Article
Biochemistry & Molecular Biology
Isolde van Riemsdijk, Jan W. Arntzen, Wieslaw Babik, Serge Bogaerts, Michael Franzen, Konstantinos Kalaentzis, Spartak N. Litvinchuk, Kurtulus Olgun, Jan Willem P. M. Wijnands, Ben Wielstra
Summary: This study utilizes parallel tagged amplicon sequencing to obtain nuclear DNA markers for banded newts and investigates population structure, interspecific gene flow, and phylogenetic relationships. The results confirm the genetic distinctiveness of the three proposed species and suggest a sister relationship between O. nesterovi and O. ophryticus. Limited introgression between the two species is found. Intraspecific structuring is extensive, with the recognized subspecies O. vittatus cilicensis representing the most distinct lineage. Mitochondrial DNA shows some discrepancies with nuclear DNA patterns among the banded newt species.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Jessie F. Salter, Peter A. Hosner, Whitney L. E. Tsai, John E. McCormack, Edward L. Braun, Rebecca T. Kimball, Robb T. Brumfield, Brant C. Faircloth
Summary: Phylogenomics with historical specimen-driven analysis is becoming increasingly important in filling gaps in evolutionary history of diverse groups. Analyzing subclades can help distinguish artifactual causes of discordance introduced by historical samples.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2022)
Article
Biochemical Research Methods
Timo Lassmann
Summary: SAMStat is an efficient program for extracting quality control metrics from fastq and SAM/BAM files. It displays sequence composition, base quality composition, and mapping error profiles based on mapping quality, allowing users to quickly identify reasons for poor mapping. A major update to SAMStat now supports paired-end and long-read data, with quality control plots drawn using the ploty javascript library.
Review
Zoology
Rafael R. Ferrari, Laurence Packer
Summary: This study provides a morphological phylogeny of Colletinae, supporting the subfamily's monophyly with four unique synapomorphies. It confirms that Colletinae can be subdivided into two major clades, one comprising Mourecotelles and Xanthocotelles, and the other including Colletes and Hemicotelles. Additionally, the study offers a fully illustrated key for generic identification of Colletinae.
ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY
(2021)
Review
Medicine, General & Internal
Syahzuwan Hassan, Rosnah Bahar, Muhammad Farid Johan, Ezzeddin Kamil Mohamed Hashim, Wan Zaidah Abdullah, Ezalia Esa, Faidatul Syazlin Abdul Hamid, Zefarina Zulkafli
Summary: Thalassemia is a highly heterogeneous disease with over a thousand recorded mutation types worldwide. Conventional PCR-based DNA analysis for thalassemia diagnosis is time-consuming and resource-intensive due to phenotype variability, disease complexity, and test limitations. Advanced molecular techniques such as next-generation sequencing (NGS) and third-generation sequencing (TGS) offer more suitable and valuable options for DNA analysis of thalassemia. The continuous improvement of sequencing methods and bioinformatics tools, particularly for identifying copy number variations and homologous genes, will lead to more accurate thalassemia detection.
Review
Clinical Neurology
Christian Mawrin, Ralf Koch, Natalie Waldt, I. Erol Sandalcioglu, Werner E. K. Braunsdorf, Jan-Peter Warnke, Felix Goehre, Hans-Juergen Meisel, Christian Ewald, Sina Neyazii, Ulrich Schueller, Elmar Kirches
Summary: This study utilizes a custom-made next generation sequencing meningioma panel to detect mutations in 11 different genes in a cohort of 109 meningioma patients. The most frequent mutations were found in NF2, AKT1(E17K), and TRAF7. Combinations of different gene mutations were common, and different mutations were associated with different meningioma subtypes and pathological grades.
