Article
Biochemistry & Molecular Biology
Nhan Ly-Trong, Suha Naser-Khdour, Robert Lanfear, Bui Quang Minh
Summary: Sequence simulators are important in phylogenetics for evaluating methods, hypothesis testing, and generating data. AliSim is a new tool that efficiently simulates biologically realistic alignments, outperforming popular software in terms of speed and efficiency.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Han Yan, Zhirui Hu, Gregg W. C. Thomas, Scott Edwards, Timothy B. Sackton, Jun S. Liu
Summary: The paper introduces PhyloAcc-GT, a method that extends PhyloAcc by modeling gene tree heterogeneity, to effectively identify lineage-specific accelerations in substitution rate while accounting for incomplete lineage sorting. The method outperforms other methods in detecting complex patterns of rate shifts and is robust to population size parameter specification.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Plant Sciences
Hiroshi Yamamoto, Nozomi Sato, Toshiharu Shikanai
Summary: The chloroplast NADH dehydrogenase-like (NDH) complex plays a crucial role in the electron transport chain in plants. The assembly and stability of subcomplex A (SubA) is dependent on the biosynthesis of the NdhA protein. Knockout mutants of ndhA in tobacco plants revealed the essential role of NdhA in stabilizing specific subunits of the NDH complex.
PLANT AND CELL PHYSIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Sudhir Kumar
Summary: Molecular evolutionary analysis requires computationally intensive steps that have a significant environmental impact. However, innovative methods and heuristics can reduce the carbon footprint, lower environmental costs, and promote green evolutionary computing.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Genetics & Heredity
Yuqi Huang, Minghao Sun, Lenan Zhuang, Jin He
Summary: This study provides a comprehensive molecular phylogenetic analysis of vertebrate AIGs, revealing loss or gain of AIG members in different species during evolution. The findings can be used for future functional characterization of AIGs.
Article
Oncology
Antonia Chroni, Sayaka Miura, Lauren Hamilton, Tracy Vu, Stephen G. Gaffney, Vivian Aly, Sajjad Karim, Maxwell Sanderford, Jeffrey P. Townsend, Sudhir Kumar
Summary: By analyzing the genetic heterogeneity of tumors in cancer patients, we found that the migration histories of metastasis are often best described by a hybrid model of metastatic tumor evolution. We discovered that new tumor seedings arise from clones of pre-existing metastases as frequently as they do from clones from primary tumors. Additionally, there were many clone exchanges between the source and recipient tumors.
Article
Biochemistry & Molecular Biology
Lina Kloub, Sean Gosselin, Matthew Fullmer, Joerg Graf, Johann Peter Gogarten, Mukul S. Bansal
Summary: Horizontal gene transfer (HGT) is crucial for prokaryotic evolution, yet little is known about the scale of individual HGT events. A computational framework called HoMer is introduced to infer single-gene HGT events and potential multiple-gene transfers, aiding a better understanding of HGT and microbial evolution on a larger scale through systematic inference of HMGTs.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Plant Sciences
Xiaolin Gu, Lingling Li, Sicong Li, Wanxin Shi, Xiaona Zhong, Yingjuan Su, Ting Wang
Summary: Our study analyzed the adaptive evolution and co-evolution of Pteridaceae chloroplast DNAs (cpDNAs). The results showed that the residues undergoing adaptive evolution and co-evolution were mostly independent, with only a few residues being simultaneously involved in both processes, and these overlapping residues tended to exhibit high mutation rates. Furthermore, our data demonstrated that Pteridaceae chloroplast genes are under purifying selection. Regardless of species grouping, positively selected residues mainly targeted photosynthetic genes.
Article
Plant Sciences
Yujiao Yang, Xiaolei Yu, Pei Wei, Chenlai Liu, Zhuyifu Chen, Xiaoyan Li, Xing Liu
Summary: In this study, the chloroplast genomes and transcriptomes of six Isoetes individuals were sequenced, assembled, and annotated. The results showed that the gene organization, genome size, and GC contents of the chloroplast genomes are highly conserved across the genus. Positive selection analyses suggested the presence of positively selected genes in the Isoetes chloroplast genomes and transcriptome data. Additionally, a high number of RNA editing sites were identified in the chloroplast genomes, possibly contributing to the formation of functional protein structures.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Evolutionary Biology
Leticia Chiara Baldassio de Paula, Rodrigo de Vilhena Perez Dios, Filipe Macedo Gudin, Marcelo Domingos de Santis, Deivys Moises Alvarez-Garcia, Manuel Antunes Junior, Beatriz Vieira Freire, Fernando Portella de Luna Marques, Daniel Jose Galafasse Lahr, Silvio Shigueo Nihei
Summary: Tachinidae is the second largest and species-rich family in Diptera, with all members being parasitoids. This study presents the first phylogenomic analysis of Tachinidae using transcriptomic data, revealing the subfamilial relationships and the existence of a fifth lineage.
