Article
Microbiology
Emma O. Fuentes-Ramirez, Miriam Vazquez-Acevedo, Alfredo Cabrera-Orefice, Sergio Guerrero-Castillo, Diego Gonzalez-Halphen
Summary: This study provides a morphological and proteomic characterization of the colorless alga Polytomella parva, identifying several plastid proteins involved in various metabolic pathways. The results contribute to a better understanding of the metabolism and biological activities of this unicellular, free-living alga.
MICROBIOLOGICAL RESEARCH
(2021)
Article
Multidisciplinary Sciences
Vivien Hotter, David Zopf, Hak Joong Kim, Anja Silge, Michael Schmitt, Prasad Aiyar, Johanna Fleck, Christian Matthaus, Julian Hniopek, Qing Yan, Joyce Loper, Severin Sasso, Christian Hertweck, Jurgen Popp, Maria Mittag
Summary: The interaction between algae and bacteria involves a complex molecular strategy, with bacteria using protegencin and orfamide A to disrupt the visual system and behavior of algae. This study highlights the multifaceted ways in which microorganisms can impact the growth and development of algae in nature.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Plant Sciences
Michela Cecchin, Jooyeon Jeong, Woojae Son, Minjae Kim, Seunghye Park, Luca Zuliani, Stefano Cazzaniga, Andrea Pompa, Chan Young Kang, Sangsu Bae, Matteo Ballottari, EonSeon Jin
Summary: This study generated lpa2 knockout mutants in Chlamydomonas reinhardtii using the CRISPR-Cas9 system and found that the absence of LPA2 protein resulted in impaired PSII assembly and function, leading to compromised photoautotrophic growth.
Article
Plant Sciences
Zheng-Ren Zhang, Xue Yang, Wei-Ying Li, Yan-Qiong Peng, Jie Gao
Summary: In this study, the chloroplast genomes of various Ficus species were sequenced and analyzed, revealing a conserved genomic structure and the presence of unique genes. The phylogenetic relationships of Ficus were found to be complex, and divergence among species likely occurred during the Miocene period.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Horticulture
Daouda Coulibaly, Xiao Huang, Shi Ting, Shahid Iqbal, Zhaojun Ni, Kenneth Omondi Ouma, Faisal Hayat, Wei Tan, Guofeng Hu, Chengdong Ma, Benjamin Karikari, Mahmoud Magdy, Zhihong Gao
Summary: This study compared the agronomical and chloroplast genome characteristics of ten Japanese apricot accessions from three Chinese provinces, revealing significant differences in phenotype and genome composition among accessions from different provinces, leading to clustering based on geographic origin.
Article
Genetics & Heredity
Nripendra Vikram Singh, Prakash Goudappa Patil, Roopa P. Sowjanya, Shilpa Parashuram, Purushothaman Natarajan, Karuppannan Dhinesh Babu, Ram Krishna Pal, Jyotsana Sharma, Umesh K. Reddy
Summary: Comprehensive chloroplast genome analysis of 16 pomegranate genotypes revealed variability in genome size and conservation in gene content, with distinct differences among genotypes and clear divergence from other taxa. The study also identified varietal-specific SNP/indel markers and provided valuable genomic resources for future genetic, taxonomical, and phylogenetic research in pomegranate.
FRONTIERS IN GENETICS
(2021)
Article
Genetics & Heredity
Hocheol Kim, Ji Hyun Yang, Danilo E. Bustamante, Martha S. Calderon, Andres Mansilla, Christine A. Maggs, Gayle I. Hansen, Hwan Su Yoon
Summary: The widely distributed genus Ahnfeltia has 11 accepted species names, with A. plicata and A. fastigiata possibly diverging genetically due to past geographic changes. Genome size differences and conserved gene contents were found between the two species. Phylogenetic analysis supported the monophyly of the Ahnfeltiophycidae, while individual gene trees indicated genetic diversification within Ahnfeltia populations in accordance with geographic distribution.
FRONTIERS IN GENETICS
(2021)
Article
Plant Sciences
Jingling Li, Jianmin Tang, Siyuan Zeng, Fang Han, Jing Yuan, Jie Yu
Summary: This study presents the plastid genomes of four Pilea taxa, revealing their typical structure, gene content, and high sequence divergence. Hypervariable regions were identified as potential DNA barcodes, and phylogenetic analysis showed the placement of Pilea within Urticaceae with strong support. The results contribute to plastid genome resources and provide valuable insights into interspecific diversity and molecular markers development in Pilea research.
