Article
Biochemistry & Molecular Biology
Weidong Huang, Pingzhou Zhu, Mingxia Wen, Zhimo Li, Xiang Yang, Hongkui Huang, Tao Jia, Chunyang Huang, Fan Song
Summary: This study sequenced four mitogenomes of click-beetles and found variations in length and control region characteristics. Phylogenetic analysis revealed the relationships among different subfamilies of Elateridae.
ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY
(2023)
Article
Genetics & Heredity
Enzhi Liu, Junjian Li, Siyang Ou, Bingjun Dong, Baotian Yang, Yu Zhou
Summary: Semblis atrata, found in clean brooks and streams in northern Eurasia, has a complete mitochondrial genome with a length of 14,909 bp, consisting of 13 protein-coding genes, 2 rRNA genes, and 22 tRNA genes. The nucleotide composition is highly AT biased, making it valuable for population genetics and phylogenetic analyses of this species.
MITOCHONDRIAL DNA PART B-RESOURCES
(2022)
Article
Genetics & Heredity
Min Li, Min Liu, Shi-Yun Hu, Fang-Zhen Luo, Ming-Long Yuan
Summary: This study analyzed the mitogenomes of ten spider species and found that nucleotide composition and codon usage were conserved within the RTA clade, but there was diversity in sequence length and structure in the control region. Most protein-coding genes were undergoing purifying selection.
FRONTIERS IN GENETICS
(2022)
Article
Genetics & Heredity
Emma M. Rempel, Jeffrey M. Marcus, Jillian T. Detwiler
Summary: The ramshorn snail Planorbella pilsbryi from North America is a widespread herbivorous freshwater snail with a complete nuclear rRNA sequence and circular mitogenome obtained through genome skimming. Phylogenetic reconstruction places P. pilsbryi as a sister taxon to Planorbella duryi within the family Planorbidae, consistent with previous hypotheses.
MITOCHONDRIAL DNA PART B-RESOURCES
(2021)
Article
Biotechnology & Applied Microbiology
Baojun Zhao, Shengtao Gao, Mingyang Zhao, Hongyu Lv, Jingyu Song, Hao Wang, Qifan Zeng, Jing Liu
Summary: This study investigates the mitochondrial genomes of three marine mussels and suggests that the absence of atp8 in some bivalve species might be due to annotation difficulties rather than actual gene loss. The study also provides evidence that mitochondrial genes may contribute to the adaptation of Mytilidae to different environments.
Article
Biotechnology & Applied Microbiology
Yoamel Milian-Garcia, Christopher A. Hempel, Lauren A. A. Janke, Robert G. Young, Tara Furukawa-Stoffer, Aruna Ambagala, Dirk Steinke, Robert H. Hanner
Summary: By sequencing the mitochondrial genomes of two Culicoides species, comparing different assembly tools, and identifying the best strategy and tools, this study provides a basis for molecular identification of Culicoides species.
Article
Agriculture, Dairy & Animal Science
Hang Wang, Qian Wen, Tongfei Wang, Fanrong Ran, Meng Wang, Xulei Fan, Shujun Wei, Zhonghu Li, Jiangli Tan
Summary: This study describes the mtgenomes of four wasps and provides new evidence for the two-origin hypothesis of eusociality in the Vespidae. The results contribute to the understanding of species evolution and phylogeny in the family Vespidae.
Article
Biochemistry & Molecular Biology
Hao Tan, Yang Yu, Yu Fu, Tianhai Liu, Yong Wang, Weihong Peng, Bo Wang, Jian Chen
Summary: This study investigated the mitogenome of the golden-needle mushroom and identified unique features. Primers were designed as markers for rapid identification of the mushroom.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Zoology
Wanqing Zhao, Dajun Liu, Qian Jia, Xin Wu, Hufang Zhang
Summary: Mitogenomes are essential in studies of phylogenetic relationships and evolutionary history. The analysis of the scentless plant bug's mitogenome revealed purifying selection in gene evolution and provided insights into its classification within the larger evolutionary tree.
