Review
Genetics & Heredity
Ron Mizrahi, Sofia Shevtsov-Tal, Oren Ostersetzer-Biran
Summary: Mitochondria are organelles responsible for cellular energy production. Plant mitochondria have introns that play a significant role in protein splicing. These splicing processes are regulated by various protein factors and may be associated with cellular and environmental signals.
Article
Plant Sciences
Sofia Shevtsov-Tal, Corinne Best, Roei Matan, Sam A. Chandran, Gregory G. Brown, Oren Ostersetzer-Biran
Summary: Plant organellar introns have degenerated during evolution, relying on host-acting protein cofactors for splicing, which may link cellular signals with respiratory functions.
Article
Plant Sciences
Shi-Kai Cao, Rui Liu, Miaodi Wang, Feng Sun, Aqib Sayyed, Hong Shi, Xiaomin Wang, Bao-Cai Tan
Summary: This study identified the role of a small P-type pentatricopeptide repeat protein, SPR2, in mediating the splicing of over half of the Group II introns in maize mitochondria. SPR2 interacts with PPR-SMR1 and other splicing factors, suggesting its involvement in the formation of a splicing complex.
Article
Plant Sciences
Kaijian Fan, Qinghui Fu, Qianhan Wei, Sinian Jia, Anqi Zhao, Tengteng Wang, Jie Cao, Yan Liu, Zhenjing Ren, Yunjun Liu
Summary: This study identified a maize ZmnMAT1 gene encoding a maturase with specific biological functions in maize and involvement in intron splicing in mitochondria. Loss of ZmnMAT1 resulted in reduced splicing efficiency, arrested embryogenesis, and endosperm development.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Dario Monachello, Marc Lauraine, Sandra Gillot, Francois Michel, Maria Costa
Summary: Mobile group II introns are retrotransposable elements that insert themselves into DNA target sites with the help of base-pairing interactions and the reverse transcriptase enzyme. A new base-pairing interaction named EBS2a-IBS2a has been identified, which is crucial for intron mobility by driving unwinding of the DNA duplex and is stabilized by the reverse transcriptase in a non-sequence-specific manner. This discovery has important implications for the biotechnological applications of group II introns in bacterial gene targeting.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Plant Sciences
Qiqi Chen, Pan Shen, Ralph Bock, Shengchun Li, Jiang Zhang
Summary: A global survey of plastid gene expression during fruit ripening in kiwifruit reveals cis-elements that can potentially trigger high-level transgene expression in edible tissues, providing valuable resources for analyzing plastid gene expression and future efforts to engineer the plastid genome of kiwifruit.
PLANT CELL REPORTS
(2022)
Article
Plant Sciences
Keiko Inaba-Hasegawa, Ayumi Ohmura, Masayo Nomura, Masahiro Sugiura
Summary: Chloroplast genomes in land plants contain approximately 20 intron-containing genes, similar to group II introns found in fungi, algae, and some bacteria, but lacking self-splicing capability. Researchers developed an in vitro system using tobacco chloroplasts to study splicing reactions, revealing differences in splicing mechanisms between chloroplast pre-mRNA and self-splicing group II introns.
PLANT AND CELL PHYSIOLOGY
(2021)
Article
Multidisciplinary Sciences
Kevin Chung, Ling Xu, Pengxin Chai, Junhui Peng, Swapnil C. Devarkar, Anna Marie Pyle
Summary: Group II introns are ribozymes that catalyze self-excision and function as retroelements invading DNA. In this study, cryo-electron microscopy structures were determined for a complete IIc intron maturation as a retroelement, revealing its poised integration into a DNA stem-loop motif. These findings provide insights into the design principles of retroelements and support the hypothesis that group II introns are ancient elements of genetic diversification.
