Article
Microbiology
Arya Suresh, Sabiha Shaik, Ramani Baddam, Amit Ranjan, Shamsul Qumar, Savita Jadhav, Torsten Semmler, Irfan A. Ghazi, Lothar H. Wieler, Niyaz Ahmed
Summary: The genotoxin colibactin produced by pathogenic E. coli strains is increasingly recognized for its critical implications in human health. This study analyzed the distribution, horizontal transmission, and evolution patterns of the island in different E. coli subtypes, shedding light on how pathogenic islands contribute to the clinical implications of infections.
Article
Multidisciplinary Sciences
Yuan Yuan, Yaolei Zhang, Peijun Zhang, Chang Liu, Jiahao Wang, Haiyu Gao, A. Rus Hoelzel, Inge Seim, Meiqi Lv, Mingli Lin, Lijun Dong, Haoyang Gao, Zixin Yang, Francesco Caruso, Wenzhi Lin, Rute R. da Fonseca, Ding Wang, Xianyan Wang, Marianne H. Rasmussen, Mingming Liu, Jinsong Zheng, Liyuan Zhao, Paula F. Campos, Hui Kang, Maria Iversen, Yue Song, Xinyu Guo, Jiao Guo, Yating Qin, Shanshan Pan, Qiwu Xu, Lingfeng Meng, A. Yunga, Shanshan Liu, Simon Ming-Yuen Lee, Xin Liu, Xun Xu, Huanming Yang, Guangyi Fan, Kun Wang, Songhai Li
Summary: The study generated high-quality genome assemblies of 17 marine mammals, revealing unique and convergent genomic variations associated with the transition to aquatic life in marine mammal lineages. The research advances understanding of the timing, pattern, and molecular changes associated with the evolution of mammalian lineages adapting to aquatic life.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Taylor S. Steele, John K. Brunson, Yukari Maeno, Ryuta Terada, Andrew E. Allen, Mari Yotsu-Yamashita, Jonathan R. Chekan, Bradley S. Moore
Summary: The biosynthetic pathways of domoic acid differ between diatoms and red macroalgae, with the absence of a critical enzyme in red macroalgae. Red macroalgae produce domoic acid via isodomoic acid B, with a unique origin of the rad genes compared to diatoms. The production of domoic acid in diatoms and red macroalgae involves a combination of native eukaryotic CYP450 neofunctionalization and horizontal gene transfer.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Peter Fuchs, Corinne Drexler, Sonia Ratajczyk, Leopold Eckhart
Summary: The evolutionary transition from land to water in cetaceans led to the loss of multiple epithelial keratins, including EPPK1, suggesting a change in the molecular composition and regulation of epithelia.
SCIENTIFIC REPORTS
(2022)
Article
Biochemistry & Molecular Biology
Marvin Choquet, Felix Lenner, Arianna Cocco, Gaelle Toullec, Erwan Corre, Jean-Yves Toullec, Andreas Wallberg
Summary: This study used comparative genomics to investigate the genetic variation and adaptation potential of 20 krill species collected from different oceans. The results showed that Antarctic krill species had lower levels of genetic variation and evolutionary rates, indicating a potentially lower adaptive potential to rapid climate change. Additionally, the study identified several candidate genes associated with adaptive evolution in Antarctic krill.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Biotechnology & Applied Microbiology
Yuki Kimura, Masato Nikaido
Summary: Type I and type II keratins are subgroups of intermediate filament proteins that provide toughness to the epidermis and protect it from water loss. Ancient fish lineages share keratin gene clusters, with a novel subcluster found in reedfish. Molecular evolutionary analyses suggest that amphibians' epidermal keratin gene subclusters originated from non-terrestrial ancestors.
Article
Genetics & Heredity
Virginia T. Scarlett, John T. Lovell, Mingqin Shao, Jeremy Phillips, Shengqiang Shu, Joanna Lusinska, David M. Goodstein, Jerry Jenkins, Jane Grimwood, Kerrie Barry, Boulos Chalhoub, Jeremy Schmutz, Robert Hasterok, Pilar Catalan, John P. Vogel
Summary: This study compares and analyzes the chromosome-scale reference genome of the natural allotetraploid grass Brachypodium hybridum, revealing gradual gene loss and chromosome rearrangement during genome integration. However, no signs of homeologous recombination or pronounced transposable element activation were found, indicating a relatively mild genome dominance.
