Article
Biotechnology & Applied Microbiology
Jian-Wei Zheng, Yang Lu, Yu-Feng Yang, Dan Huang, Da-Wei Li, Xiang Wang, Yang Gao, Wei-Dong Yang, Yuanfang Guan, Hong-Ye Li
Summary: This study analyzed the transcriptomes of 34 Conus species and identified conotoxin genes, revealing that some of these genes underwent positive natural selection. The genome of C. betulinus was also reassembled and annotated, uncovering 221 conotoxin-encoding genes. The presence of transposon elements in the flanking regions and adjacent introns of conotoxin genes may contribute to the extensive variability observed in conotoxins.
Review
Biotechnology & Applied Microbiology
Shengrui Wu, Pingfang Tian, Tianwei Tan
Summary: This review summarizes transposons from fermentation bacteria and provides valuable insights for strain improvement based on transposons.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Andrew B. Morgenthaler, Ryan K. Fritts, Shelley D. Copley
Summary: New enzymes often evolve from duplication and divergence of genes encoding enzymes with promiscuous activities. Amplifications that increase gene copy number commonly amplify many surrounding genes, which must be removed during or after evolution of a new enzyme. Amplicon remodeling, along with mutations elsewhere in the genome, leads to complex population dynamics and emergence of clones with improved fitness through different mechanisms.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Virology
Jie Tao, Benqiang Li, Jinghua Cheng, Ying Shi, Changtao Qiao, Zhi Lin, Huili Liu
Summary: Porcine astrovirus (PAstV) is an important diarrheic pathogen with a global distribution. In this study, a PAstV-4 strain was isolated and identified as a recombination of two previous strains. Proteomics analysis revealed that viral infection induces global protein changes, with mitochondria being a primary target. There is crosstalk between autophagy and apoptosis, and the NLRX1 protein may play a crucial role in antagonizing viral infection through autophagy.
Article
Agronomy
Zhiguo Wu, Wei Xi, Zixuan Han, Yanhua Wu, Yongzhuo Guan, Yuxian Zhu
Summary: In this study, a method called matrix-TE was used to comprehensively investigate the differentiation of LTR/TEs in plant genomes. The results showed that there were six LTR/TE superfamilies in Indica and Japonica rice genomes, and the divergence between the two genomes was mainly caused by Ty3/Gypsy insertion events.
Article
Biochemistry & Molecular Biology
Max A. English, Miguel A. Alcantar, James J. Collins
Summary: In this study, a synthetic transposon platform is developed for continuous genome-wide mutagenesis and dynamic rewiring of gene networks in bacteria. The platform is used to investigate the impact of transposon functionalization on the evolution of Escherichia coli populations and to demonstrate the emergence of inducible multigenic phenotypes. A modular assembly pipeline is also developed for the functionalization of transposons with gene regulatory elements and DNA barcodes. This work establishes a valuable tool for optimizing bacterial strains and understanding the dynamics of gene networks.
MOLECULAR SYSTEMS BIOLOGY
(2023)
Article
Environmental Sciences
Songqian Huang, Yuki Ichikawa, Kazutoshi Yoshitake, Shigeharu Kinoshita, Md Asaduzzaman, Fumito Omori, Kaoru Maeyama, Kiyohito Nagai, Shugo Watabe, Shuichi Asakawa
Summary: This study revealed the PIWI/piRNA pathway in the pearl oyster P. fucata, showing that piRNAs play different roles in somatic and gonadal tissues. Silencing of a single piRNA in P. fucata led to differential expression of hundreds of endogenous genes, indicating a potential role of somatic piRNAs in gene regulation.
FRONTIERS IN MARINE SCIENCE
(2021)
Article
Multidisciplinary Sciences
Wenwen Wang, Yujia Yang, Suxu Tan, Tao Zhou, Yang Liu, Changxu Tian, Lisui Bao, De Xing, Baofeng Su, Jinhai Wang, Yu Zhang, Shikai Liu, Huitong Shi, Dongya Gao, Rex Dunham, Zhanjiang Liu
Summary: The X and Y chromosomes of channel catfish have the same gene contents. The X-borne hydin-1 gene is silenced, while the Y-borne hydin-1 gene is expressed, resulting in monoallelic expression of hydin-1 responsible for sex determination, similar to genomic imprinting. Treatment with a methylation inhibitor, 5-aza-dC, erases the epigenetic marks and causes sex reversal.
