new miRNA families are established.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Review
Biochemistry & Molecular Biology
Emily Anna Baker, Alison Woollard
Summary: Duplicated genes play a crucial role in evolutionary processes as both substrates and catalysts, contributing to the phenotypic evolution of all life on Earth. Recent research on paralogues from across the tree of life challenges the classical framework and provides insights into the ways in which duplicated genes shape genetic architecture.
ESSAYS IN BIOCHEMISTRY
(2022)
Article
Plant Sciences
Jennifer A. Noble, Nicholas Bielski, Ming-Che James Liu, Thomas A. DeFalco, Martin Stegmann, Andrew D. L. Nelson, Kara McNamara, Brooke Sullivan, Khanhlinh K. Dinh, Nicholas Khuu, Sarah Hancock, Shin-Han Shiu, Cyril Zipfel, Alice Y. Cheung, Mark A. Beilstein, Ravishankar Palanivelu
Summary: This study investigates the evolution of the LLG gene family and the function and expression of angiosperm LLGs. The results show that LLG diversity is mainly due to lineage-specific duplication events, and expression divergence explains the retention of LLG paralogs. The expression of LLG duplicates in angiosperms is also found to be divergent.
Article
Plant Sciences
Seongmin Hong, Yong Pyo Lim, Suk-Yoon Kwon, Ah-Young Shin, Yong-Min Kim
Summary: In polyploids, whole genome duplication plays a significant role in genome expansion, evolution, and diversification. The flowering-time gene family, one of the largest expanded gene families in plants, has functionally diversified through evolution, providing advantages for plant adaptation and survival.
FRONTIERS IN PLANT SCIENCE
(2021)
Editorial Material
Biochemistry & Molecular Biology
Filip Kolar
Summary: Polyploidy, resulting from whole genome duplication, is widespread in Eukaryotic kingdoms and plays a significant role in plant evolution. However, tools for population genetic and genomic analysis of polyploid systems are limited, leading to a lag in research compared to diploid systems. The development of software specifically designed for polyploid population genomic analysis has opened up new opportunities in the field.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Biodiversity Conservation
Pamela S. Soltis, Douglas E. Soltis
Summary: The study of plant genomes helps understand the evolutionary history of plants, guiding crop improvement, medicine discovery, and species conservation. Plant genomes show diversity and carry evolutionary history, but our knowledge of them is limited.
PLANTS PEOPLE PLANET
(2021)
Article
Biochemistry & Molecular Biology
Christina B. Azodi, Jeremy Pardo, Robert VanBuren, Gustavo de los Campos, Shin-Han Shiu
Article
Biotechnology & Applied Microbiology
Nicholas L. Panchy, John P. Lloyd, Shin-Han Shiu
Article
Plant Sciences
Birte Schwarz, Christina B. Azodi, Shin-Han Shiu, Petra Bauer
Article
Multidisciplinary Sciences
Yan Bao, Wei-Meng Song, Peipei Wang, Xiang Yu, Bei Li, Chunmei Jiang, Shin-Han Shiu, Hongxia Zhang, Diane C. Bassham
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Biology
Pengxiang Fan, Peipei Wang, Yann-Ru Lou, Bryan J. Leong, Bethany M. Moore, Craig A. Schenck, Rachel Combs, Pengfei Cao, Federica Brandizzi, Shin-Han Shiu, Robert L. Last
Article
Multidisciplinary Sciences
Wen-Yu Liu, Hsin-Hung Lin, Chun-Ping Yu, Chao-Kang Chang, Hsiang-June Chen, Jinn-Jy Lin, Mei-Yeh Jade Lu, Shih-Long Tu, Shin-Han Shiu, Shu-Hsing Wu, Maurice S. B. Ku, Wen-Hsiung Li
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Biotechnology & Applied Microbiology
Peipei Wang, Fanrui Meng, Bethany M. Moore, Shin-Han Shiu
Summary: This study identified factors contributing to variable coverage regions in plant genome assemblies, particularly in tomato. High coverage regions were found to have higher simple sequence repeat and tandem gene densities, with a significant proportion potentially misassembled due to duplicate sequences. Additionally, a predictive model showed that misassembled, high coverage regions were often surrounded by simple sequence repeats, pseudogenes, and transposon elements. Further testing is needed to determine the generality of these factors in other species.