Article
Biochemistry & Molecular Biology
Zheng-Yang Wen, Yu-Jian Kang, Lan Ke, De-Chang Yang, Ge Gao
Summary: Gene loss is a common source of genetic variation in genome evolution. We developed a new pipeline that integrates orthologous inference and genome alignment to effectively identify loss events. We discovered 33 gene loss events that give rise to novel lncRNAs with distinct expression features and potential functions related to growth, development, immunity, and reproduction in humans. Our data also revealed variable rates of protein gene loss and functional biases among different lineages.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Chun-Hong Nie, Na-An Zhang, Yu-Long Chen, Zhen-Xia Chen, Gui-Ying Wang, Qing Li, Ze-Xia Gao
Summary: Skeletogenesis is a complex process that requires rigorous control at multiple levels during osteogenesis. By constructing a skeletogenesis database, it was found that over 55% of genes are conserved in the six species, with 181 specific genes identified in the human genome.
COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS
(2021)
Review
Genetics & Heredity
Aisha Yousaf, Junfeng Liu, Sicheng Ye, Hua Chen
Summary: The availability of high-quality genome sequences of great ape species has provided unprecedented opportunities for genomic analyses. This review summarizes recent progress in evolutionary comparative genomic studies of human, chimpanzee, bonobo, gorilla, and orangutan, focusing on evolutionary history, natural selection, structural variations, and new genes, offering insights into the origin of human-specific phenotypes.
FRONTIERS IN GENETICS
(2021)
Article
Biochemistry & Molecular Biology
Colbie J. Reed, Geoffrey Hutinet, Valerie de Crecy-Lagard
Summary: Members of the DUF34 family, also known as the NIF3 protein superfamily, have been widely annotated as GTP cyclohydrolase I type 2, but new research suggests they may serve as metal ion insertases, chaperones, or metallocofactor maturases. This diverse molecular function could explain their involvement in pathways such as cell differentiation, metal ion homeostasis, pathogen virulence, redox, and universal stress responses.
Article
Genetics & Heredity
Yang Zhang, Fan Mao, Shu Xiao, Haiyan Yu, Zhiming Xiang, Fei Xu, Jun Li, Lili Wang, Yuanyan Xiong, Mengqiu Chen, Yongbo Bao, Yuewen Deng, Quan Huo, Lvping Zhang, Wenguang Liu, Xuming Li, Haitao Ma, Yuehuan Zhang, Xiyu Mu, Min Liu, Hongkun Zheng, Nai-Kei Wong, Ziniu Yu
Summary: By sequencing the genome of C. hongkongensis and comparing it to other reference bivalve genomes, this study identified the genomic determinants driving the shift from byssal to cemented attachment in oysters. The loss of the Antennapedia gene and expansion of lineage-specific extracellular gene families were found to be implicated in this transition. Transcriptomic analysis revealed significant differences in gene expression profiles between the asymmetrical C. hongkongensis and the symmetrical P. fucata, including elevated expression of orthologous transcription factor genes and lineage-specific shell-related gene families.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2022)
Article
Microbiology
Jose Luis Maturana, Juan P. Cardenas
Summary: Blautia, a genus established in 2008, is a relatively abundant taxonomic group in the microbiome of human and other mammalian gastrointestinal tracts. Despite the increasing knowledge about Blautia, its diversity is still poorly understood. Pangenome analysis of 225 Blautia genomes revealed 33 potential species, 17 of which were previously undescribed.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Cell Biology
Xuanjing Li, Pengcheng Wang, Qi Pan, Gaoming Liu, Weiqiang Liu, Olatunde Omotoso, Juan Du, Zihao Li, Yang Yu, Yun Huang, Pingfen Zhu, Meng Li, Xuming Zhou
Summary: This study generated a high-quality genome of the Asian elephant and identified expanded gene families related to tumor-associated pathways. Comparative genomic analysis revealed genes with positive selection in long-lived mammals, which enhanced the inhibition of tumor cell migration.
Article
Microbiology
Yang Liu, Tao Pei, Juan Du, Qing Yao, Ming-Rong Deng, Honghui Zhu
Summary: The study revealed the genetic diversity, metabolic versatility, and environmental adaptation of the genus Qipengyuania using comparative genomics. Fifteen new species of this genus have been established. This study provides an overall view of the genus Qipengyuania at the genomic level, contributing to a better understanding of its ecological roles and evolutionary history.