Article
Immunology
Min Kong, Wei Li, Qingsheng Kong, Haixin Dong, Aizhong Han, Liqing Jiang
Summary: This study describes a case of a child infected with tuberculosis after being wounded. The use of metagenomic next-generation sequencing (mNGS) helped in identifying the specific pathogen and facilitating early treatment, leading to improved prognosis.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Adrian Dockery, Laura Whelan, Pete Humphries, G. Jane Farrar
Summary: Inherited retinal diseases (IRDs) encompass a variety of genetically diverse conditions with phenotypic variations, researchers utilize cutting-edge sequencing techniques to identify elusive causes, providing accurate diagnoses and informed prognoses for family planning and medical interventions.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Plant Sciences
Cecilia Plesken, Patrick Pattar, Bianka Reiss, Zinnia Naoshin Noor, Lisha Zhang, Klaus Klug, Bruno Huettel, Matthias Hahn
Summary: Botrytis cinerea, a plant pathogen causing gray mold rot on various crops, was studied using a multilocus sequence typing (MLST) scheme to evaluate genetic diversity. Through MLST analysis, high-resolution strain differentiation and robust species separation were achieved. The study revealed unknown populations of B. cinerea and genetically distinct strains on Iris pseudacorus.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Oncology
Bassel Nazha, Tony Z. Zhuang, Hiba Dada, Leylah M. Drusbosky, Jacqueline T. Brown, Deepak Ravindranathan, Bradley C. Carthon, Omer Kucuk, Jamie Goldman, Viraj A. Master, Mehmet Asim Bilen
Summary: This study evaluated the genomic landscape of adrenocortical carcinoma (ACC) using blood-based DNA testing. The findings suggest that a significant proportion of ACC patients have actionable mutations, which could inform personalized treatment options or clinical trials for this aggressive malignancy.
Review
Biochemistry & Molecular Biology
Pasquale Tripodi
Summary: This review examines the application of genomic technologies in studying the diversity of tomatoes, with a focus on next-generation sequencing strategies and methods. It also discusses how genomics has provided insights into the domestication process of tomatoes and presents perspectives on utilizing natural variation for breeding purposes through pan-genome construction and graphical pan-genome development.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Multidisciplinary Sciences
Yen-Yi Liu, Bo-Han Chen, Chih-Chieh Chen, Chien-Shun Chiou
Summary: This study evaluated the robustness of different read lengths, read depths, and assemblers in recovering genes from reference genomes. The quality of assemblies was found to be mainly affected by read depth, regardless of the assembler used. Recommendations for cutoff values and cost-effective combinations for cgMLST were provided.
Article
Biochemical Research Methods
Christopher Paul Wardell, Cody Ashby, Michael Anton Bauer
Summary: FiNGS is a software developed to improve the precision of variant caller outputs for somatic variants, with demonstrated reliability and better performance than other tools for the same task. It provides researchers with a simple, configurable, and reproducible tool for filtering somatic variants in sequencing data.
BMC BIOINFORMATICS
(2021)
Article
Evolutionary Biology
Jesus Gomez-Zurita, Anabela Cardoso
Summary: Cryptocephalinae, with 5,300 species, is the fourth largest subfamily of Chrysomelidae beetles. A molecular phylogenetic study confirmed its sister-group relationship with Lamprosomatinae and identified Eumolpinae as its closest relative, while also providing insights into the systematics of this diverse group.
