Article
Biochemistry & Molecular Biology
Tiange Yang, Saimire Aishan, Jiale Zhu, Yonghua Qin, Jiao Liu, Hong Liu, Jun Tie, Jiangqing Wang, Rui Qin
Summary: This study assembled and compared the chloroplast genomes of several Carthamus species, finding that their chloroplast genome structures were highly conserved. Phylogenomic analysis supported Carthamus as a monophyletic taxon, divided into two sections. This study expanded our understanding of Carthamus chloroplast genomes and provided support for more comprehensive phylogenetic studies.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Plant Sciences
Dong-Mei Li, Jie Li, Dai-Rong Wang, Ye-Chun Xu, Gen-Fa Zhu
Summary: This study sequenced, assembled, and analyzed ten complete chloroplast genomes of Zingiberoideae plants, providing valuable resources for understanding molecular evolutionary dynamics in the Zingiberaceae family. Divergent hotspots identified in the genomes can be used for developing molecular markers for phylogenetic inference and species identification.
Article
Marine & Freshwater Biology
Yu Wang, Yi Yang, Lingfeng Kong, Takenori Sasaki, Qi Li
Summary: In this study, the higher-level phylogeny of the Imparidentia superorder in Heterodonta was investigated by adding new mitochondrial sequences. The results provided a clearer understanding of the overall structure of the Imparidentia tree and the relationships among major lineages. Additionally, the molecular divergence times of nine nodes in the Imparidentia tree were inferred. Overall, this study contributes to a better-resolved phylogeny of Imparidentia based on mitochondrial genomes.
MARINE LIFE SCIENCE & TECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Huihui Zhang, Tao Huang, Qi Zhou, Qianqian Sheng, Zunling Zhu
Summary: This study sequenced the complete chloroplast genome of two Bougainvillea species and identified highly variable sites as potential markers for breeding cold-tolerant cultivars. The findings contribute to understanding the response of the cp genome to low-temperature stress and elucidating evolutionary characteristics and phylogenetic relationships among Bougainvillea species.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Genetics & Heredity
Wei Zhang, Ran Li, Changfa Zhou
Summary: Current research on Ephemeroptera focuses on morphology due to limited mitogenome data. This study sequenced and compared the mitogenomes of Epeorus carinatus and E. dayongensis, finding an extra tRNA(Met) gene that may be a molecular synapomorphy for part of Heptageniidae. Phylogenetic analyses suggest E. carinatus and E. dayongensis should be grouped into different subgenera within Heptageniidae.
Article
Biotechnology & Applied Microbiology
Dongzhu Jiang, Xiaodong Cai, Min Gong, Maoqin Xia, Haitao Xing, Shanshan Dong, Shuming Tian, Jialin Li, Junyao Lin, Yiqing Liu, Hong-Lei Li
Summary: This study conducted comparative genomics and phylogenetic analysis on the Zingiber genus. The results showed that the chloroplast genomes of Zingiber species have typical structures and conservative characteristics. Positive selection was identified in certain genes. The study also provided the complete chloroplast genome sequences of Zingiber species, which can be used for future research on molecular evolutionary dynamics and population variation.
Article
Biotechnology & Applied Microbiology
Jiaojun Yu, Jun Fu, Yuanping Fang, Jun Xiang, Hongjin Dong
Summary: In this study, eight chloroplast genomes of Rubus from the Dabie Mountains in Central China were sequenced and analyzed. The results showed that these genomes had similar structures and gene compositions, and identified markers for genetic diversity and phylogenetic analysis. The study demonstrated the potential use of the whole plastome as a powerful tool in phylogenetic studies of this genus.
Article
Biochemical Research Methods
Nicolas Serge Matthieu Robert, Fatih Sarigol, Elisabeth Zieger, Oleg Simakov
Summary: This method bridges the gap between micro- and macrosynteny detection, providing detailed information on both synteny conservation and transformation throughout the evolutionary history of animal genomes.
