Article
Biochemistry & Molecular Biology
Kenneth K. Askelson, Garth M. Spellman, Darren Irwin
Summary: Analysis of genomic variation reveals high differentiation among white-breasted nuthatch populations, suggesting the existence of at least three species. It also shows evidence of introgression between a ghost lineage and a current population, contributing to differentiation.
Article
Ecology
Mohammed Ahmed, Nickellaus G. Roberts, Funmilola Adediran, Ashleigh B. Smythe, Kevin M. Kocot, Oleksandr Holovachov
Summary: This study conducted phylogenomic analyses on different suborders within the phylum Nematoda, revealing the phylogenetic relationships of Trichinellida, Spirurina, Rhabditina, and Tylenchina. Additionally, a phylum-wide analysis was performed, resulting in the phylogenetic tree of Nematoda.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Jeremias N. Brand, Gudrun Viktorin, R. Axel W. Wiberg, Christian Beisel, Lukas Schaerer
Summary: This study reports on a global sampling campaign aimed at increasing taxon sampling and geographic representation of the genus Macrostomum. Using extensive transcriptome and single-locus data, the researchers generated phylogenomic hypotheses including 145 species. The results show consistent clades across different phylogenetic methods, but the exact grouping is unclear, possibly due to a radiation early in Macrostomum evolution. Additionally, the study reveals a large undescribed diversity, with 94 of the studied species likely being new to science, and identifies multiple novel morphological traits.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Kateryna Gaertner, Craig Michell, Riikka Tapanainen, Steffi Goffart, Sina Saari, Manu Soininmaki, Eric Dufour, Jaakko L. O. Pohjoismaki
Summary: Speciation, a fundamental evolutionary process, leads to genetic differentiation of populations and results in discrete morphological, physiological and behavioural differences. This study analyzed the genetic and gene regulation differences between fibroblasts of two closely related mammals, the arctic/subarctic mountain hare and the temperate steppe-climate adapted brown hare, and discovered a species-specific expression pattern of 1623 genes, indicating differences in cell growth, cell cycle control, respiration, and metabolism.
Article
Biodiversity Conservation
Jakub Sawicki, Katarzyna Krawczyk, Monika Slipiko, Monika Szczecinska
Summary: Nowellia curvifolia is a widespread Holarctic species with a plastome that is the second smallest among photosynthetic liverworts. There is a low level of genetic differentiation between European and North American specimens, while Asian specimens show higher genetic diversity. Newly sequenced mitogenomes from European specimens exhibit identical gene content and structure to previously published ones, with low intercontinental differentiation.
Article
Genetics & Heredity
Pedro Andrade, Mariana L. Lyra, Juliana Zina, Deivson F. O. Bastos, Andres E. Brunetti, Delio Baeta, Sandra Afonso, Tuliana O. Brunes, Pedro P. G. Taucce, Miguel Carneiro, Celio F. B. Haddad, Fernando Sequeira
Summary: This article describes the genomic resources of the Neotropical leaf-frog Phyllomedusa bahiana, including genome, mitogenome, and transcriptome assemblies. These assemblies represent important additions to the catalog of genomic resources available for amphibians.
G3-GENES GENOMES GENETICS
(2022)
Article
Multidisciplinary Sciences
Elena Pomari, Giovanni Malerba, Laura Veschetti, Alessandra Franceschi, Lucas Moron Dalla Tor, Michela Deiana, Monica Degani, Manuela Mistretta, Cristina Patuzzo, Andrea Ragusa, Antonio Mori, Zeno Bisoffi, Dora Buonfrate
Summary: This study successfully identified the miRNAs of early and larval stages of S. stercoralis, providing important data for further research on the role of small molecules in its lifecycle and clinical diagnostics.
SCIENTIFIC REPORTS
(2022)
Article
Marine & Freshwater Biology
Laura Hagemann, Katharina. M. M. Mauer, Thomas Hankeln, Hanno Schmidt, Holger Herlyn
Summary: The present study aims to reconstruct the genome and transcriptome of the last common ancestor of Syndermata. The results suggest that the ancestral genome was compact, with a coding portion of >= 40%, and contained approximately 17,000 protein-coding genes with an average of 4-6 exons and 3-5 introns per gene.