Review
Biochemistry & Molecular Biology
Katherine Dwyer, Neha Agarwal, Lori Pile, Athar Ansari
Summary: Introns play a crucial role in eukaryotic organisms by impacting various aspects of gene expression, including transcription. Studies in yeast have shown that introns contribute to the formation of multi-looped gene architecture, enhancing transcription through interactions like promoter-5 ' splice site, terminator-3 ' splice site, and promoter-terminator interactions. This splicing-facilitated changes in gene architecture may provide insight into transcriptional regulation in yeast and higher eukaryotes.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Review
Genetics & Heredity
Kaitlin N. Girardini, Anouk M. Olthof, Rahul N. Kanadia
Summary: This article focuses on the role of introns in eukaryotic gene expression by using an intron-centric approach. It discusses how intron architecture influences splicing mechanisms and the impact of spliceosomal snRNAs and their variants on intron splicing. Additionally, the article explores how the presence of introns and the need for splicing affect transcription regulation. Despite the abundant presence of introns in the eukaryotic genome and their emerging role in gene expression regulation, there are still many unexplored areas. Therefore, the article refers to introns as the "dark matter" of the eukaryotic genome and discusses some unresolved questions in the field.
FRONTIERS IN GENETICS
(2023)
Article
Plant Sciences
Weiwei Chen, Yu Cui, Zheyuan Wang, Rongrong Chen, Cheng He, Yan Liu, Xuemei Du, Yunjun Liu, Junjie Fu, Guoying Wang, Jianhua Wang, Riliang Gu
Summary: In maize, the maturase-related protein ZmnMAT3 is crucial for seed embryogenesis and the assembly of mitochondrial complex I. Loss of function results in reduced splicing efficiency of introns and abnormal expression of alternative oxidases, indicating its importance in kernel development.
PLANT AND CELL PHYSIOLOGY
(2021)
Article
Microbiology
Judith Ryll, Rebecca Rothering, Francesco Catania
Summary: The conventional distinction between exons and introns in eukaryotic genes is actually blurred. This article provides evidence, through studies on Paramecium, that resolves the disconnect between traditional views on introns and the role of RNA splicing.
Review
Plant Sciences
Syed Sarfaraz Hussain, Manzar Abbas, Sammar Abbas, Mingke Wei, Ahmed H. El-Sappah, Yuhan Sun, Yun Li, Arthur J. Ragauskas, Quanzi Li
Summary: Alternative splicing in plants regulates gene expression through differential transcriptional modifications, allowing adaptation to environmental stresses and different growth stages. It causes the retention of introns in messenger RNA, leading to the translation of differentially expressed proteins. Additionally, alternative splicing remodels transcription factors at the post-transcriptional level, activating or repressing transcription.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Kacper Maciszewski, Nadja Dabbagh, Angelika Preisfeld, Anna Karnkowska
Summary: Organellar genomes often carry group II introns, which occasionally encode proteins called maturases that are important for splicing. The number of introns varies among different organellar genomes, and bursts of introns have been observed in multiple eukaryotic lineages, including euglenophytes. The study found that maturase content in euglenophyte plastid genomes has a patchy distribution, and most of the maturases have lost at least one functional domain. The origins of the maturases are diversified, acquired along with the green algal plastid or horizontally transferred.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2022)
Article
Clinical Neurology
Hong-Dong Li, Cory C. Funk, Karen McFarland, Eric B. Dammer, Mariet Allen, Minerva M. Carrasquillo, Yona Levites, Paramita Chakrabarty, Jeremy D. Burgess, Xue Wang, Dennis Dickson, Nicholas T. Seyfried, Duc M. Duong, James J. Lah, Steven G. Younkin, Allan Levey, Gilbert S. Omenn, Nilufer Ertekin-Taner, Todd E. Golde, Nathan D. Price
Summary: In this study, intron retention (IR) was found to play a role in Alzheimer's disease (AD) through genome-wide analysis of genetic, transcriptomic, and proteomic data. Thousands of IR events were identified, along with differentially expressed genes associated with AD and splicing-related genes that may regulate IR. The findings provide a new resource for exploring new AD biomarkers and pathological mechanisms.
ALZHEIMERS & DEMENTIA
(2021)
Article
Ecology
Todd J. Widhelm, Felix Grewe, Jen-Pan Huang, Karolis Ramanauskas, Roberta Mason-Gamer, H. Thorsten Lumbsch
Summary: The study reveals that populations of P. glabra from Australia, Chile, and New Zealand are genetically distinct, but frequent long-distance dispersal may have prevented speciation.
