Article
Multidisciplinary Sciences
Shakibur Rahman, Sergei L. Kosakovsky Pond, Andrew Webb, Jody Hey
Summary: Research shows that synonymous codon substitutions are not always selectively neutral, and conventional dN/dS analyses may overestimate the frequency of positive diversifying selection and underestimate the strength of purifying selection. By analyzing two classes of synonymous substitutions, it was found that this discrepancy can be adequately explained by very weak selection with a mean product of population size and selection coefficient, Ns = 0.8.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Zhengting Zou, Jianzhi Zhang
Summary: Through comparative genomics research, it has been discovered that whether nonsynonymous transversions are more deleterious than nonsynonymous transitions depends on the species, and the variance in eta can primarily be explained by the among-species disparity in amino acid exchangeabilities.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Letter
Biochemistry & Molecular Biology
Roberto Del Amparo, Miguel Arenas
Summary: Selecting the best-fitting substitution model is recommended for accurately reconstructing ancestral sequences.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Multidisciplinary Sciences
Yasuka Toda, Meng-Ching Ko, Qiaoyi Liang, Eliot T. Miller, Alejandro Rico-Guevara, Tomoya Nakagita, Ayano Sakakibara, Kana Uemura, Timothy Sackton, Takashi Hayakawa, Simon Yung Wa Sin, Yoshiro Ishimaru, Takumi Misaka, Pablo Oteiza, James Crall, Scott Edwards, William Buttemer, Shuichi Matsumura, Maude W. Baldwin
Summary: An early sensory shift involving the umami receptor conferred sweet-sensing abilities in songbirds, shaping the sensory biology of an entire evolutionary radiation of birds.
Article
Biochemistry & Molecular Biology
Alexander G. Lucaci, Jordan D. Zehr, David Enard, Joseph W. Thornton, Sergei L. Kosakovsky Pond
Summary: Inference and interpretation of evolutionary processes are influenced by statistical models and tests. Failing to consider certain aspects of the substitution process and model variation can bias estimates of model parameters and affect selection detection. This study develops an analytical framework to incorporate multinucleotide substitutions and variation in synonymous substitution rate into selection analyses. The results show that these factors have a significant impact on the detection of positive selection, highlighting the need for their routine inclusion in selection analysis.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Biochemical Research Methods
Galya Klink, Olga Kalinina, Georgii Bazykin
Summary: Fitness conferred by the same allele may differ between genotypes and environments, and these differences shape variation and evolution. In this study, a new method is developed to detect individual amino acids that confer different fitness in different groups of species. The method combines sequence and phylogenetic data, and is validated using simulated evolution and applied to HIV-1 and influenza A. The results are consistent with fitness differences observed in experiments.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Review
Genetics & Heredity
Manoj Kumar Gupta, Ramakrishna Vadde
Summary: Numerous substitution models have been developed to estimate the evolutionary history of any sequence/organism, and the codon substitution model is the most powerful. However, due to higher computational demand, only a few studies have used this model for genome-scale analysis. Hence, there is a need to develop more robust and less computationally demanding codon substitution models. This review article explores the basis of different codon substitution models and discusses how to develop more efficient models.
FRONTIERS IN GENETICS
(2023)
Article
Genetics & Heredity
Roberto Del Amparo, Miguel Arenas
Summary: Probabilistic phylogenetic tree reconstruction has traditionally been performed by selecting the best-fitting substitution model of molecular evolution. Recent studies have proposed that this step is unnecessary, leading to a debate in the field. However, in the case of protein sequences, the selection of a substitution model has a significant influence on phylogenetic tree reconstruction. Our analysis of real and simulated data shows that phylogenetic trees reconstructed using the best-fitting substitution model of protein evolution are the most accurate in terms of topology and branch lengths.
Article
Multidisciplinary Sciences
Tian Xia, Lei Zhang, Guolei Sun, Xiufeng Yang, Honghai Zhang
Summary: This study identified eight canonical SOCS genes in reptiles and found that these genes had highly conserved evolutionary dynamics across the reptile lineages. Positive selection signals were detected in SOCS4 across reptile lineages, while SOCS2 showed selection signals specifically in the crocodilian lineage. The study also revealed different negative selection pressures on SOCS genes compared to reptile lineages and highlighted the rapid evolution in the crocodilian lineage.
