Article
Biotechnology & Applied Microbiology
Chuanxue Liu, Pei Peng, Weiguo Li, Changrong Ye, Shuhua Zhang, Ruiying Wang, Dong Li, Shiwu Guan, Lanmin Zhang, Xiaoqun Huang, Zhenhua Guo, Junxiang Guo, Yu Long, Le Li, Guojun Pan, Bingchuan Tian, Jinhua Xiao
Summary: This study resequenced 239 japonica rice elites to reveal the genetic diversity and relationships among them, constructed a japonica rice pan-genome, predicted numerous novel genes, and detected strong selection signals in genomic regions. The results provide a foundation for future whole genome sequences-enabled breeding in rice and serve as a paradigm for other species.
Article
Biochemistry & Molecular Biology
Marta Vohnoutova, Anastazie Sedlakova, Radka Symonova
Summary: The organization of the AT/GC composition in vertebrate genomes is not well understood, especially in comparing amniotes and anamniotes. Recent studies have shown exceptions to the previous understanding, particularly in a specific fish lineage. This suggests the need for a reevaluation of genome composition, considering new data and tools. Through in silico analysis, we found a discrepancy between previous plots of GC% and the actual distribution of GC% values in fish genomes, indicating that previous approaches distorted results and contributed to the confusion about fish genome composition. Chromosome size and transposons may play a role in the observed AT/GC heterogeneity in mammalian chromosomes, but to a lesser extent in fishes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Genetics & Heredity
Cindy Ruan, Brian R. Morton
Summary: A common genome composition pattern in eubacteria is an asymmetry between the leading and lagging strands resulting in opposite skew patterns in the two replichores that lie between the origin and terminus of replication. This pattern has been found in the plastid genome of species from several diverse lineages, such as euglenozoa and rhodophytes, but is not apparent in other lineages. The implications of this pattern for plastid evolution analyses are discussed.
Article
Genetics & Heredity
Dominik Matoulek, Bruno Jezek, Marta Vohnoutova, Radka Symonova
Summary: It has been traditionally believed that fish genomes have low guanine-cytosine (GC%) content compared to higher vertebrates. However, through analysis of animal genomes, it was found that fish genomes actually have comparable or even higher GC% content than higher vertebrates. Furthermore, it was discovered that GC% content increases from DNA to cDNA to exons in all animal genomes, and not just in higher vertebrates. This research provides important insights into the understanding of fish genome composition.
Article
Plant Sciences
Taihua Yang, Bowei Cai, Zhibo Jia, Yu Wang, Jing Wang, Graham J. King, Xianhong Ge, Zaiyun Li
Summary: Sinapis alba and Sinapis arvensis are mustard crops that have important genetic potential for crop improvement. Through genomic analysis and comparison, it was found that both species retained evidence of a whole-genome triplication event approximately 20.5 million years ago. Subgenome dominance was observed in key genetic factors. The findings provide insights into the genome evolution and phylogenetic relationships of Brassiceae, and have implications for genetic improvement of these plants.
Article
Multidisciplinary Sciences
Baoxing Song, Santiago Marco-Sola, Miquel Moreto, Lynn Johnson, Edward S. Buckler, Michelle C. Stitzer
Summary: This study introduces a genome alignment method called AnchorWave, which shows significant improvement when applied to species with complex genomes. It can accurately identify multikilobase indels and improve the recall rate of transcription factor-binding sites.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Microbiology
Marianoel Pereira-Gomez, Lucia Carrau, Alvaro Fajardo, Pilar Moreno, Gonzalo Moratorio
Summary: Live-attenuated vaccines have been successfully used to prevent diseases caused by RNA viruses by eliciting strong and long-lasting immune responses. Recent research has focused on achieving viral attenuation through rational genetic design, with advancements in synthetic biology providing a framework for new strategies.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biochemical Research Methods
Joshua Rees-Garbutt, Jake Rightmyer, Oliver Chalkley, Lucia Marucci, Claire Grierson
Summary: Theoretical minimal gene sets for Mycoplasma genitalium have been simulated and found to be unable to produce dividing cells, indicating the need to reintroduce specific genes. This underscores the importance of identifying species-specific low essential genes and their interactions.