Article
Multidisciplinary Sciences
Florian C. Boucher, Cedric Dentant, Sebastien Ibanez, Thibaut Capblancq, Marti Boleda, Louise Boulangeat, Jan Smycka, Cristina Roquet, Sebastien Lavergne
Summary: Through plant surveys and genomic research, this study found that plant diversity in high-elevation temperate mountains was enriched during the Pleistocene, driven by the combined action of geography and geology.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Jana Kabus, Sarah Cunze, Andrea Dombrowski, Ioannis Karaouzas, Spase Shumka, Jonas Jourdan
Summary: This study explores the differences in ecological niches among genetic lineages within a cryptic species complex. By sampling and identifying genetic lineages of the Gammarus roeselii species complex, the researchers found varying degrees of differences in the Grinnellian niches of different lineages, with some lineages having similar niches despite geographical separation and others having clearly different niches. These results suggest that a closer inspection of cryptic species is needed in the context of conservation and biodiversity.
Article
Genetics & Heredity
Yue Xie, Sen Wang, Shuangyang Wu, Shenghan Gao, Qingshu Meng, Chengdong Wang, Jingchao Lan, Li Luo, Xuan Zhou, Jing Xu, Xiaobin Gu, Ran He, Zijiang Yang, Xuerong Peng, Songnian Hu, Guangyou Yang
Summary: This study reveals the host adaptation of Baylisascaris schroederi to the giant panda and provides insights into the evolutionary trajectory of host-shift events in ascaridoid parasite lineages. The specific adaptations of B. schroederi to survive in the gut of giant pandas, such as increasing cuticle thickness and efficient utilization of host nutrients, are characterized. The findings of this study will aid in the development of prevention and treatment measures to protect giant panda populations from roundworm parasitism.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2022)
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)
Review
Ecology
Caren P. Shin, Warren D. Allmon
Summary: Methodological and biological considerations are intertwined when studying cryptic species. The frequency and definition of cryptic species in taxonomic groups are not well documented, causing ambiguity in interpreting their significance. Based on recent literature on shelled marine gastropods, this study reviews the definition and implications of cryptic species, concluding that most gastropod species are not cryptic.
ECOLOGY AND EVOLUTION
(2023)
Article
Plant Sciences
Ying Li, Deqiang Zhang, Shuqin Zhang, Yongfeng Lou, Xinmin An, Zehui Jiang, Zhimin Gao
Summary: This study analyzed the regulatory networks involved in primary thickening and their dynamics during bamboo growth, revealing the role of miRNA-gene-phytohormone networks. The findings provide insights into the molecular mechanisms underlying wood formation and properties in bamboo.
Article
Biochemistry & Molecular Biology
Lin Yang, Fuwen Wei, Xiangjiang Zhan, Huizhong Fan, Pengpeng Zhao, Guangping Huang, Jiang Chang, Yinghu Lei, Yibo Hu
Summary: This study investigates the genomics of takins and reveals the existence of two phylogenetic species and recent speciation. Two genetically divergent subspecies were also identified. The findings provide insights into the scientific conservation of takins and the biogeography of the Himalaya-Hengduan biodiversity hotspot.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Food Science & Technology
Soeren Lukas Hellmann, Fabian Ripp, Sven-Ernoe Bikar, Bertil Schmidt, Rene Koeppel, Thomas Hankeln
EUROPEAN FOOD RESEARCH AND TECHNOLOGY
(2020)
Article
Biochemical Research Methods
Robin Kobus, Jose M. Abuin, Andre Mueller, Soeren Lukas Hellmann, Juan C. Pichel, Tomas F. Pena, Andreas Hildebrandt, Thomas Hankeln, Bertil Schmidt
BMC BIOINFORMATICS
(2020)
Article
Multidisciplinary Sciences
Katharina Mauer, Soeren Lukas Hellmann, Marco Groth, Andreas C. Froebius, Hans Zischler, Thomas Hankeln, Holger Herlyn
Article
Genetics & Heredity
Sacha Heerschop, Zahra Fagrouch, Ernst J. Verschoor, Hans Zischler
Summary: Research on PRDM9 and PRDM7 evolution in primates sheds light on their roles in hybrid sterility and evolution. The origin of PRDM7 is shown to be more recent than previously expected, with different characteristics observed in different primates.
