Article
Plant Sciences
Hui Liu, Hai-Meng Lyu, Kaikai Zhu, Yves Van de Peer, Zong-Ming (Max) Cheng
Summary: This study identified multiple gene families in plant genomes containing intronless or intron-poor genes, which play important roles in response to drought and salt stress, epigenetic processes, and plant development. The origin, evolution, and potential functions of these intronless and intron-poor sub-families provide insights into plant genome evolution and gene functional divergence.
Article
Plant Sciences
Negin Mirghasemi, Elena Fanelli, Salar Jamali, Mohammed Mehdi Sohani, Francesca De Luca
Summary: The study characterized and evolution of three ss-1,4-endoglucanase genes in the root-lesion nematode Pratylenchus loosi, showing they resulted from gene duplication followed by sequence and gene structure diversification. The Pl-eng-2 gene was fully determined and found to be localized in the secretory esophageal glands of all life stages, while Pl-eng-3 and Pl-eng-4 were only partially sequenced, with loss of the linker domain and carbohydrate-binding domain during evolution.
Article
Forestry
Jianlun Zhao, Enkai Xu, Qirui Wang
Summary: The AT-hook motif nuclear-localized (AHL) family members in peach were identified and analyzed. The genes were classified into two clades (Clade-A and Clade-B) and three subfamilies. The expression patterns, evolution, and duplication events of PpAHLs were investigated, and their roles in plant development and response to drought stress were discovered.
Article
Multidisciplinary Sciences
Christina Akirtava, Gemma E. May, C. Joel McManus
Summary: The study found that the putative IRESes previously reported in Hox gene hTLs are rarely included in transcript leaders and instead function independently as transcriptional promoters. Additionally, the proposed RNA structure of the putative Hoxa9 IRES is not conserved. The majority of hTLs with putative IRES activity overlap with transcriptional promoters, enhancers, and 3' splice sites, arguing against widespread IRES-like activities from hTLs.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biotechnology & Applied Microbiology
Ailan Wang, Wei Chen, Shiheng Tao
Summary: In the Caenorhabditis genus, extensive species-specific tandem duplications and occasional gene loss drove the rapid evolution of the F-box gene family, leading to complex gene structural variation and diversified functions affecting growth and development within and among Caenorhabditis species. Functional divergence of F-box genes in Caenorhabditis species was suggested to be achieved through sub-functionalization by highly divergent stage-specific expression patterns. This study lays the foundation for future functional studies on the evolution of F-box genes in the Caenorhabditis genome.
Article
Biochemistry & Molecular Biology
Gabriela Giannina Schaefer, Lukas Joerg Grebe, Robin Schinkel, Bernhard Lieb
Summary: The study reveals multiple gene duplications and intron gains within Caenogastropoda, indicating these as general features of Apogastropoda hemocyanins. While exon-intron structures are consistent within Tectipleura lineages, they vary significantly within Caenogastropoda and even among paralogous hemocyanin genes of the same species. This suggests that intron accumulation occurred gradually within Caenogastropoda, leading to a multitude of introns.
JOURNAL OF MOLECULAR EVOLUTION
(2021)
Article
Plant Sciences
Wei Wang, Xiaoning Li, Shugao Fan, Yang He, Meng Wei, Jiayi Wang, Yanling Yin, Yanfeng Liu
Summary: In this study, we conducted a comprehensive analysis of L. perenne and identified 3,770 tandem duplication genes (TDGs). Evolutionary analysis revealed a duplication event in L. perenne approximately 7.69 million years ago. Functional analysis showed that these TDGs were mainly enriched in photosynthesis, hormone-mediated signaling pathways, and stress responses, indicating their contribution to environmental adaptability. Expression profile analysis demonstrated that TDGs had highly conserved expression levels and were significantly lower compared to all genes in different tissues, but had a higher frequency of differentially expressed genes (DEGs) in response to low-temperature stress. Furthermore, analysis of an important gene family revealed that ELIPs were likely responsible for low temperature responses and adaptation in L. perenne. This study provides evidence for the genetic basis of low-temperature adaptation and valuable resources for stress resistance improvement in L. perenne.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Forestry
Nan Xu, Xue-Min Han, Yuan Xue, Xiang-Lin Zhuge, Chao-Nan Guan, Hai-Ling Yang
Summary: This study provides a comprehensive analysis of laccase copies in the Populus trichocarpa genome and explores the evolutionary process and functional divergence of terrestrial plant laccases.