Article
Multidisciplinary Sciences
Adan F. Mar-Silva, Pindaro Diaz-Jaimes, Cristina Dominguez-Mendoza, Omar Dominguez-Dominguez, Jonathan Valdiviezo-Rivera, Eduardo Espinoza-Herrera
Summary: This study found that oceanographic conditions and habitat characteristics have an impact on genetic structure in marine species, using Lutjanus guttatus as an example. The Gulf of Panama, as part of the Tropical Eastern Pacific, acts as a barrier to gene flow due to its complex current system and heterogeneous environment. The results suggest that adaptive selection plays a crucial role in population differentiation for Lutjanus guttatus.
Article
Immunology
Lara Wahlster, Jeffrey M. Verboon, Leif S. Ludwig, Susan C. Black, Wendy Luo, Kopal Garg, Richard A. Voit, Ryan L. Collins, Kiran Garimella, Maura Costello, Katherine R. Chao, Julia K. Goodrich, Stephanie P. DiTroia, Anne O'Donnell-Luria, Michael E. Talkowski, Alan D. Michelson, Alan B. Cantor, Vijay G. Sankaran
Summary: Advances in genome sequencing have helped identify causes for many rare diseases, but complex structural variants like the one described in this study may still be missed by conventional sequencing methods. The discovery of a pathogenic WAC-ANKRD26 fusion transcript resulting from a large complex structural variant highlights the importance of utilizing long-read whole-genome sequencing for comprehensive genetic analyses.
JOURNAL OF EXPERIMENTAL MEDICINE
(2021)
Article
Biochemistry & Molecular Biology
Dong Liang, Pengju Zhao, Jingfang Si, Lingzhao Fang, Erola Pairo-Castineira, Xiaoxiang Hu, Qing Xu, Yali Hou, Yu Gong, Zhengwen Liang, Bing Tian, Huaming Mao, Marnoch Yindee, Md Omar Faruque, Siton Kongvongxay, Souksamlane Khamphoumee, George E. Liu, Dong-Dong Wu, James Stuart F. Barker, Jianlin Han, Yi Zhang
Summary: This study revealed that a 2,809-bp-long LINE-1 insertion in the ASIP gene is the causative mutation for the white coat phenotype in swamp buffalo. This LINE-1 insertion acts as a strong proximal promoter leading to increased transcription of ASIP, which prevents melanocyte maturation and results in absence of pigment in white buffalo skin and hairs. Phylogenetic analyses suggest the white buffalo-specific ASIP allele originated from a recent genetic transposition event. Furthermore, a similar LINE-1 insertion was identified in the cattle ASIP gene, indicating a convergent mechanism of coat color evolution in the Bovini tribe.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Plant Sciences
Mengqi Li, Yilong Feng, Qi Han, Ying Yang, Yining Shi, Dongyang Zheng, Wenli Zhang
Summary: This study reveals how sequence and structural variations control agronomic traits in rice and provides genome-editing targets for improving favorable agronomic properties.
Article
Multidisciplinary Sciences
Yingnan Gao, Martin Wu
Summary: This study demonstrates the presence and prevalence of pulsed evolution in microbial genomic trait evolution using a likelihood-based framework. The findings support the predictions of punctuated equilibrium and quantum evolution theories.
Article
Biotechnology & Applied Microbiology
Shuhua Zhan, Cortland Griswold, Lewis Lukens
Summary: The study revealed that mapping bias significantly affects gene transcript abundance estimation in maize, particularly when RNA-seq reads are aligned to a single reference genome. Bias varies across different chromosomal features, with genes at distinct chromosomal ends being more affected. Accurate transcript estimation across genetically variable individuals may require individual genome or transcriptome templates.
Article
Biochemistry & Molecular Biology
Fushi Ke, Liette Vasseur, Huiqin Yi, Lihua Yang, Xiao Wei, Baosheng Wang, Ming Kang
Summary: The study analyzed 132 genomes from five recently divergent species in Primulina genus, showing that both gene flow and linked selection have contributed to the genome-wide variation landscape. Lineage-specific genomic islands may have facilitated adaptation of certain species to special habitats.