Article
Plant Sciences
Melinda R. Grosser, Samantha K. Sites, Mayara M. Murata, Yolanda Lopez, Karen C. Chamusco, Kyra Love Harriage, Jude W. Grosser, James H. Graham, Fred G. Gmitter, Christine D. Chase
Summary: Plant genomes contain nuclear, plastid, and mitochondrial components which have different inheritance and evolutionary patterns. Genetic markers from these three genomes can be used to study inheritance, genetic relationships, and phenotypic contributions. Developing mitochondrial markers is challenging due to their high variability in size, gene order, and non-coding sequences, as well as their conservation in protein-coding sequences. PCR amplification of introns using conserved flanking exons is an effective method for developing polymorphic nuclear genome markers.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Engineering, Environmental
Zexin Tao, Xiaojuan Lin, Yao Liu, Feng Ji, Suting Wang, Ping Xiong, Li Zhang, Qing Xu, Aiqiang Xu, Ning Cui
Summary: This study collected sewage samples from Jinan, China from 2018 to 2019, and analyzed classic and novel HAstVs using real-time quantitative PCR and next generation sequencing. The results showed that sewage contains a high diversity of astroviruses, and there are multiple co-circulating lineages within each local HAstV genotype.
Article
Genetics & Heredity
Shaoke Guo, Xiaoyun Wu, Rende Song, Xita Za, Qingzhang Zhao, Jiye Li, Haiqing Ma, Fude Wu, Chunnian Liang, Jie Pei, Xian Guo
Summary: In this study, the complete mitochondrial genome of Yanglong yak was successfully assembled, showing the same gene order as other yak breeds. Phylogenetic analysis revealed a close relationship between this breed and other yak varieties.
MITOCHONDRIAL DNA PART B-RESOURCES
(2021)
Article
Genetics & Heredity
Jeffrey M. Marcus, Jan-Glynnis C. Alex, Mackenzie R. Alexiuk, Katrina J. Audet, Somtochukwu D. Azubuike, Amber S. Bezte, Madison B. Boychuk, Natalie L. Cale, Lara A. Carroll, Gabriela Y. Castro, Joshua Cheng, Janam Chopra, Gregory A. Corkal, Carla Louise M. Dizon, Moeez Farooq, Cecilia C. Flores, Ruzzell C. Flores, Tadbeer Grewal, Maria Haguisan, Kousha Kamal, Haziqa B. Kassim, Spencer J. Kauenhofen, Anushka Kothari, Suseong Lee, Yanju Li, Raju Majumdar, Ana Markovic, Hope K. Mcauley, Ashley M. Mckay, Deesha Nayar, Gurasis Osahan, Jordan A. Paul, Dhruvrajsinh Raolji, Alexandria Reimer, Talia R. Shafai, Simarjit Singh, Shloke Srivastava, Jackie Wang, Tristan B. Wolfe, Shirly J. Xie
Summary: In this study, the genome of a smudged butterfly species from Central and South America was sequenced, resulting in the assembly of its complete mitochondrial genome. The mitogenome was found to be AT-rich and contains protein-coding genes and tRNAs. Phylogenetic reconstruction suggests a close relationship between this butterfly species and Hamadryas.
MITOCHONDRIAL DNA PART B-RESOURCES
(2022)
Article
Multidisciplinary Sciences
Jiequn Yi, Han Wu, Jianbai Liu, Jihu Li, Yinglin Lu, Yifei Zhang, Yinjie Cheng, Yi Guo, Dunsong Li, Yuxing An
Summary: In this study, the mitogenome of A. fulloi was sequenced and characterized, revealing large-scale rearrangements and a novel gene arrangement. Phylogenetic analysis showed that the phylogenetic relationship of 6 superfamilies could be presented as Mymaridae + (Eupelmidae + (Encyrtidae + (Trichogrammatidae + (Pteromalidae + Eulophidae)))).
SCIENTIFIC REPORTS
(2022)
Article
Biotechnology & Applied Microbiology
Mingsheng Yang, Junhao Li, Silin Su, Hongfei Zhang, Zhengbing Wang, Weili Ding, Lili Li
Summary: This study generated 13 mitochondrial genomes of eight tortricid species and conducted a detailed comparative mitogenomics study of Tortricidae for the first time. The results revealed the evolutionary architectures of tortricid mitogenomes and provide a foundation for future studies on population genetics and phylogenetic investigations in this group.