Article
Microbiology
Quan Wang, Haolin Luo, Jieyi Zhuang, Xinyi Li, Danqiong Huang, Zhangli Hu, Guiying Zhang
Summary: This article describes the research on the synthetic mitochondrial genome of C. reinhardtii. By designing and assembling a synthetic mitochondria left arm genome, it was transferred into a respiratory defect strain and the internal function was verified. This research provides valuable guidance for synthetic biology and algae industry, and opens up possible directions for future research.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Plant Sciences
Eka Giorgashvili, Katja Reichel, Calvinna Caswara, Vuqar Kerimov, Thomas Borsch, Michael Gruenstaeudl
Summary: This study examines the effects of sequencing coverage and assembly software on plastid genome assembly in the endemic shrub Calligonum bakuense. The results show that software choice significantly influences the accuracy and reproducibility of plastid genome assembly, while a sequencing coverage between 500x and 100x can reduce sequence variability and computation time.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Genetics & Heredity
Sisi Chen, Ting Wang, Jiangping Shu, Qiaoping Xiang, Tuo Yang, Xianchun Zhang, Yuehong Yan
Summary: This study investigates the plastomic diversity and evolutionary patterns of three lycophyte families, providing insights into the phylogenetic relationships and characteristics of these ancient vascular plants. The comparative analysis of plastid phylogenomics and plastomic diversity sets a foundation for further studies in biology and evolution in lycophytes and vascular plants.
Article
Biochemistry & Molecular Biology
Romain Gastineau, Nikolai A. Davidovich, Olga I. Davidovich, Claude Lemieux, Monique Turmel, Rafal J. Wrobel, Andrzej Witkowski
Summary: In this study, the plastid genomes of three diatoms from the genus Climaconeis were sequenced, with two strains of Climaconeis scalaris having the largest genomes ever sequenced among diatoms. Significant rearrangements of gene order were identified in the two populations of Climaconeis cf. scalaris. Another sequenced Climaconeis chloroplast genome was 1.5 times smaller than those of the Climaconeis cf. scalaris strains and had a different quadripartite structure. Extensive structural changes in the Climaconeis genus were compared with those seen in other algae and plants with large plastid genomes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
Xiaojie Pang, Wojciech J. Nawrocki, Pierre Cardol, Mengyuan Zheng, Jingjing Jiang, Yuan Fang, Wenqiang Yang, Roberta Croce, Lijin Tian
Summary: Weak acids produced during fermentation can suppress both photosynthesis and aerobic respiration. This effect is widespread among photosynthetic organisms and helps algae adapt to changing environmental conditions.
NATURE COMMUNICATIONS
(2023)
Article
Biotechnology & Applied Microbiology
Joonhyung Jung, Changkyun Kim, Joo-Hwan Kim
Summary: This study provides detailed information on 15 complete plastid genomes of Commelinoideae taxa, revealing structural variations and resolving problematic positions among genera in the family.
Article
Biochemistry & Molecular Biology
David M. Edwards, Ellen C. Royrvik, Joanna M. Chustecki, Konstantinos Giannakis, Robert C. Glastad, Arunas L. Radzvilavicius, Iain G. Johnston
Summary: A comprehensive genetic model has been constructed to explain how different mechanisms segregate and decrease damage in organelle DNA (oDNA) across eukaryotes. Gene conversion is identified as a powerful mechanism to increase beneficial cell-to-cell variance without depleting oDNA copy number, explaining the advantage of observed oDNA recombination in diverse organisms. This framework provides insights into how eukaryotes avoid Muller's ratchet and explains the puzzling oDNA differences across taxa.
Editorial Material
Biochemistry & Molecular Biology
David Roy Smith
Summary: Mini-circular organelle genomes, which have never been observed in plants before, have now been found in the holoparasite Rhopalocnemis phalloides. The mitochondrial genome of this parasitic plant consists of 21 highly heteroplasmic mini-circles, providing an exceptional example of convergent organelle evolution across different lineages.