Article
Biochemistry & Molecular Biology
Wen-Ye Yuan, Motonori Tomita
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2015)
Article
Biotechnology & Applied Microbiology
Motonori Tomita, Kazuo Ishii
BIOMED RESEARCH INTERNATIONAL
(2018)
Article
Biochemistry & Molecular Biology
Yoshiki Naito, Motonori Tomita
BIOCHEMICAL GENETICS
(2013)
Article
Genetics & Heredity
Y. -Z. Ma, M. Tomita
CYTOLOGY AND GENETICS
(2013)
Article
Biochemistry & Molecular Biology
Motonori Tomita, Shiho Yazawa, Yoshimasa Uenishi
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2019)
Article
Genetics & Heredity
Motonori Tomita, Jun Tanaka
Article
Plant Sciences
Motonori Tomita, Keiichiro Ishimoto
Article
Multidisciplinary Sciences
M. Z. Islam, M. Arifuzzaman, S. Banik, M. A. Hossain, J. Ferdous, M. Khalequzzaman, B. R. Pittendrigh, M. Tomita, M. P. Ali
Article
Agronomy
M. Tomita, H. Tanaka, K. Takahashi
Summary: Researchers successfully isolated the rye serine/threonine protein kinase (S/T PK) gene from the large genome of rye, which plays a vital role in intracellular signal transduction mediated by ABA following drought stress. By screening and sequencing a cDNA library, they determined the characteristics of the S/T PK gene and its transcription via ABA. Northern hybridization confirmed that the S/T PK gene is transcribed in ABA-treated leaves, suggesting its involvement in intracellular signal transduction.
CEREAL RESEARCH COMMUNICATIONS
(2021)
Article
Biotechnology & Applied Microbiology
Motonori Tomita, Takaaki Kanzaki, Eri Tanaka
Summary: A new class of Revolver transposon-like elements were analyzed in rye cultivar Petkus using FISH method, with standard elements showing weak hybridization throughout the chromosomes while nonautonomous elements were widely distributed. The Revolver elements exhibited a clustered nature, which is a significantly rare case in genomics research.
JOURNAL OF APPLIED GENETICS
(2021)
Article
Biochemistry & Molecular Biology
Motonori Tomita, Ryotaro Tokuyama, Shosuke Matsumoto, Kazuo Ishii
Summary: We identified the key genes controlling the late maturation of the Japonica cultivar Isehikari and elucidated their effect on maturity. This study provides important genetic information for a better understanding and improvement of rice cultivation.
INTERNATIONAL JOURNAL OF GENOMICS
(2022)
Article
Biology
Motonori Tomita, Ryotaro Tokuyama
Summary: In this study, we developed semidwarf and late-maturing isogenics of Koshihikari to achieve stable high yield and avoid high temperature maturation. Through whole-genome analysis, we identified the SNP mutations in Hd16 and sd1 genes and analyzed the integration of DNA fragments and accompanying genes. The semidwarf and late-maturing variety, Koshihikari sd1Hd16, showed significant differences in flowering time, plant height, and yield compared to Koshihikari.
Article
Green & Sustainable Science & Technology
Motonori Tomita, Hideumi Ebata, Kohei Nakayama
Summary: In this study, a new variety of rice, Koshihikari sd1GW2, incorporating the large-grain gene GW2 and semidwarf gene sd1, was developed and successfully integrated into the genome of the leading Japonica rice cultivar, Koshihikari. This new variety showed higher thousand-grain weight and grain yield, and was found to be less susceptible to lodging, which is commonly observed in heavier panicle weight cultivars.
Article
Biochemistry & Molecular Biology
Motonori Tomita, Masakazu Yamashita, Akihiro Omichi
Summary: The study analyzed the gene structures of three types of vacuolar-type antiporters transcribed in wheat under salt stress and identified three vacuolar-type Na+/H+ antiporter genes, TaNHXa, b, and c. These genes encode transmembrane domains characteristic of vacuolar-type Na+/H+ antiporter, such as the amyloid binding site in the third domain.
GENETICS AND MOLECULAR BIOLOGY
(2021)
Article
Biology
Motonori Tomita, Takatoshi Tanisaka