Article
Multidisciplinary Sciences
Ruslan Kalendar, Ulykbek Kairov, Daniyar Karabayev, Akbota Aitkulova, Nuray Tynyshtykbayeva, Asset Daniyarov, Zhenis Otarbay, Saule Rakhimova, Ainur Akilzhanova, Dos Sarbassov
Summary: We have developed a comprehensive set of multiplexed primers for universal SARS-CoV-2 genome sequencing using the Oxford Nanopore Rapid Barcoding library kit. These primers can be used to set up any variant of primer pools for whole-genome sequencing of SARS-CoV-2 with the Oxford Nanopore, using single- or double-tiled amplicons ranging from 1.2 to 4.8 kb. Additionally, this primer set is also applicable for targeted SARS-CoV-2 genome sequencing. We propose an optimized protocol for cDNA synthesis using Maxima H Minus Reverse Transcriptase and a set of SARS-CoV-2 specific primers, which allows efficient cDNA synthesis from a wide range of RNA amounts and quality, and enables whole-genome sequencing of SARS-CoV-2 with long tiled amplicons up to 4.8 kb, even in low-titer virus samples and degraded RNA.
SCIENTIFIC REPORTS
(2023)
Article
Medicine, Research & Experimental
Ming Chen, Pengqiang Zhong, Mengzhi Hong, Jinfeng Tan, Xuegao Yu, Hao Huang, Juan Ouyang, Xiaoping Lin, Peisong Chen
Summary: In this study, low coverage whole genome sequencing (LCWGS) was used to detect suspicious pelvic masses for ovarian cancer, showing high diagnostic value and complementarity with traditional diagnostic methods. The results suggest that LCWGS could be a promising tool for the identification of ovarian cancer.
JOURNAL OF TRANSLATIONAL MEDICINE
(2021)
Article
Environmental Sciences
Halina Binde Doria, Pauline Hannappel, Markus Pfenninger
Summary: This study investigated the evolutionary adaptation and genomic basis of increased tolerance in Chironomus riparius to cadmium exposure. The results showed a strong genome-wide selective response in all replicates, with pathways related to microtubules and organelles and cellular movement being specifically selected by cadmium exposure.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Fisheries
Hailiang Song, Boyu Zhu, Tian Dong, Wei Wang, Mou Hu, Xiaoyu Yan, Shijian Xu, Hongxia Hu
Summary: In this study, 11 candidate genes related to caviar yield trait of Russian sturgeon were identified, providing important insights into the genetic mechanism of caviar yield and future genome-assisted breeding.
Article
Zoology
Cheng-Fei Sun, Xin-Hui Zhang, Jun-Jian Dong, Xin-Xin You, Yuan-Yuan Tian, Feng-Ying Gao, He-Tong Zhang, Qiong Shi, Xing Ye
Summary: This study sequenced 149 largemouth bass fish and identified genomic regions with genes associated with improved traits. Through selective signal analysis, hundreds of potential candidate genes subjected to selection were identified. These candidate genes may serve as genomic markers for improving important traits of biological and commercial interest.
ZOOLOGICAL RESEARCH
(2023)
Article
Microbiology
Katarzyna Parys, Nicholas R. Colaianni, Ho-Seok Lee, Ulrich Hohmann, Natalie Edelbacher, Alen Trgovcevic, Zuzana Blahovska, Duhwa Lee, Alexander Mechtler, Zsuzsanna Muhari-Portik, Mathias Madalinski, Niklas Schandry, Isaac Rodriguez-Arevalo, Claude Becker, Elisabeth Sonnleitner, Arthur Korte, Udo Blasi, Niko Geldner, Michael Hothorn, Corbin D. Jones, Jeffery L. Dangl, Youssef Belkhadir
Summary: The study explores how microbial genes encoding MAMPs drive microbe elimination by activating immune responses in the presence of a host, and how the functionality of these genes is balanced against their immunogenicity. Decoding the immunogenic and motility profiles of a flagellin epitope in plants, the research identifies synthetic mutational tracks that undermine the detection activities of a plant flagellin receptor, leading to the discovery of antagonist or weaker agonist activities in the epitopes. This study also finds signatures of these mutational tracks in natural Pseudomonads.
CELL HOST & MICROBE
(2021)
Article
Biochemistry & Molecular Biology
Owen J. Holland, Madeline Toomey, Collin Ahrens, Ary A. Hoffmann, Laurence J. Croft, Craig D. H. Sherman, Adam D. Miller
Summary: This study provides evidence of rapid genomic changes in wild Australian blacklip abalone following a major population crash associated with an infectious disease. The findings suggest that rapid evolutionary changes may determine the recovery of abalone stocks and enhance virus resistance. This is a novel example of rapid adaptation in natural populations of a nonmodel marine organism, highlighting the potential pace at which selection can act to counter diseases in wildlife communities.