Article
Biochemistry & Molecular Biology
Liina Kinkar, Robin B. Gasser, Bonnie L. Webster, David Rollinson, D. Timothy J. Littlewood, Bill C. H. Chang, Andreas J. Stroehlein, Pasi K. Korhonen, Neil D. Young
Summary: This study demonstrates how third-generation long-read sequencing and informatic methods can accurately characterize long non-coding, tandem-repetitive regions in mitochondrial genomes, overcoming challenges faced by conventional sequencing methods. The discovery of a large tandem-repetitive non-coding region in a metazoan organism raises questions about the evolution and function of potential control regions in mt genomes, prompting further exploration using Nanopore-informatic workflows.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Genetics & Heredity
William L. Macken, Annie Godwin, Gabrielle Wheway, Karen Stals, Liliya Nazlamova, Sian Ellard, Ahmed Alfares, Taghrid Aloraini, Lamia AlSubaie, Majid Alfadhel, Sulaiman Alajaji, Htoo A. Wai, Jay Self, Andrew G. L. Douglas, Alexander P. Kao, Matthew Guille, Diana Baralle
Summary: This study identified a novel recessive coatopathy characterized by severe developmental delay, cataracts, and variable microcephaly. Genetic analysis revealed variants in the COPB1 gene in two families, and CRISPR/Cas9 modelling in Xenopus tropicalis replicated the human syndrome features. This research highlights the importance of COPI subunits in brain development and human health, demonstrating the utility of exome and genome sequencing combined with Xenopus tropicalis CRISPR/Cas modelling for identifying and characterizing rare disease genes.
Article
Developmental Biology
Marcela M. Moreno, William B. Barrell, Annie Godwin, Matthew Guille, Karen J. Liu
Summary: Neuroblastoma is a common and deadly pediatric cancer, often found near the adrenal glands. The study demonstrates high conservation of the ALK protein among vertebrates and its expression in frog embryos, suggesting a potential role in neuroblastoma initiation. High levels of alk expression in tadpole stages indicate its involvement in tumorigenesis.
GENE EXPRESSION PATTERNS
(2021)
Article
Infectious Diseases
Euripide F. G. A. Avokpaho, Parfait Houngbegnon, Manfred Accrombessi, Eloic Atindegla, Elodie Yard, Arianna Rubin Means, David S. Kennedy, D. Timothy J. Littlewood, Andre Garcia, Achille Massougbodji, Sean R. Galagan, Judd L. Walson, Gilles Cottrell, Moudachirou Ibikounle, Kristjana Hronn Asbjornsdottir, Adrian J. F. Luty
Summary: Despite previous deworming campaigns targeting school-aged children, there is still a persistent reservoir of soil-transmitted helminth infections in adults and pre-school aged children that require targeted control measures. Expanding mass drug administration to target the whole community, instead of just school-aged children, may be necessary to achieve the goal of eliminating soil-transmitted helminths as a public health problem.
PLOS NEGLECTED TROPICAL DISEASES
(2021)
Article
Biochemistry & Molecular Biology
Natalia Fraija-Fernandez, Andrea Waeschenbach, Andrew G. Briscoe, Suzanne Hocking, Roman Kuchta, Tommi Nyman, D. Timothy J. Littlewood
Summary: This study established a robust phylogenetic framework for diphyllobothriidean tapeworms through sequencing mitochondrial genomes and nuclear ribosomal operon. Results indicate Cephalochlamydidae as an early diverging lineage, with Solenophoridae and Diphyllobothriidae as sister groups. While diphyllobothriideans likely originated in freshwater, later lineages show shifts between freshwater and marine habitats, with definitive hosts including marine and terrestrial mammals and birds.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2021)
Article
Microbiology
Yao-Dong Wu, Guo-Dong Dai, Li Li, D. Timothy J. Littlewood, John Asekhaen Ohiolei, Lin-Sheng Zhang, Ai-Min Guo, Yan-Tao Wu, Xing-Wei Ni, Nigus Abebe Shumuye, Wen-Hui Li, Nian-Zhang Zhang, Bao-Quan Fu, Yong Fu, Hong-Bin Yan, Wan-Zhong Jia
Summary: Cyclophyllidea is the most species-rich order of tapeworms, with significant health impact on wildlife, livestock, and humans. Through collection and sequencing of specimens from rodents in Qinghai-Tibet Plateau, several putative new species were identified. Additionally, three known species were found, suggesting their wide distribution in western China. The divergence time estimates indicate a strong association between species differentiation and biogeographic changes resulting from the uplift of the QTP, supporting the hypothesis of host-parasite co-evolution.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Developmental Biology
Alice M. Godden, Marco Antonaci, Nicole J. Ward, Michael van der Lee, Anita Abu-Daya, Matthew Guille, Grant N. Wheeler
Summary: Researchers used CRISPR-Cas9 knockout methods to study the role of miRNAs in the development of Xenopus neural crest. They designed a new approach to effectively 'drop out' miRNAs and studied their functions and effects through phenotype validation and gene analysis.
DEVELOPMENTAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Ahmet Tuncay, Anna Noble, Matthew Guille, James N. Cobley
Summary: RedoxiFluor is a novel antibody technology that enables accurate quantification of target-specific protein thiol redox state in percentages and moles on a microplate. It can operate in global mode and array mode, making it highly versatile. Extensive validation in diverse biological contexts demonstrates the reliability and utility of this technology.
FREE RADICAL BIOLOGY AND MEDICINE
(2022)
Review
Parasitology
Marina Papaiakovou, D. Timothy J. Littlewood, Stephen R. Doyle, Robin B. Gasser, Cinzia Cantacessi
Summary: This article evaluates the strengths and limitations of existing methods for diagnosing gastrointestinal helminth infections in humans and animals. It also explores the use of high-throughput sequencing approaches to define the taxonomic composition of these infections. Additionally, the article discusses the interactions between helminths and microbiota in the host gut.
PARASITES & VECTORS
(2022)
Article
Genetics & Heredity
Vardha Ismail, Linda G. Zachariassen, Annie Godwin, Mane Sahakian, Sian Ellard, Karen L. Stals, Emma Baple, Kate Tatton Brown, Nicola Foulds, Gabrielle Wheway, Matthew O. Parker, Signe M. Lyngby, Miriam G. Pedersen, Julie Desir, Allan Bayat, Maria Musgaard, Matthew Guille, Anders S. Kristensen, Diana Baralle
Summary: In this study, individuals carrying GRIA1 variants were identified and found to be associated with neurodevelopmental disorders, mainly affecting cognition and speech. Functional evaluation and animal models further confirmed the impact of these variants on AMPAR function.
AMERICAN JOURNAL OF HUMAN GENETICS
(2022)
Article
Evolutionary Biology
Peter G. Foster, Dominik Schrempf, Gergely J. Szollosi, Tom A. Williams, Cymon J. Cox, T. Martin Embley
Summary: Long branches and compositional heterogeneity in protein sequences can pose problems in phylogenetic reconstruction. Recoding alignments can help mitigate these issues, but the effectiveness depends on the specific characteristics of the data. Exchangeability-based recoding generally improves accuracy, while Chi-squared-based recoding may decrease accuracy. However, the impact of recoding on accuracy varies when dealing with alignments that exhibit different types of compositional heterogeneity. It is important to exercise caution when interpreting trees generated from recoded amino acid data sets and consider alternative models that directly account for the patterns in the data.
SYSTEMATIC BIOLOGY
(2023)
Article
Anatomy & Morphology
Narmadha Alles, Matthew Guille, Dariusz C. Gorecki
Summary: This study adapted the Zebrafish Embryonic Genotyper for rapid genomic DNA extraction from Xenopus frogs, allowing for rapid genotyping during the early stages of development. The results showed that the extraction process did not have any detrimental effects on the subsequent tadpole development or morphology, and high-quality DNA was successfully extracted.
DEVELOPMENTAL DYNAMICS
(2023)
Article
Biology
Heather E. Grant, Andrew N. Ostrovsky, Helen L. Jenkins, Leandro M. Vieira, Dennis P. Gordon, Peter G. Foster, Olga N. Kotenko, Abigail M. Smith, Bjoern Berning, Joanne S. Porter, Javier Souto, Wayne K. Florence, Kevin J. Tilbrook, Andrea Waeschenbach
Summary: Parental care is crucial for the survival and evolutionary success of offspring in metazoan groups. This study investigated the evolution of incubation chambers in bryozoans and found that at least 10 different types of brood chambers evolved in the Cheilostomatida order. The modular nature of bryozoans likely contributed to the diverse array of incubation chambers observed.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Article
Multidisciplinary Sciences
Joao M. Brazao, Peter G. Foster, Cymon J. Cox
Summary: In this study, the computational efficiency and accuracy of five methods for estimating substitution models were tested. Data-specific models were found to perform better than empirical models, with IQ-TREE and P4 (maximum likelihood) being the most accurate at estimating data-specific models. Additionally, the use of data-specific protein models resulted in a better fit to the data and different tree topologies compared to empirical models when re-analyzing published datasets.
Article
Parasitology
B. Neov, G. P. Vasileva, G. Radoslavov, P. Hristov, D. T. J. Littlewood, B. B. Georgiev
Summary: This study aimed to test a hypothesis for phylogenetic relationships among mammalian hymenolepidid tapeworms using molecular analyses and phylogenetics, revealing diverse host switching and evolutionary events among different clades.
JOURNAL OF HELMINTHOLOGY
(2021)