Review
Biochemistry & Molecular Biology
Huijing Ma, Mengxia Wang, Yong E. Zhang, Shengjun Tan
Summary: Since the discovery of the first transposon by Dr. Barbara McClintock, the prevalence and diversity of transposable elements (TEs) have been gradually recognized. TEs contribute to organismal evolution through functional sequences and shuffling genomic sequences. TE-mediated gene duplications result in exon shuffling and neofunctionalization. The future of this field involves studying the mechanisms and functions of TE-mediated duplicates.
JOURNAL OF GENETICS AND GENOMICS
(2023)
Article
Medicine, General & Internal
Harry P. Erba, Pau Montesinos, Hee-Je Kim, Elzbieta Patkowska, Radovan Vrhovac, Pavel Zak, Po -Nan Wang, Tsvetomir Mitov, James Hanyok, Yasser Mostafa Kamel, Jaime E. Connolly Rohrbach, Li Liu, Aziz Benzohra, Arnaud Lesegretain, Jorge Cortes, Alexander E. Perl, Mikkael A. Sekeres, Herve Dombret, Sergio Amadori, Jianxiang Wang, Mark J. Levis, Richard F. Schlenk
Summary: The aim of the study was to compare the effect of Quizartinib versus placebo on overall survival in patients with FLT3-ITD-positive newly diagnosed AML. The results showed that the addition of Quizartinib to standard chemotherapy can improve overall survival in adult patients with FLT3-ITD-positive newly diagnosed AML.
Article
Mathematics, Applied
Mengwei Xu, Jane J. Ye
Summary: This paper introduces the relaxed constant positive linear dependence constraint qualification (RCPLD) for disjunctive systems, which are composed of multiple polyhedral convex sets. The RCPLD introduced in this paper is weaker but still a constraint qualification compared to the one introduced for a more general system. To obtain the local error bound for the disjunctive system, the piecewise RCPLD is proposed, under which the error bound property holds under certain conditions. The results are further applied to specific types of disjunctive programs, such as MPEC, MPVC, and MPSC, achieving error bound properties and introducing new constraint qualifications.
SET-VALUED AND VARIATIONAL ANALYSIS
(2023)
Article
Evolutionary Biology
Kevin T. Bilyk, Xuan Zhuang, Chiara Papetti
Summary: Evolution in the chronic cold of the Southern Ocean has resulted in significant genetic changes in cryonotothenioid fishes. Positive selective pressure has led to changes in gene regulatory factors, cell cycle genes, and genes related to cellular adhesion, all of which play important roles in adapting to freezing temperatures. On the other hand, the relaxation of selective pressure has primarily affected genes related to mitochondrial function. The loss of hemoproteins, however, has had minimal impact on protein-coding genes. Overall, long-term exposure to cold has led to profound changes in cryonotothenioid genomes, making it challenging for them to adapt to a rapidly changing climate.
GENOME BIOLOGY AND EVOLUTION
(2023)
Article
Virology
Bryan P. Brown, Denis Chopera, Enock Havyarimana, Jerome Wendoh, Shameem Jaumdally, Donald D. Nyangahu, Clive M. Gray, Darren P. Martin, Arvind Varsani, Heather B. Jaspan
Summary: The study found elevated positive selection in the genomes of crAssphages, particularly in the RNA polymerase and phage tail protein encoding genes, potentially mediated by interactions between crAssphages and their bacterial partners.