Article
Biotechnology & Applied Microbiology
Chenyang Han, Rui Ding, Xiaoyan Zong, Lijie Zhang, Xuhui Chen, Bo Qu
Summary: This study determined the complete chloroplast genome sequence of Platanthera ussuriensis and compared it with other closely related orchid species. The results showed that the chloroplast genome of P. ussuriensis was relatively conserved, but there were some high variation regions that could be used as molecular markers. Phylogenetic analysis indicated a closer evolutionary relationship between P. ussuriensis and P. japonica.
Article
Biochemistry & Molecular Biology
F. Vanessa Loiacono, Dirk Walther, Stefanie Seeger, Wolfram Thiele, Ines Gerlach, Daniel Karcher, Mark Aurel Schoettler, Reimo Zoschke, Ralph Bock
Summary: RNA editing is an important process in converting cytidines to uridines in plant organellar transcripts. This study investigates the evolution and recognition of a recently gained editing site, demonstrating that changes in RNA recognition motifs allow an ancient PPR protein, QED1, to specifically target this site. The study also finds that the target specificity of PPR proteins depends on the RNA:protein ratio and the low expression levels of PPR proteins are necessary to ensure editing site selection specificity.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biodiversity Conservation
Emma K. Roberts, Emily A. Wright, Asha E. Worsham, Daniel M. Hardy, Robert D. Bradley
Summary: The extraordinary morphological diversity among extant mammals poses challenges for studies of speciation, adaptation, molecular evolution, and reproductive isolation. Despite molecular studies, uncertainties remain regarding divergence events. A phylogenetic tool based on a single reproductive molecular marker provides a solution to this longstanding issue.
Article
Biology
Edmund R. R. Moody, Tara A. Mahendrarajah, Nina Dombrowski, James W. Clark, Celine Petitjean, Pierre Offre, Gergely J. Szollosi, Anja Spang, Tom A. Williams, George H. Perry
Summary: Core gene phylogenies are important for understanding early evolution, but different gene sets and methods have led to different views of the tree of life. Recent analyses suggest that Archaea may be less divergent from Bacteria than previously thought, and estimates of inter-domain distance are inflated due to rapid evolution of ribosomal proteins. Resolving this debate is crucial for understanding the diversity of archaeal and bacterial domains and the early course of cellular evolution.
Article
Multidisciplinary Sciences
Chinmay A. Kalluraya, Alexander J. Weitzel, Brian V. Tsu, Matthew D. Daugherty
Summary: The vertebrate eye is a unique organ that evolved through the acquisition of genetic material from bacteria, which played a crucial role in the development of the vertebrate visual cycle.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biochemistry & Molecular Biology
Emiko Noro, Masaru Mori, Gakuto Makino, Yuki Takai, Sumiko Ohnuma, Asako Sato, Masaru Tomita, Kenji Nakahigashi, Akio Kanai
Article
Multidisciplinary Sciences
Yohei Hayashi, Kei Otsuka, Masayuki Ebina, Kaori Igarashi, Asuka Takehara, Mitsuyo Matsumoto, Akio Kanai, Kazuhiko Igarashi, Tomoyoshi Soga, Yasuhisa Matsui
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2017)
Article
Microbiology
Shohei Nagata, Junnosuke Imai, Gakuto Makino, Masaru Tomita, Akio Kanai
FRONTIERS IN MICROBIOLOGY
(2017)
Article
Genetics & Heredity
Satoshi Tamaki, Masaru Tomita, Haruo Suzuki, Akio Kanai
FRONTIERS IN GENETICS
(2018)
Correction
Multidisciplinary Sciences
Yohei Hayashi, Kei Otsuka, Masayuki Ebina, Kaori Igarashi, Asuka Takehara, Mitsuyo Matsumoto, Akio Kanai, Kazuhiko Igarashi, Tomoyoshi Soga, Yasuhisa Matsui
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2018)
Article
Evolutionary Biology
