Article
Multidisciplinary Sciences
Chani R. Rue, Jason D. Selwyn, Patricia M. Cockett, Bryan Gillis, Lauren Gurski, Philip Jose, Brandi L. Kutil, Sharon F. Magnuson, Luz Angela Lopez de Mesa, R. Deborah Overath, Delbert Lee Smee, Christopher E. Bird
Summary: This study assembled mitochondrial genomes of Crassostrea virginica from Texas using pooled restriction-site-associated DNA sequencing (ezRAD), and compared them with the published genome from Delaware. Genetic differentiation was observed between Delaware and Texas populations, but not among the three bays in Texas. The study highlights the utility of mitochondrial DNA for comparing historic data and emphasizes the importance of reliable mitochondrial genome assembly to facilitate cross-study comparisons.
Article
Genetics & Heredity
Paul J. Worden, Daniel R. Bogema, Melinda L. Micallef, Jeffrey Go, Ania T. Deutscher, Maurizio Labbate, Timothy J. Green, William L. King, Michael Liu, Justin R. Seymour, Cheryl Jenkins
Summary: This study investigated the multifactorial disease causing stock losses in Pacific oyster summer mortality events. Through genomic analysis, multiple potentially pathogenic bacteria were identified, with Vibrio species being the most dominant in these events. The analysis also revealed limited and inconsistent associations between isolate species and their geographical origins or host health status, suggesting the need for strain-level identification.
MICROBIAL GENOMICS
(2022)
Article
Genetics & Heredity
Qi Chen, Lu Chen, Cheng-Qing Liao, Xing Wang, Min Wang, Guo-Hua Huang
Summary: This study integrated 794 mitogenomes from 26 lepidopteran superfamilies for comparative genomic and phylogenetic analysis, revealing gene codon differences and unique base overlaps in primitive taxon, as well as uncovering the main phylogenetic relationships within Lepidoptera.
Article
Chemistry, Medicinal
Monika Dhanji-Rapkova, Andrew D. Turner, Craig Baker-Austin, Jim F. Huggett, Jennifer M. Ritchie
Summary: A potent and heat-stable toxin, TTX, accumulates in various marine bivalve species, including Pacific oysters, with the highest concentrations found in the digestive gland. TTX levels vary significantly between different geographical locations and within populations of oysters, suggesting high variability in toxin distribution.
Article
Biochemistry & Molecular Biology
Shi-Jie Ke, Ding-Kun Liu, Xiong-De Tu, Xin He, Meng-Meng Zhang, Meng-Jia Zhu, Di-Yang Zhang, Cui-Li Zhang, Si-Ren Lan, Zhong-Jian Liu
Summary: In this study, the complete mitochondrial genome of Apostasia shenzhenica was sequenced and assembled, revealing its genetic diversity and phylogenetic relationships among monocotyledons. The mitochondrial genome was 672,872 bp in length and contained 36 protein-coding genes, 16 tRNAs, two rRNAs, and two copies of nad4L. Repeat sequence analysis showed the presence of medium and small repeats, accounting for 1.28% of the mitogenome sequence. Selection pressure analysis indicated high conservation of the mitogenome in related species. RNA editing identified 416 sites in the protein-coding region. Additionally, 44 chloroplast genomic DNA fragments were transferred to the mitogenome, with five plastid-derived genes remaining intact. Phylogenetic analysis showed well-determined evolution and classification of most monocots. These findings contribute to the genetic resources of orchids and provide valuable insights into the taxonomy and molecular evolution of monocots.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Microbiology
Marion Soree, Francois Delavat, Christophe Lambert, Solen Lozach, Mathias Papin, Bruno Petton, Delphine Passerini, Lionel Degremont, Dominique Hervio Heath
Summary: The study revealed that oysters grown in controlled environments accumulated more Vibrio parahaemolyticus than those grown in intertidal environments, possibly due to immune priming in the latter. However, both types of oysters showed similar depuration rates for V. parahaemolyticus.
ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Physiology
Sheng Liu, Hongqiang Xu, Shoushuo Jian, Qinggang Xue, Zhihua Lin
Summary: The study compared the taste and micronutrient content of Portuguese oysters and Kumamoto oysters, revealing differences in protein, glycogen, calcium, copper, zinc, as well as volatile organic compounds. However, free amino acids and flavor nucleotides may not be the key contributors to the special taste of Kumamoto oysters.