JOURNAL OF BIOGEOGRAPHY
(2021)
Article
Ecology
Elisa Lagostina, Mikhail Andreev, Francesco Dal Grande, Felix Grewe, Aline Lorenz, H. Thorsten Lumbsch, Ricardo Rozzi, Ulrike Ruprecht, Leopoldo Garcia Sancho, Ulrik Sochting, Mayara Scur, Nora Wirtz, Christian Printzen
Summary: The genetic structure of three lichen species in the Maritime Antarctic and southern South America was studied, revealing that different dispersal strategies and migration histories influence their genetic diversity levels.
JOURNAL OF BIOGEOGRAPHY
(2021)
Article
Plant Sciences
Alejandrina Barcenas-Pena, Steven D. Leavitt, Felix Grewe, H. Thorsten Lumbsch
Summary: The study sampled 38 Xanthoparmelia species from around the world and identified 18 species-level lineages in central Mexico. Traditional taxonomy and species delimitation in the genus Xanthoparmelia need revision, and molecular evidence is emphasized for more robust species delimitations.
ANALES DEL JARDIN BOTANICO DE MADRID
(2021)
Article
Mycology
Todd J. Widhelm, Felix Grewe, Bernard Goffinet, Mats Wedin, Trevor Goward, Luis F. Coca, Isabel Distefano, Alica Kosuthova, H. Thorsten Lumbsch
Summary: The evolutionary history of the lichenized fungal order Peltigerales, particularly the Collematineae, has been successfully resolved using phylogenomic data, despite conflicting signal in exon trees. Rapid diversification events were identified in the early evolution of the suborder. A minimum subset of exons that could reconstruct phylogenetic relationships with higher support than the complete dataset was identified. Comparisons between the minimum and complete datasets showed similar results in species tree inferences, bipartition analyses, and divergence time estimations, although errors in divergence time estimations were higher in the minimum dataset. Target capture datasets yielded higher support values compared to topologies reconstructed using traditional nuclear and mitochondrial markers.
Article
Biochemistry & Molecular Biology
Runxian Yu, Chenyu Sun, Yan Zhong, Ying Liu, M. Virginia Sanchez-Puerta, Jeffrey P. Mower, Renchao Zhou
Summary: The mitochondrial genome of the parasitic plant Rhopalocnemis phalloides displays a highly modified structure consisting of 21 mini-circular chromosomes. Despite its small size, this mitogenome contains a typical set of genes and introns within unique regions of each chromosome. The presence of extreme heteroplasmy and various mutations suggests a complex evolutionary history for this particular species, offering insight into the replication and gene expression mechanisms of plant mitochondrial genomes.
Article
Multidisciplinary Sciences
Huihui Yu, Mu Li, Jaspreet Sandhu, Guangchao Sun, James C. Schnable, Harkamal Walia, Weibo Xie, Bin Yu, Jeffrey P. Mower, Chi Zhang
Summary: The study developed computational pipelines to identify microexons in plants and showed their importance and diversity in plant evolution.
NATURE COMMUNICATIONS
(2022)
Article
Ecology
Claudio G. Ametrano, H. Thorsten Lumbsch, Isabel Di Stefano, Ek Sangvichien, Lucia Muggia, Felix Grewe
Summary: In this study, the coevolutionary effects of mutualistic interactions in lichens were investigated, revealing slower rates of evolution in independently evolved lichen clades. This evolutionary pattern is hypothesized to be linked to the longer generation time of lichenized fungi rather than different selection strengths.
ECOLOGY AND EVOLUTION
(2022)
Article
Ecology
Sarah A. Cowles, Christopher C. Witt, Elisa Bonaccorso, Felix Grewe, J. Albert C. Uy
Summary: Understanding the factors behind the diversification of geographically variable species is crucial. This study focused on the Amazilia Hummingbird, which is found along the Pacific coast from Ecuador to Peru. The researchers found that there are six subspecies of the Amazilia Hummingbird, with genetic isolation and gene flow contributing to their evolution. Additionally, one subspecies in Ecuador may be genetically distinct enough to be considered a separate species.