Motofumi Saito, Asako Sato, Shohei Nagata, Satoshi Tamaki, Masaru Tomita, Haruo Suzuki, Akio Kanai
GENOME BIOLOGY AND EVOLUTION
(2019)
Editorial Material
Genetics & Heredity
Akio Kanai, Tohru Yoshihisa
FRONTIERS IN GENETICS
(2019)
Article
Reproductive Biology
Yohei Hayashi, Masaru Mori, Kaori Igarashi, Keiko Tanaka, Asuka Takehara, Yumi Ito-Matsuoka, Akio Kanai, Nobuo Yaegashi, Tomoyoshi Soga, Yasuhisa Matsui
BIOLOGY OF REPRODUCTION
(2020)
Article
Genetics & Heredity
Trieu-Duc Vu, Yuki Lwasaki, Shuji Shigenobu, Akiko Maruko, Kenshiro Oshima, Erica Lioka, Chao-Li Huang, Takashi Abe, Satoshi Tamaki, Yi-Wen Lin, Chih-Kuan Chen, Mei-Yeh Lu, Masaru Hojo, Hao-Ven Wang, Shun-Fen Tzeng, Hao-Jen Huang, Akio Kanai, Takashi Gojobori, Tzen-Yuh Chiang, H. Sunny Sun, Wen-Hsiung Li, Norihiro Okada
Article
Microbiology
Masahiro C. Miura, Shohei Nagata, Satoshi Tamaki, Masaru Tomita, Akio Kanai
Summary: This study developed a bioinformatic pipeline to systematically collect and analyze Group II introns (G2Is) in prokaryotes. The results showed the presence of G2Is in both bacteria and archaea, with their numbers defined almost at the phylum level. Furthermore, a comprehensive sequence analysis led to the identification of three new categories of intron-encoded proteins (IEPs), and it was observed that about 30% of IEPs are non-canonical. The study also analyzed the relationship between genomic signatures and the mechanism of G2I increases.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Megumi Tsurumaki, Motofumi Saito, Masaru Tomita, Akio Kanai
Summary: The candidate phyla radiation (CPR) bacteria, consisting mainly of uncultured lineages, have smaller cells and genomes compared to non-CPR bacteria. They lack certain ribosomal proteins and exhibit unique protein lengths and sequences. The ribosomes of CPR bacteria appear to be smaller with simplified surface structures, which may contribute to their distinct characteristics.
Article
Microbiology
Teppei Morita, Nadim Majdalani, Masahiro C. Miura, Rerina Inose, Taku Oshima, Masaru Tomita, Akio Kanai, Susan Gottesman
Summary: The regulatory function of many bacterial small RNAs (sRNAs) is dependent on the RNA chaperone Hfq binding to the 3' portion of the sRNA intrinsic terminator. This study identified several genes, including an sRNA gene (cyaR) and three protein-coding genes (cspD, ygjH, and rof), that attenuate the termination of SgrS in Escherichia coli. Overexpression of the protein attenuators CspD and Rof resulted in increased readthrough at terminators of SgrS and other sRNAs, reducing their regulatory effects on target mRNAs. Further analysis revealed the unexpected role of Rho in sRNA termination and the stabilizing effect of CspD on both terminated and readthrough transcripts. This study provides evidence of the modulation of intrinsic termination as an additional layer of regulation in sRNA signaling.
Article
Biochemistry & Molecular Biology
Motofumi Saito, Rerina Inose, Asako Sato, Masaru Tomita, Haruo Suzuki, Akio Kanai
Summary: The Clp1 family proteins play an essential role in RNA processing in eukaryotes, and their diversification is mainly due to gene duplication and alternative splicing. Our study reveals that the Clp1 and Nol9/Grc3 groups were already formed in the eukaryotic ancestor, and the protist phylum Euglenozoa has a particularly high number of Clp1 family proteins. This research provides valuable insights into the evolutionary history of Clp1 family proteins in different species.
JOURNAL OF MOLECULAR EVOLUTION
(2023)
Review
Geography, Physical
Naota Takeyama, Yuka Takahashi, Shohei Nagata, Yusuke Sawaki, Tomohiko Sato, Shigenori Maruyama, Akio Kanai
JOURNAL OF GEOGRAPHY-CHIGAKU ZASSHI
(2020)
Review
Geography, Physical
Megumi Tsurumaki, Motofumi Saito, Shigenori Maruyama, Akio Kanai
JOURNAL OF GEOGRAPHY-CHIGAKU ZASSHI
(2020)