Article
Immunology
Liyan Zeng, Ming Chen, Min Wang, Liuyao Zhu, Jingjing Yan, Xiaoyan Zhang, Jianqing Xu, Shuye Zhang
Summary: Analyzing the codon usage patterns of different strains of enterovirus A (EV-A), we found that there are variations in codon usage bias among different strains and these patterns are clade-specific. Natural selection plays a dominant role in shaping the codon usage preference of EV-A strains, and the unique codon usage patterns affect protein expression levels. We also identified host-specific codon adaptation patterns of EV-A strains in different clades.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Louis Duchemin, Vincent Lanore, Philippe Veber, Bastien Boussau
Summary: This paper investigates the performance of six amino-acid profile methods in detecting changes in the direction of selection, and compares them to a widely used d(N)/d(S) approach. The results show that all methods have reduced performance in the presence of biased gene conversion, but the best method, Pelican, performs as well as codeml in most conditions. It is fast and enables genome-scale searches for site-wise changes in the direction of selection associated with phenotypic changes.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Ecology
Fang Wang, Yonas I. Tekle
Summary: The evolution and diversity of the Amoebozoa supergroup is complex and poorly understood. Natural selection plays a crucial role in its evolution, and there is heterogeneity in selection across different lineages, potentially related to their ecological environment and adaptation optimization.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Ali Mostafa Anwar, Saif M. Khodary, Eman Ali Ahmed, Aya Osama, Shahd Ezzeldin, Anthony Tanios, Sebaey Mahgoub, Sameh Magdeldin
Summary: The tRNA adaptation index (tAI) is a translation efficiency metric that considers codon-tRNA wobble interaction efficiencies. The initial implementation had flaws due to species-specific variations in gene expression. The species-specific approach (stAI) was developed, but it struggled to find the global optimum. We developed a new approach called genetic tAI (gtAI) using a genetic algorithm to optimize weights and improve the correlation with the codon adaptation index (CAI) and protein abundance prediction.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2023)
Article
Biochemical Research Methods
Meng Wu, Fulei Nie, Haibin Liu, Tianyang Zhang, Miaomiao Li, Xiaoming Song, Wei Chen
Summary: This study investigated 1592 m(6)A modification regulators from 65 representative plant species and analyzed their phylogenetic relationships, sequence structure, selection pressure, and codon usage. The study found that regulators from different species or subfamilies were distinguishable based on phylogenetic trees. The gene structure of regulators was conserved, but unique exon/intron structures and motif organizations were observed among different families. The analysis also demonstrated that regulators experienced purifying selection, and the selection pressure was more relaxed in higher plants, suggesting they might have acquired new functions during evolution. Additionally, different codon usage preferences were observed for different kinds of regulators.
Article
Infectious Diseases
Qi Peng, Xue Zhang, Jizong Li, Wenlong He, Baochao Fan, Yanxiu Ni, Maojun Liu, Bin Li
Summary: This study presents a comprehensive analysis of 54 representative PDCoV strains, revealing a certain codon usage bias in the S gene and a higher adaptation level of PDCoV to humans and chickens than to pigs. These findings contribute to our understanding of PDCoV's evolution, adaptability, and inter-species transmission.
TRANSBOUNDARY AND EMERGING DISEASES
(2022)
Article
Plant Sciences
Jane D. Ray, Siti Subandiyah, Vivian A. Rincon-Florez, Ady B. Prakoso, I. W. Mudita, Lilia C. Carvalhais, Jenny E. R. Markus, Cecilia A. O'Dwyer, Andre Drenth
Summary: Blood disease in bananas caused by Ralstonia syzygii subsp. celebesensis is a bacterial wilt causing significant crop losses in Indonesia and Malaysia. There is no known varietal resistance to this disease in the Musa genus, and the disease has a rapidly expanding geographical range, making it an emerging threat to banana production in Southeast Asia and beyond.
Article
Plant Sciences
Jane D. Ray, Siti Subandiyah, Vivian A. Rincon-Florez, Ady B. Prakoso, Lilia C. Carvalhais, Andre Drenth
Summary: Blood disease of banana, caused by Ralstonia syzygii subsp. celebesensis, is a vascular wilt that has economic significance in Indonesia and Malaysia. This study confirms that Cavendish and Kepok 'Kuning' banana varieties are susceptible to Blood disease, and the infection occurs through various parts of the banana inflorescence.
Article
Plant Sciences
Jane D. Ray, Siti Subandiyah, Ady B. Prakoso, Vivian A. Rincon-Florez, Lilia C. Carvalhais, Andre Drenth
Summary: This study reveals that Banana Blood disease is mainly transmitted by insects and other means. The ooze from infected male bell and the sap from various symptomatic plant parts are infective and can be easily transmitted through tools. Long-distance dispersal can occur through contaminated planting material. Disease management strategies are discussed based on these findings.