Article
Biochemistry & Molecular Biology
Min-Min Chen, Miao Zhang, Zong-Suo Liang, Qiu-Ling He
Summary: This study investigated the evolutionary relationships and germplasm identification of the Uncaria genus, a traditional Chinese medicine. The researchers sequenced and annotated the chloroplast genomes of various Uncaria species, identifying highly variable loci and SSRs that can be used as molecular markers. Phylogenetic analysis revealed the relationships between five Uncaria species. This research provides valuable insights for identifying genuine Uncaria species and their counterfeits.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Hoseong Choi, Yeonhwa Jo, Soo Yeon Choi, Sang-Min Kim, Yu Mi Choi, Jin-Sung Hong, Bong Choon Lee, Won Kyong Cho
Summary: Using RNA sequencing, we obtained 7 SMV genomes from soybean germplasms and conducted a comprehensive evolutionary and phylogenetic study of 143 SMV genomes from various plant species and countries. The study revealed the existence of nine clades of SMV isolates/strains and identified 76 recombinant events and 141 recombinants in total. The study also found that recombination and plant host adaptation are important factors driving the genetic diversity of the SMV genome.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Entomology
Yupeng Wu, Hui Fang, Jiping Wen, Juping Wang, Tianwen Cao, Bo He
Summary: In this study, the mitogenomes of Hestina persimilis and Hestinalis nama were obtained via sanger sequencing. Comparative analysis revealed that these two mitogenomes are highly conservative and share a close evolutionary relationship. Phylogenetic trees built upon the mitogenomic data show consistent relationships among Nymphalidae, with Hestinalis nama being closely related to Apatura and forming a monophyletic clade.
Article
Forestry
Yan-Feng Song, Qing-Hua Yang, Xian-Gui Yi, Zhao-Qing Zhu, Xian-Rong Wang, Meng Li
Summary: The study utilized SCUB analysis to investigate codon usage bias in subg. Cerasus, revealing natural selection as the main influencing factor, with gene expression level and GC content also impacting the usage pattern. The findings showed a consistent codon usage pattern across the 36 species, highlighting the importance of locus mutations and no-preference codons in phylogenetic reconstruction within the subgenus.
Article
Biochemistry & Molecular Biology
Ewa Gorecka, Romain Gastineau, Nikolai A. Davidovich, Olga I. Davidovich, Matt P. Ashworth, Jamal S. M. Sabir, Claude Lemieux, Monique Turmel, Andrzej Witkowski
Summary: This study presents the complete plastid and mitochondrial genomes of the monoraphid diatom Schizostauron trachyderma for the first time, showing a close relationship between S. trachyderma and fistula-bearing species of biraphid diatoms through multigene phylogenies.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Yupeng Wu, Xiaoran Liu, Yulei Zhang, Hui Fang, Junjiao Lu, Juping Wang
Summary: The mitochondrial genomes of four species belonging to the Crambidae family were successfully sequenced and analyzed, providing insights into their gene structure and phylogenetic relationships.
ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY
(2022)
Article
Environmental Sciences
Fengping Li, Jiawen Zheng, Qingxia Ma, Zhifeng Gu, Aimin Wang, Yi Yang, Chunsheng Liu
Summary: In this study, the complete mitochondrial genomes of three species from the marine gastropod Strombidae were sequenced. The phylogenetic relationships within Strombidae were explored and several morphological similarities were observed. The results suggest a possible correlation between morphological evolution in Strombidae and paleoclimate change.
FRONTIERS IN MARINE SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Rodrigo P. Baptista, Yiran Li, Adam Sateriale, Mandy J. Sanders, Karen L. Brooks, Alan Tracey, Brendan R. E. Ansell, Aaron R. Jex, Garrett W. Cooper, Ethan D. Smith, Rui Xiao, Jennifer E. Dumaine, Peter Georgeson, Bernard J. Pope, Matthew Berriman, Boris Striepen, James A. Cotton, Jessica C. Kissinger
Summary: We generated a new genome assembly and annotation for Cryptosporidium parvum IOWA and compared it with closely related species, revealing the potential genetic differences between them. The new assembly and annotation provide a more complete and accurate reference for future research.
Editorial Material
Parasitology
James A. Cotton, Stephen R. Doyle
Summary: The reduced efficacy of anthelmintic drug PZQ in controlling schistosomiasis is a major public health concern. Le Clec'h et al. identified a gene responsible for PZQ resistance in experimentally selected Schistosoma mansoni, but its importance in natural infections is yet to be determined.