FRONTIERS IN PHYSIOLOGY
(2021)
Article
Agriculture, Dairy & Animal Science
Di Xu, Mengyao Sun, Zenghao Gao, Yiping Zhou, Qingqian Wang, Lei Chen
Summary: In this study, the mitochondrial genomes of 14 Talpidae species were compared, and it was found that variations in the control region repeats are responsible for the differences in mitochondrial genome lengths. The phylogenetic tree of Talpidae was reconstructed using the mitochondrial genome Cyt b genes as biomarkers. The divergence of Talpidae was found to be closely related to historical global climate changes, providing valuable experimental data for the systematic evolution and ecological adaptability of Talpidae.
Article
Multidisciplinary Sciences
Xinghao Li, Nan Song, Heng Zhang
Summary: The research sequenced complete or nearly complete mitogenomes of seven species in the tribe Coccinellini and found that they all share the same gene content and order as the putative ancestral insect mitogenome. Through comparative analysis of over 30 coccinellid species, the study confirmed the monophyletic nature of the Coccinellidae family.
Article
Entomology
Jing Liu, Yuyu Wang, Ruyue Zhang, Chengmin Shi, Weicheng Lu, Jing Li, Ming Bai
Summary: This study sequenced and analyzed three complete mt genomes of Erotylinae for the first time and conducted a comparative mt genomic analysis with Languriinae. The results revealed similarities in mt genome characteristics between Erotylinae and Languriinae, providing valuable information for future research. Mitochondrial genomes of Erotylinae showed consistent arrangements with other Coleoptera species, while differences in start and stop codons were observed between Languriinae and Erotylinae species. Phylogenetic analyses supported the monophyly of Erotylidae and showed the close relationship between Erotylinae and Xenocelinae, with Languriinae nested within Erotylidae.
Article
Environmental Sciences
Kayla Mladinich, Bridget A. Holohan, Sandra E. Shumway, J. Evan Ward
Summary: This study examines the relationship between microplastics and eastern oysters in Long Island Sound. The results show low concentrations of microplastics in oysters and their surrounding environment, with no clear correlation. This suggests that oysters are not a reliable bioindicator species for microplastic pollution.
MARINE ENVIRONMENTAL RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Weidong Huang, Changhua Zhang, Tingzhen Zhang, Ye Xu, Shiwen Xu, Li Tian, Hu Li, Wanzhi Cai, Fan Song
Summary: This study investigates the characteristics and evolution of the control region (CR) in Tortricidae, a type of moth. Through mitochondrial genome analysis, the researchers found that the CR sequences in Tortricidae exhibit high structural diversity, indicating the plasticity of the mitochondrial DNA molecule in this insect group.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Biotechnology & Applied Microbiology
Yan Cheng, Xiaoxue He, S. V. G. N. Priyadarshani, Yu Wang, Li Ye, Chao Shi, Kangzhuo Ye, Qiao Zhou, Ziqiang Luo, Fang Deng, Ling Cao, Ping Zheng, Mohammad Aslam, Yuan Qin
Summary: In this study, the mitochondrial genome of a halophytic model plant S. glauca was assembled and annotated, providing insights into the genome characteristics and variation of mt genomes in plants. The subsequent analysis revealed the importance of protein-coding genes in the mt genomes and their negative selections.
Article
Entomology
Lilan Yuan, Xueying Ge, Guanglin Xie, Haoyu Liu, Yuxia Yang
Summary: The family Melyridae, including Dasytinae and Malachiinae, is distributed worldwide and is the largest family of Cleroidea. Recent molecular phylogenetic studies have shown conflicting results on the relationships within this family, highlighting the need for reliable markers for further research. The annotated complete mitogenome of Cordylepherus sp. provides valuable insights into the organization and genetic characteristics of this family. Further large-scale analyses are necessary to confirm the relationships within Melyridae.
Article
Agronomy
Xiaoyan Li, Qiuju Han, Mengyao Li, Qing Luo, Shunhua Zhu, Yangxia Zheng, Guofei Tan
Summary: In this study, the mitochondrial genome of watercress was assembled using Illumina and Nanopore sequencing platforms, revealing a circular structure of 384,074 bp with 28 tRNA genes, 3 rRNA genes, and 34 protein-coding genes. The study also identified watercress's codon preference for leucine, isoleucine, and serine, and its close evolutionary relationship with species such as Bupleurum, Apium, Angelica, and Daucus. This research provides a valuable resource for the study of watercress evolution and molecular breeding.