Article
Plant Sciences
Vivian A. Rincon-Florez, Jane D. Ray, Lilia C. Carvalhais, Cecilia A. O'Dwyer, Siti Subandiyah, Dzarifah Zulperi, Andre Drenth
Summary: This study developed a novel real-time PCR assay for the detection of banana Blood disease with high specificity and sensitivity. The assay was validated and proven to be reliable for the diagnosis of Blood disease, outperforming other PCR-based diagnostic methods.
Article
Multidisciplinary Sciences
Alan Soffan, Siti Subandiyah, Arman Wijonarko, Widhi Dyah Sawitri
Summary: Tea Mosquito Bug (TMB) is a major pest infesting tea and cocoa plantations worldwide. RNA-seq analysis of TMB antennae identified several genes involved in odorant reception, providing valuable molecular resources for developing olfaction-based control methods.
Article
Plant Sciences
Ady B. Prakoso, Tri Joko, Alan Soffan, Juli P. Sari, Jane D. Ray, Andre Drenth, Siti Subandiyah
Article
Agriculture, Multidisciplinary
Retno Pangestuti, Endang Sulistyaningsih, Budiastuti Kurniasih, Rudi Hari Murti, Stephen Harper, Siti Subandiyah
Summary: This study describes for the first time the growth stages of shallot plants from true seed, and develops an extended BBCH scale for identifying these stages. According to the scale, tropical shallot from seed in lowland areas exhibits five principal growth stages.
ANNALS OF APPLIED BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Junaidi, Tri Rini Nuringtyas, Anne Clement-Vidal, Albert Flori, Afdholiatus Syafaah, Fetrina Oktavia, Sigit Ismawanto, Martini Aji, Siti Subandiyah, Pascal Montoro
Summary: This study analyzed the effects of antioxidants and other latex diagnosis parameters on harvesting stress and tapping panel dryness (TPD). The results showed that the variation in reduced thiol content (RSH) is related to tapping frequency and ethephon stimulation, as well as the occurrence of TPD.
Article
Plant Sciences
Masanto Masanto, Arif Wibowo, Nur Fathurahman Ridwan, Widhi Dyah Sawitri, Koji Kageyama, Siti Subandiyah
Summary: This study revealed the expression and regulation mechanism of pathogenicity-related genes in causing black pod rot disease by Phytophthora palmivora through qPCR analysis, showing heterogeneity in gene expression among different isolates during the incubation periods.
JOURNAL OF PLANT INTERACTIONS
(2021)
Article
Plant Sciences
Ruth Feti Rahayuniati, Siti Subandiyah, Sedyo Hartono, Susamto Somowiyarjo, Ruly Eko Kusuma Kurniawan, Ady Bayu Prakoso, Kathy Crew, Megan E. Vance, Jane D. Ray, John E. Thomas
Summary: The study found that banana bunchy top virus (BBTV) is present in banana plants across various islands in Indonesia, with molecular analysis showing that BBTV isolates mainly belong to the South East Asian subgroup. Additionally, natural infections of BBTV were also observed on other plants such as abaca and wild banana.
TROPICAL PLANT PATHOLOGY
(2021)
Article
Entomology
Varsha Salsabillah, Nugroho Susetya Putra, Abdulrahman Saad Aldawood, Alan Soffan
Summary: This study found that chitosan significantly inhibits the population growth of green peach aphids by causing increased energy consumption due to frequent stylet withdrawal and intracellular puncture. Chitosan may act as a plant defense elicitor, but further research is needed to explore this mechanism.
INTERNATIONAL JOURNAL OF TROPICAL INSECT SCIENCE
(2021)
Proceedings Paper
Biodiversity Conservation
Woro Anindito Sri Tunjung, Dina Maulidia, Alfa Nadiya, Agnes Iskandar, Asti Fitri Widyasari, Siti Subandiyah
6TH INTERNATIONAL CONFERENCE ON BIOLOGICAL SCIENCE (ICBS 2019) - BIODIVERSITY AS A CORNERSTONE FOR EMBRACING FUTURE HUMANITY
(2020)
Article
Multidisciplinary Sciences
Ady B. Prakoso, Anisa A. Anjani, Tri Joko, Andre Drenth, Alan Soffan, Siti Subandiyah