TRENDS IN PARASITOLOGY
(2022)
Article
Microbiology
Adam J. Roberts, Han B. Ong, Simon Clare, Cordelia Brandt, Katherine Harcourt, Susanne U. Franssen, James A. Cotton, Nicole Mueller-Sienerth, Gavin J. Wright
Summary: This study aims to discover essential proteins for in vitro growth and host infection of Leishmania spp., with the goal of identifying subunit vaccine candidates. Through in silico analysis and genome editing, potential subunit vaccine candidates have been identified. Preclinical trials in a murine model showed significant levels of protection against splenic infection.
Article
Infectious Diseases
Yegnasew Takele, Emebet Adem, Tadele Mulaw, Ingrid Muller, James Anthony Cotton, Pascale Kropf
Summary: Neutrophil activation status and effector functions are not fully restored in Visceral leishmaniasis (VL) patients co-infected with HIV (VL/HIV patients), suggesting impaired host defence against pathogens in these patients.
PLOS NEGLECTED TROPICAL DISEASES
(2022)
Article
Infectious Diseases
Yegnasew Takele, Emebet Adem, Susanne Ursula Franssen, Rebecca L. Womersley, Myrsini C. Kaforou, Michael L. Levin, Ingrid C. Mueller, James Anthony L. Cotton, Pascale C. Kropf
Summary: The study found that lymphocytes from visceral leishmaniasis patients expressed a marker called PD1, and the ligand of this marker, PDL1, was also expressed on different blood cells. Blocking the interaction between PD1 and PDL1 increased the production of IFN gamma, suggesting that therapy using immune checkpoint inhibitors may improve disease control.
PLOS NEGLECTED TROPICAL DISEASES
(2022)
Article
Microbiology
Duncan J. Berger, Elsa Leger, Geetha Sankaranarayanan, Mariama Sene, Nicolas D. Diouf, Muriel Rabone, Aidan Emery, Fiona Allan, James A. Cotton, Matthew Berriman, Joanne P. Webster
Summary: Hybridization between different species of parasites is a major concern for public and veterinary health. Recent research has shown that viable hybrids and introgressed lineages between Schistosoma spp. are common in Africa and beyond. It is unclear whether these hybrids represent recent or ancient hybridization events.
Article
Microbiology
Roz Laing, Stephen R. Doyle, Jennifer McIntyre, Kirsty Maitland, Alison Morrison, David J. Bartley, Ray Kaplan, Umer Chaudhry, Neil Sargison, Andy Tait, James A. Cotton, Collette Britton, Eileen Devaney
Summary: Through crossbreeding and gene expression analysis, we have identified certain genes associated with ivermectin resistance and proposed a novel mechanism that allows resistant worms to survive treatment. This is crucial for understanding ivermectin resistance and response to treatment in parasitic helminths.
Article
Immunology
Hugo O. Valdivia, Bruno M. Roatt, Rodrigo de Paula Baptista, Jennifer Ottino, Anderson Coqueiro-dos-Santos, Mandy J. Sanders, Alexandre B. Reis, James A. Cotton, Daniella C. Bartholomeu
Summary: Visceral leishmaniasis, an important global health problem, is particularly prevalent in Brazil. This study reveals a turnover of parasite populations in a re-emergent focus in Brazil, which presents new challenges for disease control efforts.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Cell Biology
Stephen R. Doyle, Roz Laing, David Bartley, Alison Morrison, Nancy Holroyd, Kirsty Maitland, Alistair Antonopoulos, Umer Chaudhry, Ilona Flis, Sue Howell, Jennifer McIntyre, John S. Gilleard, Andy Tait, Barbara Mable, Ray Kaplan, Neil Sargison, Collette Britton, Matthew Berriman, Eileen Devaney, James A. Cotton
Summary: Understanding the genetic basis of anthelmintic drug resistance in parasitic nematodes is crucial for improving parasite control. By using an in vivo genetic cross, this study successfully mapped resistance loci for three major classes of anthelmintics and identified new alleles for resistance. The study also implicated a transcription factor in ivermectin resistance and demonstrated the feasibility of high-resolution forward genetics in parasitic nematodes.
Article
Infectious Diseases
Sarah M. Coker, Erin K. Box, Natalie Stilwell, Elizabeth A. Thiele, James A. Cotton, Ellen Haynes, Michael J. Yabsley, Christopher A. Cleveland
Summary: Dracunculus medinensis, or Guinea worm, is a parasitic nematode that causes the debilitating disease dracunculiasis in humans. The global Guinea Worm Eradication Program has made significant progress in reducing human infections. However, the detection of animal infections poses challenges. To improve species confirmation time, a quantitative PCR assay targeting the mitochondrial cytochrome b gene of Guinea worm was developed. The assay demonstrated high sensitivity and specificity and can potentially eliminate the need for DNA sequencing.