MICROBIOLOGY SPECTRUM
(2022)
Review
Biodiversity Conservation
Gernot Segelbacher, Mirte Bosse, Pamela Burger, Peter Galbusera, Jose A. Godoy, Philippe Helsen, Christina Hvilsom, Laura Iacolina, Adla Kahric, Chiara Manfrin, Marina Nonic, Delphine Thizy, Ivaylo Tsvetkov, Nevena Velickovic, Carles Vila, Samantha M. Wisely, Elena Buzan
Summary: Recent technological advances in genomics have provided new tools for conservation managers and practitioners, but choosing the right tools remains a crucial challenge. Inspirational case studies show how new technologies can help address conservation challenges, while also highlighting the need to consider the feasibility of different techniques.
CONSERVATION GENETICS
(2022)
Article
Cell Biology
Sara Lado, Jan Futas, Martin Plasil, Tom Loney, Pia Weidinger, Jeremy V. Camp, Jolanta Kolodziejek, Dafalla O. Kannan, Petr Horin, Norbert Nowotny, Pamela A. Burger
Summary: Dromedaries, important livestock, can act as a vector for transmitting zoonotic viruses such as MERS-CoV and CCHFV to humans. A recent study in the UAE found that CCHFV is endemic in dromedaries and camel ticks. The study identified two candidate immune genes, FCAR and CLEC2B, which play important roles in host defense against viral infections.
Article
Agriculture, Dairy & Animal Science
Morteza Bitaraf Sani, Zahra Roudbari, Omid Karimi, Mohammad Hossein Banabazi, Saeid Esmaeilkhanian, Nader Asadzadeh, Javad Zare Harofte, Ali Shafei Naderi, Pamela Anna Burger
Summary: This project aimed to find biological themes affecting growth in dromedaries. By analyzing candidate SNPs and related genes, the main biological functions related to growth were identified, providing potential candidate genes for camel breeding programs.
Article
Biochemistry & Molecular Biology
Zhipeng Jia, Surong Hasi, Claus Vogl, Pamela A. Burger
Summary: In this study, a complete genome of W. magnifica was obtained and its evolutionary and comparative analysis was performed. The results revealed a close phylogenetic relationship between W. magnifica and Sarcophaga bullata, and expansions of gene families with various functions, including immunity, insecticide-resistance mechanisms, heat stress response, and cuticle development. This study provides important genomic resources for studying the evolution of dipterous flies and the biology of W. magnifica.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Agriculture, Dairy & Animal Science
Amal Al-Kharusi, Elshafie Ibrahim Elshafie, Senan Baqir, Asim Faraz, Aliya Al-Ansari, Pamela Burger, Osman Mahgoub, Kaadhia Al-Kharousi, Halima Al-Duhli, Mohammed Al-Sinani, Raqiya Al-Hatali, Derek Roberts
Summary: Camels play a crucial role in the pastoral economy, especially in arid and semi-arid areas. Their milk and meat are important for human health, making it vital to consider their health, risks, and associated diseases. This investigation detected trypanosomoses in dromedary camels in Northern Oman and found two species of trypanosomes in the samples.
Article
Agriculture, Dairy & Animal Science
Morteza Bitaraf Sani, Javad Zare Harofte, Mohammad Hossein Banabazi, Asim Faraz, Saeid Esmaeilkhanian, Ali Shafei Naderi, Nader Salim, Abbas Teimoori, Ahmad Bitaraf, Mohammad Zadehrahmani, Pamela Anna Burger, Nader Asadzadeh, Mohammad Silawi, Afsaneh Taghipour Sheshdeh, Behrouz Mohammad Nazari, Mohammad Ali Faghihi, Zahra Roudbari
Summary: This study identified SNPs associated with coat color in dromedaries using GBS and highlighted the role of the SNAI1 gene in melanin biosynthesis and pigmentation. Despite the absence of distinct genetic clusters based on coat color phenotypes, admixture was observed in the four different coat color groups.