Editorial Material
Biochemistry & Molecular Biology
David R. Smith
Editorial Material
Biochemistry & Molecular Biology
David R. Smith
Summary: While David Smith will not declare the genome paper dead again, the question remains whether its existence as a zombie still serves science.
Review
Plant Sciences
Norman P. A. Huner, David R. Smith, Marina Cvetkovska, Xi Zhang, Alexander G. Ivanov, Beth Szyszka-Mroz, Isha Kalra, Rachael Morgan-Kiss
Summary: The review explores the mechanisms by which polar photoautotrophs maintain cellular energy balance to overcome the potential energy imbalance in low temperature environments. Photopsychrophiles are obligately adapted to low temperature, while photopsychrotolerant species can tolerate a broad range of temperatures. The study compares the photoprotective mechanisms in different polar organisms and discusses how genomic redundancy in photopsychrophilic genomes may confer energy balance, photoprotection, and resilience in harsh environments.
JOURNAL OF PLANT PHYSIOLOGY
(2022)
Article
Plant Sciences
Marina Cvetkovska, Xi Zhang, Galyna Vakulenko, Samuel Benzaquen, Beth Szyszka-Mroz, Nina Malczewski, David R. Smith, Norman P. A. Huner
Summary: The Antarctic green alga Chlamydomonas sp. UWO241 is an obligate psychrophile that thrives in cold conditions but struggles to adapt to temperatures outside its preferred range. Despite accumulating stress markers at low temperatures, it does not exhibit a robust heat stress response when exposed to higher temperatures.
PLANT CELL AND ENVIRONMENT
(2022)
Article
Genetics & Heredity
Alex S. Torson, Alexandra M. A. Hicks, Claire E. Baragar, David R. Smith, Brent J. Sinclair
Summary: In this study, the complete mitochondrial genomes of the spring field cricket and the variable field cricket were assembled using RNA-seq reads. The genomes of both species contained the expected genes and exhibited arrangements consistent with closely related Orthoptera. Phylogenetic analysis revealed their clustering with other Gryllus species in the Gryllidae clade.
MITOCHONDRIAL DNA PART B-RESOURCES
(2022)
Editorial Material
Biochemistry & Molecular Biology
David R. Smith
Article
Plant Sciences
Qiao-Ping Xiang, Jun-Yong Tang, Ji-Gao Yu, David Roy Smith, Yan-Mei Zhu, Ya-Rong Wang, Jong-Soo Kang, Jie Yang, Xian-Chun Zhang
Summary: This study discovered that the plastome of Selaginella sinensis has accelerated substitution rates, a low GC content, pervasive repeat elements, and a dynamic network structure. It also lacks certain related recombinases. The study suggests that the interplay between a deficient DNA-RRR system and high repeat content has led to the unique divergence of the S. sinensis plastome.
Editorial Material
Biochemistry & Molecular Biology
David R. Smith
Summary: Writing and receiving reference letters have become more important in the time of COVID.
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
Plant Sciences
Alexandra E. DeShaw, Francisco Figueroa-Martinez, Thomas Proschold, Maike Lorenz, Aurora M. Nedelcu, David R. Smith, Adrian Reyes-Prieto
Summary: This study explores the plastid genomes of Hyalomonas and Hyalogonium, which show independent losses of photosynthesis. The plastid genome of Hyalomonas is moderately sized with a reduced gene complement, while the plastome of Hyalogonium is the largest observed in nonphotosynthetic plants or algae. These findings suggest that plastid genome compaction is not obligatory following the loss of photosynthesis in free-living algae.
Editorial Material
Biochemistry & Molecular Biology
David R. Smith
Editorial Material
Biochemistry & Molecular Biology
David R. Smith
Summary: Early adoption of coping strategies can help in managing the challenges and uncertainties in both science and life.
Editorial Material
Biochemistry & Molecular Biology
David R. Smith
Article
Mathematical & Computational Biology
Xi Zhang, Yining Hu, David Roy Smith
Summary: Gene duplication is an important evolutionary mechanism that provides new genetic material for organisms to adapt to their environment. However, identifying and categorizing highly similar duplicate genes (HSDs) can be difficult. This study presents HSDatabase, an online sequence repository that collects and curates HSDs from various organisms. The database includes statistics on HSDs, sequence alignments, and links to other databases, and is a valuable resource for comparative genomic analyses.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2022)