Article
Biochemistry & Molecular Biology
Siobhan A. Cusack, Peipei Wang, Serena G. Lotreck, Bethany M. Moore, Fanrui Meng, Jeffrey K. Conner, Patrick J. Krysan, Melissa D. Lehti-Shiu, Shin-Han Shiu
Summary: Genetic redundancy refers to a situation where an individual with a loss-of-function mutation in one gene does not show an apparent phenotype until one or more paralogs are also knocked out. Machine learning models were established to predict whether a gene pair is likely redundant in Arabidopsis thaliana, with features such as recent duplication events, annotation as a transcription factor, downregulation during stress conditions, and similar expression patterns under stress conditions being important predictors.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Plant Sciences
Peipei Wang, Bethany M. Moore, Sahra Uygun, Melissa D. Lehti-Shiu, Cornelius S. Barry, Shin-Han Shiu
Summary: Plant metabolites from various pathways play important roles in plant survival, human nutrition, and medicine. This study explores different data combinations and strategies to predict plant pathway memberships accurately, emphasizing the importance of data quality. Unsupervised learning performs better in prediction, and models based on gene-to-pathway expression similarities outperform those based solely on expression levels.
Article
Biochemistry & Molecular Biology
Bethany M. Moore, Yun Sun Lee, Peipei Wang, Christina Azodi, Erich Grotewold, Shin-Han Shiu
Summary: The modeling and experimental validation of transcriptional response to wounding and jasmonic acid identified temporal cis-regulatory codes and new regulatory sequences important for wound response. The study provides a global predictive model for wound response and highlights the significance of regulatory factors and open chromatin regions in different types of wound response.
Review
Plant Sciences
Peipei Wang, Ally M. Schumacher, Shin-Han Shiu
Summary: Predicting plant metabolic pathways is crucial for metabolic engineering and the production of plant metabolite-derived medicine. Recent progress has been made in using multi-omics data and computational approaches to predict the pathways, complementing traditional genetic and biochemical approaches.
CURRENT OPINION IN PLANT BIOLOGY
(2022)
Article
Plant Sciences
Peipei Wang, Fanrui Meng, Paityn Donaldson, Sarah Horan, Nicholas L. Panchy, Elyse Vischulis, Eamon Winship, Jeffrey K. Conner, Patrick J. Krysan, Shin-Han Shiu, Melissa D. Lehti-Shiu
Summary: This study measured fitness traits in Arabidopsis using image segmentation and object detection methods, and found fitness effects for certain genes. The object detection-based algorithm yielded more accurate results compared to the segmentation-based method, providing near-perfect seed counts and highly accurate fruit counts.
Article
Multidisciplinary Sciences
Wen-Yu Liu, Chun-Ping Yu, Chao-Kang Chang, Hsiang-June Chen, Meng-Yun Li, Yi-Hua Chen, Shin-Han Shiu, Maurice S. B. Ku, Shih-Long Tu, Mei-Yeh Jade Lu, Wen-Hsiung Li
Summary: The superior photosynthetic efficiency of C-4 leaves over C-3 leaves is due to their unique Kranz anatomy. This study identified the regulators and underlying molecular mechanisms of Kranz anatomy development in maize leaves. The researchers analyzed transcriptomic data and identified transcription factors and auxin transporter genes that are involved in early Kranz development. They constructed a gene regulatory network and provided insights into the regulation of early leaf development.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Yun Sun Lee, Shin-Han Shiu, Erich Grotewold
Summary: The association of bHLH and ACT-like domains is unique to the plantae kingdom, suggesting a common origin. The ACT-like domains mediate homodimer formation and negatively affect DNA binding of the associated bHLH domains. The evolution of the ACT-like domains is constrained by the bHLH domains.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biochemistry & Molecular Biology
Amy Baetsen-Young, Huan Chen, Shin-Han Shiu, Brad Day
Summary: The study compared the response of Fusarium virguliforme in maize and soybean hosts, revealing that induction of senescence dampening transcriptional regulators occurred in infected maize, while senescence-associated processes were observed in soybean, suggesting root senescence as a key factor in symptomatic versus asymptomatic host-fungal interactions. This process supports the lifestyle and virulence of F. virguliforme during biotrophy to necrotrophy transitions, indicating a transcriptomic reprogramming favoring susceptibility and induction of pathways associated with senescence during the necrotrophic stage of fungal development within symptomatic hosts.