Article
Biodiversity Conservation
M. Magliolo, V. N. Naude, V. C. van der Merwe, S. Prost, P. Orozco-terWengel, P. A. Burger, A. Kotze, J. P. Grobler, D. L. Dalton
Summary: In South Africa, the cheetah population is divided into free-roamers, managed metapopulation, and captive facilities. To preserve overall genetic variation, interventions such as genetic exchanges and supplementation with unrelated individuals are proposed. Simulation results showed that without intervention or with only genetic exchanges, there were significant losses of heterozygosity and an increase in the frequencies of close relatives. However, introducing individuals from captive facilities maintained genetic diversity and relatedness.
ANIMAL CONSERVATION
(2023)
Article
Biochemistry & Molecular Biology
Attila Placido Sachslehner, Marta Surbek, Bahar Golabi, Miriam Geiselhofer, Karin Jaeger, Claudia Hess, Ulrike Kuchler, Reinhard Gruber, Leopold Eckhart
Summary: The study focuses on the localization of transglutaminase activity in various integumentary structures in mammals and birds. Transglutaminase activity was found in different layers of human epidermis, sweat glands, hair follicles, and nails. It was also present in claws, feathers, and keratinocytes of feathers in chickens. Additionally, transglutaminase activity was detected in tongue papillae of mice and chickens. The study suggests that transglutamination contributes to the cornification of hard skin appendages.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Cell Biology
Caterina Barresi, Heidemarie Rossiter, Maria Buchberger, Johannes Pammer, Supawadee Sukseree, Maria Sibilia, Erwin Tschachler, Leopold Eckhart
Summary: Autophagy is a degradation mechanism that plays a critical role in cellular homeostasis. Inhibition of autophagy has been found to slow down the growth of skin tumors.
Editorial Material
Agriculture, Dairy & Animal Science
Marcel Smits, Han Joosten, Bernard Faye, Pamela A. Burger
Summary: Until recently, dromedaries were used for various purposes such as transportation and production of meat, milk, and wool. However, the production of dromedary milk has steadily increased in recent decades due to its perceived health benefits. This has led to changes in animal welfare, gene composition, and the need for improved regulation and legislation to ensure food safety and well-being of dromedaries.
Article
Evolutionary Biology
Sven Winter, Rene Meissner, Carola Greve, Alexander Ben Hamadou, Petr Horin, Stefan Prost, Pamela A. Burger
Summary: This study presents a new genome assembly of the cheetah using PacBio long reads and Hi-C proximity ligation data. The assembly is of high quality and will greatly benefit conservation and evolutionary genomic analyses. It also provides a valuable resource for gaining a detailed understanding of immune response gene function and diversity in felids.
JOURNAL OF HEREDITY
(2023)
Article
Agriculture, Dairy & Animal Science
Badjibassa Akounda, Dominique Ouedraogo, Albert Soudre, Pamela A. Burger, Benjamin D. Rosen, Curtis P. Van Tassell, Johann Soelkner
Summary: This study explores the morphological differences between different goat populations in Burkina Faso using morphometric traits. The results show that there is no strict distinction between the two populations, indicating a close genetic relationship. Four groups were identified based on body size, representing the main breeds and their crosses. These different goat morphotypes are the result of farmers breeding practices. The study highlights the need for sustainable genetic improvement approaches for the use of these adapted local goat genetic resources.
Article
Immunology
Leopold Eckhart, Wolfgang Sipos
Summary: This study identified inactivating mutations of OAS genes in primates through comparative genomics and revealed a diversifying evolution pattern of the OAS gene family. The study also found that camelids lack OAS2 and OAS3 genes, Asian pangolins lack both OASL and OAS3 genes, and a new OAS gene (OAS5) is present in the bat suborder Yangochiroptera. These differences may affect innate immune responses to coronaviruses and other RNA viruses.
Article
Entomology
Zhipeng Jia, Surong Hasi, Deng Zhan, Bin Hou, Claus Vogl, Pamela A. Burger
Summary: In this study, two sex-determination genes in Wohlfahrtia magnifica were isolated and characterized, providing a foundation for genetic control strategies against this species. Additionally, transcriptome analysis revealed five candidate genes that may be involved in Cas9-based gene drive systems, potentially contributing to the control of myiasis infestation caused by W. magnifica.
Review
Biochemistry & Molecular Biology
Marta Surbek, Supawadee Sukseree, Leopold Eckhart
Summary: The skin protects the body and its metabolism of iron is regulated by differentially expressed genes in the epidermal keratinocytes, supporting the recycling of iron and preventing its release from the skin surface.