ECOLOGY AND EVOLUTION
(2022)
Article
Plant Sciences
Weishu Fan, Fang Liu, Qiaoya Jia, Haiyuan Du, Wu Chen, Jiwei Ruan, Jiajun Lei, De-Zhu Li, Jeffrey P. Mower, Andan Zhu
Summary: Plant mitochondrial DNA evolves rapidly in structure but slowly in sequence. The noncoding portions of plant mitogenomes are not homologous among species, which raises questions about the rate and spectrum of mutations in noncoding regions. The study shows that plant mitogenomes have low point mutations genome-wide but exceptionally high structural variations, supporting a gain-and-loss model for the rapid loss of homology among plant mitogenomes.
Article
Biochemistry & Molecular Biology
Xiao-Jian Qu, Xue-Jie Zhang, Dong-Ling Cao, Xiu-Xiu Guo, Jeffrey P. Mower, Shou-Jin Fan
Summary: Koenigia, a genus proposed by Linnaeus, has a contentious taxonomic history. The relationships among species and the circumscription of the genus relative to Aconogonon remain uncertain. In this study, genome skimming was used to explore the phylogenetic relationships of Koenigia and to establish the timing of major evolutionary diversification events. The results showed that K. delicatula has lost functional copies of certain genes and has gene rearrangements in its plastome. The conflicting relationships among plastome and mitochondrial trees and among gene trees complicate the circumscription of Koenigia, which may be due to rapid diversification within a short period of time. Furthermore, the study revealed correlated variation in substitution rates among Persicarieae species, suggesting a shared underlying mechanism promoting evolutionary rate variation in both organellar genomes. The divergence of K. delicatula from other Koenigia species may be associated with climatic events and the uplift of certain geographical areas.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2022)
Article
Microbiology
Ana Otero, Alejandrina Barcenas-Pena, H. Thorsten Lumbsch, Felix Grewe
Summary: This study used RADseq technology to analyze the evolutionary history of neuropogonoid lichens. Two new species and three resurrected species were discovered, and the timeframe for neuropogonoid lichen diversification was inferred. This study provided important support for filling the gap of fungal diversity and raised new questions about factors that may trigger complex evolutionary scenarios.
Article
Plant Sciences
Hans Ter Steege, Elenice A. Fortes, Danae M. A. Rozendaal, Roy H. J. Erkens, Daniel Sabatier, Gerardo Aymard, Elza Duijm, Marcel Eurlings, Felix Grewe, Maihyra M. Pombo, Vitor F. Gomes, Vidal F. de Mansano, Sylvia M. de Oliveira
Summary: This study investigates the evolution of different inflorescence types within the Amazonian hyperdominant genus Eperua. The results show that the shift from bat to bee and bee to bat pollination has occurred multiple times within the genus, but the bee to bat pollination doesn't always lead to a pendant inflorescence.
AMERICAN JOURNAL OF BOTANY
(2023)
Article
Plant Sciences
Alejandrina Barcenas-Pena, Harrie J. M. Sipman, Volkmar Wirth, Felix Grewe, H. Thorsten Lumbsch
Summary: This study investigated the diversity of Xanthoparmelia in southern Africa by examining morphological features, secondary metabolites, and DNA sequences. A total of 37 species were recorded, including three new species. The study also identified phylogenetic differences among other species.
Article
Mycology
Tuan Anh Duong, Janneke Aylward, Claudio Gennaro Ametrano, Barsha Poudel, Quentin Carlo Santana, Pieter Markus Wilken, Anke Martin, Kiruba Shankari Arun-Chinnappa, Lieschen de Vos, Isabel DiStefano, Felix Grewe, Sabine Huhndorf, Helge Thorsten Lumbsch, Jostina Raesetsa Rakoma, Barsha PoudeI, Emma Theodora Steenkamp, Yukun Sun, Magriet A. van der Nest, Michael John Wingfield, Neriman Yilmaz, Brenda Diana Wingfield
Article
Biology
Felix Grewe, Marcus R. Kronforst, Naomi E. Pierce, Corrie S. Moreau
Summary: By using next-generation sequencing on a 93-year-old museum specimen, researchers were able to confirm that the Xerces blue butterfly was indeed a distinct species and was driven to extinction.