Article
Biochemistry & Molecular Biology
Markus Osaland Fjelde, Einar Timdal, Reidar Haugan, Mika Bendiksby
Summary: This study investigated the taxonomy of the crustose lichen genus Calvitimela using molecular phylogenetics and morphological observations. The results revealed evolutionarily old and deeply divergent lineages within Calvitimela, with overlapping morphological characters between different subgenera. Chemical characters were informative at the level of subgenera but often homoplastic at the species level. A practical taxonomy of Calvitimela was proposed based on these findings.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Bo-Yang Shi, Da Pan, Kang-Qin Zhang, Tian-Yu Gu, Darren C. J. Yeo, Peter K. L. Ng, Neil Cumberlidge, Hong-Ying Sun
Summary: This study investigates the evolutionary history and speciation mechanisms of montane potamids in the Hengduan Mountains Region. The results suggest that the vicariance events of these crabs are correlated with the emergence of sky islands due to the uplift of the mountains. The mountain ridges provided corridors for their dispersal and past climatic conditions played a crucial role in their evolutionary history. The mechanisms isolating sky islands are reinforced by the climatic features of dry-hot valleys and continue to affect local diversification.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Attila Nemeth, Edvard Mizsei, Levente Laczko, David Czaban, Zsolt Hegyeli, Szabolcs Lengyel, Gabor Csorba, Gabor Sramko
Summary: Species delimitation of European blind mole rats is challenging due to their small morphological differences and complex chromosomal evolution. This study provides a comprehensive framework to improve understanding of their evolutionary history and revise their taxonomy. The results reveal the presence of multiple superspecies and species, with distinct geographic patterns and rapid chromosomal evolution.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Ying Qi, Zhaoyan Zhong, Xu Liu, Xing He, Yadong Zhou, Lili Zhang, Chong Chen, Katrin Linse, Jian-Wen Qiu, Jin Sun
Summary: This study investigates the phylogenetic relationships among patellogastropod families using mitochondrial and phylogenomic data. The results show that the mitochondrial phylogeny recovers monophyly of most families, but the relationships among families are still contentious. However, a more robust family-level topology consistent with morphology is achieved by phylogenomics. Additionally, the mainly deep-water families are found to be monophyletic, suggesting a single colonization of the deep water during the Jurassic.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Yu-Jie Shi, Jin -Liang Huang, Jia-Xuan Mi, Jing Li, Fan-Yu Meng, Yu Zhong, Fang He, Fei -Fei Tian, Fan Zhang, Liang-Hua Chen, Han-Bo Yang, Hong-Lin Hu, Xue-Qin Wan
Summary: Despite numerous studies on hybrid speciation, our understanding of this process remains limited. In this study, we conducted an 18-year systematic investigation on Populus taxa on the Qinghai-Tibet Plateau and discovered three new taxa that originated from distant hybridization between two different sections. These hybrid taxa demonstrate greater ecological adaptability than their ancestral species due to heterosis. We propose a hybrid speciation process model that can explain important evolutionary concerns.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Anna Cho, Denis Tikhonenkov, Gordon Lax, Kristina I. Prokina, Patrick J. Keeling
Summary: Unlike conspicuous ochrophytes, many small and overlooked flagellates belonging to basally branching stramenopiles remain poorly characterized at the cellular or genomic level. This study describes four new species, including two new genera, of sediment-dwelling MAST-6 and provides updated phylogenomic tree of stramenopiles. The characterization of these flagellates is important due to their phylogenetic diversity and abundance in various environments.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Tian-Tian Xue, Steven B. Janssens, Bin-Bin Liu, Sheng-Xiang Yu
Summary: Phylogenomic conflicts are widespread among genomic data, with most previous studies primarily focusing on nuclear datasets instead of organellar genomes. In this study, we investigated the phylogenetic conflicts within and between plastid and mitochondrial genomes using Potentilla as a case study. We found that both plastid and mitochondrial genomes divided Potentilla into eight highly supported clades, with two newly identified clades. Our results demonstrate that mitochondrial genes can fully resolve phylogenetic relationships among major clades of Potentilla and are not always linked with plastomes in evolutionary history.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Alexandra A. Grossi, Chunpo Tian, Mengjiao Ren, Fasheng Zou, Daniel R. Gustafsson
Summary: This study suggests that the coevolutionary relationships between chewing lice, endosymbiotic bacteria, and birds are not independent, but the patterns vary depending on the analysis method used. Additionally, louse host-switching does not seem to affect bacterial strains.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Ingrid Olivares, Sergio Tusso, Maria Jose Sanin, Marylaure de La Harpe, Oriane Loiseau, Jonathan Rolland, Nicolas Salamin, Michael Kessler, Kentaro K. Shimizu, Margot Paris
Summary: Traditionally, differences between species have been associated with morphological variation. However, the discovery of cryptic diversity suggests that the evolution of distinct lineages can occur without morphological differences. Through genetic analysis, we found that a tropical montane plant lineage is composed of numerous unrecognized genetic groups that are not morphologically distinct. Geographic distance and topography play a crucial role in determining the genetic divergence of these groups.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