ACS SYNTHETIC BIOLOGY
(2021)
Article
Plant Sciences
Chenxin Li, Chaonan Cai, Yutian Tao, Zhongshuai Sun, Ming Jiang, Luxi Chen, Junmin Li
Summary: The study sequenced 27 complete chloroplast genomes of 11 wild Fragaria species and analyzed the variation among them, revealing higher variability in non-coding regions compared to coding regions. Five variable loci suitable for DNA barcoding of Fragaria species were identified. Phylogenetic analyses based on the whole cp genomes supported the clustering of species into two groups, with different geographic distributions.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Plant Sciences
Nicolas Pompidor, Carine Charron, Catherine Hervouet, Stephanie Bocs, Gaetan Droc, Ronan Rivallan, Aurore Manez, Therese Mitros, Kankshita Swaminathan, Jean-Christophe Glaszmann, Olivier Garsmeur, Angelique D'Hont
Summary: Research on the modern sugarcane cultivars reveals the existence of three founding genomes (A, B, C) originating from two presumed ancestors, suggesting the high polyploidy and interspecific hybridization model can explain the variable chromosome pairing affinity observed in Saccharum. This represents a major revision in understanding the diversity of Saccharum.
Article
Multidisciplinary Sciences
Chunyu Liu, Jessica L. Fetterman, Xianbang Sun, Kaiyu Yan, Poching Liu, Yan Luo, Jun Ding, Jun Zhu, Daniel Levy
Summary: This study compared mtDNA sequence variants between LCL and whole blood samples. The results showed that most homoplasmic variants were present in both LCL and blood samples, while most heteroplasmic variants were unique to either LCL or blood samples. LCL samples had a higher number of heteroplasmic variants compared to whole blood samples, but a similar number of homoplasmic variants. Additionally, LCL samples tended to have lower levels of heteroplasmy.
SCIENTIFIC REPORTS
(2022)
Review
Biochemical Research Methods
Zhaoqian Liu, Jingtong Feng, Bin Yu, Qin Ma, Bingqiang Liu
Summary: Bacterial genomes are recognized to closely interact with cellular processes. Researchers focus on uncovering organizational mechanisms of bacterial genomes to reveal potential cellular activities. Advances in experimental techniques and computational models provide opportunities for understanding these mechanisms, including local structures such as operons/transcription units and global constraints shaping bacterial genomes.
BRIEFINGS IN BIOINFORMATICS
(2021)
Review
Biotechnology & Applied Microbiology
Ji-Yoon Guk, Min-Jeong Jang, Jin-Wook Choi, Yeon Mi Lee, Seungill Kim
Summary: Genome phasing is a recently developed assembly method that separates heterozygous eukaryotic genomic regions and builds haplotype-resolved assemblies. Using haplotype-resolved genome assemblies in plants can reveal significant differences among haplotypes regarding chromosomal rearrangements and expression of specific alleles, contributing to the understanding of biological characteristics of plant species. However, there are limitations in current genome-phasing methods that need to be addressed for further improvements.
PLANT BIOTECHNOLOGY JOURNAL
(2022)
Article
Entomology
Yuyu Wang, Ruyue Zhang, Yunlong Ma, Jing Li, Fan Fan, Xingyue Liu, Ding Yang
Summary: Green lacewings are widely distributed natural predators within Neuroptera, playing an important role in biological pest control in agricultural ecosystems. The phylogenetic relationships among the three subfamilies of Chrysopidae have been debated, and a new study using low-coverage genomes of five species has suggested that Chrysopinae is a monophyletic sister group to Apochrysinae + Nothochrysinae. Further research in this area will contribute to a better understanding of the higher phylogeny of Chrysopidae and enhance the utilization of natural predators for pest control.
Article
Biology
Tomas Panek, Dovile Barcyte, Sebastian C. Treitli, Kristina Zahonova, Martin Sokol, Tereza Sevcikova, Eliska Zadrobilkova, Karin Jaske, Naoji Yubuki, Ivan Cepicka, Marek Elias
Summary: By studying the newly discovered non-photosynthetic lineage Leontynka, new insights into organellar genome evolution in Chlamydomonadales can be gained. Leontynka’s unique characteristics of plastid and mitochondrial genomes make it an interesting model for studying organellar genome evolution.