Article
Genetics & Heredity
Xiaoyu Luo, Jianbo Li, Chentong Xiao, Luyang Sun, Weixuan Xiang, Ningbo Chen, Chuzhao Lei, Hong Lei, Yun Long, Ting Long, Quji Suolang, Kangle Yi
Summary: This study compared the genomic variations of Xiangxi cattle with other breeds and found higher genetic diversity and weaker artificial selection in Xiangxi cattle. The study also identified important genes related to reproduction, growth, meat quality, heat tolerance, and immune response in Xiangxi cattle.
FRONTIERS IN GENETICS
(2022)
Article
Pharmacology & Pharmacy
Edin Muratspahic, Bernhard Retzl, Leopold Duerrauer, Michael Freissmuth, Christian F. W. Becker, Christian W. Gruber
Summary: Peptides have shown promise in GPCR drug discovery, particularly in the field of analgesics. By genome mining, novel KOR peptide ligands derived from blenny fish have been identified, exhibiting high affinity and potency for KOR activation.
FRONTIERS IN PHARMACOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Haruna Nakamura, Mitsuto Aibara, Rei Kajitani, Hillary D. J. Mrosso, Semvua Mzighani, Atsushi Toyoda, Takehiko Itoh, Norihiro Okada, Masato Nikaido
Summary: The cichlids of Lake Victoria exhibit rapid adaptive radiation, with low genetic differentiation among species and highly differentiated genes related to vision playing a crucial role in speciation. Comparative genomic analyses of three Lake Victoria cichlid species in different habitats revealed distinct patterns of population history and identified novel adaptive candidate genes, some with long divergent haplotypes between species, indicating selective sweep events. Phylogenetic analyses showed that much of the allelic diversity among Lake Victoria cichlids originated from standing genetic variation before the adaptive radiation. The study uncovered the species-specific adaptation processes and complex genomic substrate that facilitated this adaptation.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Agriculture, Dairy & Animal Science
Sihu Wang, Sayed Haidar Abbas Raza, Ke Zhang, Chugang Mei, Muna O. Alamoudi, Bandar H. Aloufi, Ahmed Mohajja Alshammari, Linsen Zan
Summary: Qinchuan cattle have undergone gradual improvements in body shape and growth rate through long-term breeding. Whole genome sequencing data revealed candidate genes related to the growth and development traits of Qinchuan cattle, including brain size, body characteristics, and limb development. Other genes were also found to be associated with meat quality, reproductive function, and coat color. These findings provide insights into breed formation and molecular genetic breeding, and can contribute to improving animal production and health.
ANIMAL BIOTECHNOLOGY
(2023)
Article
Agriculture, Dairy & Animal Science
Chunna Cao, Yuxin Kang, Qian Zhou, Hojjat Asadollahpour Nanaei, Didi Bo, Peiyao Liu, Yangyang Bai, Ran Li, Yu Jiang, Xianyong Lan, Chuanying Pan
Summary: This study identified candidate genes associated with the unique grey color and environmental adaptation in Romanov sheep through whole-genome sequencing. Understanding the genetic background and signatures of Romanov sheep is of great value for its conservation and utilization.
JOURNAL OF ANIMAL SCIENCE
(2023)
Article
Agriculture, Multidisciplinary
Jie Wang, Qiu-xia Lei, Ding-guo Cao, Yan Zhou, Hai-xia Han, Wei Liu, Da-peng Li, Fu-wei Li, Jie Liu
Summary: There are many different chicken breeds around the world with varying features, serving as valuable resources. However, there is currently a lack of knowledge regarding the genetic determinants responsible for the traits and characteristics of these breeds. Understanding the genetic mechanisms that explain the variations among breeds can assist breeders in developing improved chicken breeds.
JOURNAL OF INTEGRATIVE AGRICULTURE
(2023)
Article
Fisheries
Dong-Yang Zhang, Xin-Ming Liu, Wei-Jie Huang, Yao Wang, Khan Anwarullah, Li-Fei Luo, Ze-Xia Gao
Summary: In this study, the genetic variation of wild grass carp populations from the Yangtze River and the Pearl River, as well as a mono-female population, was detected using whole-genome resequencing. The mono-female population showed moderate genetic differentiation from the wild populations and exhibited selective sweeps in key genes associated with important traits. These findings have implications for molecular marker-assisted breeding and conservation strategies of grass carp germplasm resources.
Article
Genetics & Heredity
Guangqi Lyu, Chunyu Feng, Shiyu Zhu, Shuang Ren, Wanyi Dang, David M. Irwin, Zhe Wang, Shuyi Zhang
Summary: The difference in body size in Shiba Inu breeds may be related to candidate genes and specific sites, with 8 new genes requiring further study.
FRONTIERS IN GENETICS
(2021)