PLOS NEGLECTED TROPICAL DISEASES
(2022)
Article
Infectious Diseases
Tushabe John Vianney, Duncan J. Berger, Stephen R. Doyle, Geetha Sankaranarayanan, Joel Serubanja, Prossy Kabuubi Nakawungu, Fred Besigye, Richard E. Sanya, Nancy Holroyd, Fiona Allan, Emily L. Webb, Alison M. Elliott, Matthew Berriman, James A. Cotton
Summary: This study aims to understand the impact of praziquantel (PZQ) treatment on the genetics of schistosomes. The authors obtained whole-genome sequence data from 174 individual miracidia collected from fishing communities in Uganda and investigated the genetic variation and genomic signatures of natural selection in pre- and post-treatment parasite populations. The study found higher genetic diversity in pre-treatment parasite populations and identified genes with evidence of recent positive selection in post-treatment and intensively treated parasites that could be related to reduced susceptibility to PZQ treatment.
PLOS NEGLECTED TROPICAL DISEASES
(2022)
Article
Microbiology
Aya Hefnawy, Gabriel Negreira, Marlene Jara, James A. Cotton, Ilse Maes, Erika D'Haenens, Hideo Imamura, Bart Cuypers, Pieter Monsieurs, Christina Mouchtoglou, Hans De Winter, Isabel Pintelon, Jean-Pierre Timmermans, Matt Berriman, Mandy Sanders, Julio Martin, Geraldine de Muylder, Jean-Claude Dujardin, Yann G-J Sterckx, Malgorzata Anna Domagalska
Summary: The study demonstrates the importance of prospective drug resistance (DR) studies for neglected tropical diseases (NTDs) using Leishmania donovani as a paradigm. By experimentally selecting resistance to a promising compound for visceral leishmaniasis and characterizing resistant parasites, a new DR mechanism involving LdoDLP1 was discovered. This highlights the practical relevance of prospective DR studies.
Article
Parasitology
Janneke Wit, Matthew L. Workentine, Elizabeth Redman, Roz Laing, Lewis Stevens, James A. Cotton, Umer Chaudhry, Qasim Ali, Erik C. Andersen, Samuel Yeaman, James D. Wasmuth, John S. Gilleard
Summary: This study fills the knowledge gaps in the detection of selection signatures in parasitic nematodes and provides a framework for maximizing the power of genome-wide approaches in detecting drug resistance loci. The study detected clear signatures of drug selection in Haemonchus contortus populations and identified the isotype-1 6-tubulin gene as the most important resistance locus.
INTERNATIONAL JOURNAL FOR PARASITOLOGY
(2022)
Article
Immunology
Susanne U. Franssen, Mandy J. Sanders, Matt Berriman, Christine A. Petersen, James A. Cotton
Summary: This study presents genomic data from Leishmania-infected dogs in the United States, demonstrating vertical transmission of the parasites without vector transmission. The parasites were introduced to the US separately from the Old World and more recently than L. infantum from South America. The unusual genetics of the parasite population suggest limited or no sexual reproduction. The findings have important implications for the population genetics of Leishmania parasites and highlight the need to consider vertical transmission in addition to vector transmission when studying transmission in complex natural settings.
EMERGING INFECTIOUS DISEASES
(2022)
Article
Cell Biology
Yegnasew Takele, Tadele Mulaw, Emebet Adem, Caroline Jayne Shaw, Susanne Ursula Franssen, Rebecca Womersley, Myrsini Kaforou, Graham Philip Taylor, Michael Levin, Ingrid Muller, James Anthony Cotton, Pascale Kropf
Summary: (Summary in English)
Visceral leishmaniasis (VL) has a high relapse rate in HIV patients, and these patients still exhibit pathological abnormalities after treatment. Three immunological markers associated with VL relapse in HIV patients have been identified, and these markers can be measured in primary hospital settings in Ethiopia, helping to predict relapse risk and improve disease management and patient care.
CELL REPORTS MEDICINE
(2022)