FRONTIERS IN GENETICS
(2021)
Article
Biochemistry & Molecular Biology
David Rosenkranz, Hans Zischler, Daniel Gebert
Summary: The PIWI/piRNA system plays diverse roles in animals, including protection of germline cells, gene regulation, antiviral defense, and somatic transposon repression. piRNA clusters serve as the major source of piRNAs in almost all metazoan species, with highly divergent genomic loci influencing piRNA populations in different taxonomic groups.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Ecology
Yeisson Gutierrez, Marion Fresch, Soren L. Hellmann, Thomas Hankeln, Christoph Scherber, Jens Brockmeyer
Summary: Diet composition and social environment have impacts on the proteome of house crickets, but gender plays a significant role in protein abundance variation. Males exhibit enriched proteins related to metabolic pathways and locomotion, while females show higher amounts of proteins associated with genetic processes regulation and nutrient catabolism. Moreover, diet composition and social environment induce sex-specific changes in a smaller set of proteins with particular roles.
ECOLOGY AND EVOLUTION
(2021)
Article
Multidisciplinary Sciences
Iliyas Rashid, Melina Campos, Travis Collier, Marc Crepeau, Allison Weakley, Hans Gripkey, Yoosook Lee, Hanno Schmidt, Gregory C. Lanzaro
Summary: High-depth whole genome sequencing was used to estimate the nuclear mutation rate per generation in malaria vectors Anopheles coluzzii and Anopheles stephensi by detecting de novo genetic mutations. This study provides the first empirical measurement of mutation rates in Anopheles genus, which will be useful for comparative evolutionary genomics and population genetic analysis of malaria vector mosquito species.
SCIENTIFIC REPORTS
(2022)
Article
Biochemical Research Methods
Marcel Kwiatkowski, Madlen Hotze, Julia Schumacher, Abdul R. Asif, Jose Miguel Ramos Pittol, Bertram Brenig, Sanja Ramljak, Hans Zischler, Holger Herlyn
Summary: Multiple spotting in 2-DE/MS can be influenced by protein speciation, amino acid modification, and alternative splicing. The ability to resolve proteomes down to protein species can lead to enrichment of multispotting proteins in 2-DE/MS, and low sensitivity of stains and MS instruments may enhance this effect.
Article
Biochemistry & Molecular Biology
Hanno Schmidt, Katharina Mauer, Thomas Hankeln, Holger Herlyn
Summary: The inability of parasites to complete their life cycles in less suitable hosts holds important clues for parasite control. In this study, the researchers analyzed transcriptomes of thorny-headed worms and compared developmentally arrested worms from one host species to their counterparts from another host species. They found that the molecular machinery of the worms from the less suitable host was less tailored to reproduction and more focused on coping with the unsuitable environment. The researchers also identified sex-specific traits and potential targets for treatment. This comparative analysis may also provide insights into the control of other helminth pathogens in humans and livestock.
CELL AND BIOSCIENCE
(2022)
Article
Biotechnology & Applied Microbiology
Hanno Schmidt, Katharina Mauer, Manuel Glaser, Bahram Sayyaf Dezfuli, Soren Lukas Hellmann, Ana Lucia Silva Gomes, Falk Butter, Rebecca C. Wade, Thomas Hankeln, Holger Herlyn
Summary: This study presents a bioinformatics workflow for the identification of candidate target proteins in parasites. The workflow combines genomics, transcriptomics, and proteomics to reduce the time and cost in the development of new strategies against parasites. The results demonstrate the effectiveness of the workflow in identifying highly specific candidate targets in Acanthocephala (thorny-headed worms). Virtual ligand screening also identified promising compounds for the control of these parasites.
Article
Genetics & Heredity
Maurice Scheuren, Jonas Moehner, Hans Zischler
Summary: R-loops are three-stranded nucleic acid structures that play important roles in transcriptional regulation, DNA replication, and chromatin accessibility. In this study, the presence of R-loops in fully mature human and bonobo sperm heads was shown, with partial correspondence to transcribed regions and chromatin structure. The R-loop landscape in sperm resembles patterns seen in somatic cells, and R-loops are detected in both residual histone and protamine-packed chromatin. Additionally, R-loops were found to influence the transcriptomes of early developmental stage zygotes. These findings suggest that R-loops may contribute to inherited gene regulation.
FRONTIERS IN GENETICS
(2023)