Article
Immunology
Ying Liu, Huifen Wang, Yaoguang Li, Zujiang Yu
Summary: The study aimed to evaluate the clinical diagnostic value of metagenomic next-generation sequencing (mNGS) for tuberculosis (TB). Retrospective analysis of 52 patients with suspected TB infection was conducted, and multiple detection methods were performed. The results showed that mNGS had a higher detection rate of MTB compared to acid-fast staining and PCR, but no statistical difference with T-SPOT.TB assay. As an adjunctive diagnostic technology, mNGS can be combined with traditional methods to guide the diagnosis and treatment of TB.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
Editorial Material
Multidisciplinary Sciences
Guangping Huang, Xiaoge Ping, Weihua Xu, Yibo Hu, Jiang Chang, Ronald R. Swaisgood, Jiang Zhou, Xiangjiang Zhan, Zejun Zhang, Yonggang Nie, Jie Cui, Michael Bruford, Zhihe Zhang, Baoguo Li, Li Zhang, Zhi Lv, Fuwen Wei
NATIONAL SCIENCE REVIEW
(2021)
Article
Ornithology
Pengcheng Wang, Chiafen Yeh, Jiang Chang, Hongyan Yao, Yiqiang Fu, Chengte Yao, Xiao Wang, Shouhsien Li, Zhengwang Zhang
Summary: This study used genetic data and ecological niche modeling to investigate the speciation process of Chinese Bamboo Partridges and Taiwan Bamboo Partridges. The results showed that gene flow between the two species ceased before the mid-Pleistocene, and their ecological niches were highly conserved, with overlapping potential distribution ranges during the last glacial maximum. These findings suggest that speciation with gene flow may have played a role in the diversification of these species.
Article
Biodiversity Conservation
Jinzhe Qi, Jiayin Gu, Yao Ning, Dale G. Miquelle, Marcel Holyoak, Dusu Wen, Xin Liang, Shuyan Liu, Nathan James Roberts, Eryan Yang, Jianmin Lang, Fuyou Wang, Cheng Li, Zhuo Liang, Peiqi Liu, Yi Ren, Shaochun Zhou, Minghai Zhang, Jianzhang Ma, Jiang Chang, Guangshun Jiang
Summary: Efforts to restore the population of Amur tigers in northeast China have mainly focused on the Laoyeling landscape. However, the study suggests that the population recovery in other landscapes may be constrained by low prey density, highlighting the need for prey restoration and other conservation strategies to achieve a large meta-population of Amur tigers across northeast Asia.
BIOLOGICAL CONSERVATION
(2021)
Article
Biodiversity Conservation
Shan Tian, Shuai Lu, Junqin Hua, Jiang Chang, Jianqiang Li, Zhengwang Zhang, Yong Wang, Jiliang Xu, Mingxiang Zhang
Summary: This study conducted a survey on Reeves's Pheasant populations in central China and found that the existing national nature reserve network covers only a small portion of suitable habitat for the species. It suggests prioritizing currently unprotected moderately suitable habitat for conservation efforts to improve management effectiveness.
BIRD CONSERVATION INTERNATIONAL
(2022)
Article
Zoology
Hongyan Yao, Yanan Zhang, Zhen Wang, Gaoming Liu, Quan Ran, Zhengwang Zhang, Keji Guo, Ailin Yang, Nan Wang, Pengcheng Wang
Summary: This study investigates the divergence process of the cold-adapted species L. lerwa and finds that climatic oscillations played a significant role in their isolation and subsequent divergence on the Qinghai-Tibetan Plateau.
Correction
Multidisciplinary Sciences
Zhongru Gu, Shengkai Pan, Zhenzhen Lin, Li Hu, Xiaoyang Dai, Jiang Chang, Yuanchao Xue, Han Su, Juan Long, Mengru Sun, Sergey Ganusevich, Vasiliy Sokolov, Aleksandr Sokolov, Ivan Pokrovsky, Fen Ji, Michael W. Bruford, Andrew Dixon, Xiangjiang Zhan
Article
Ecology
Jin Liu, Weipan Lei, Xunqiang Mo, Chris J. Hassell, Zhengwang Zhang, Tim Coulson
Summary: The study shows that environmental change can have an impact on migration tactics and population dynamics in birds through adaptive phenotypic plasticity. The loss of staging habitat leads to increased plasticity in migration tactics, with individuals staying longer on the habitat, which affects population dynamics.
JOURNAL OF ANIMAL ECOLOGY
(2022)
Article
Ornithology
Pengcheng Wang, Simin Liu, Junhua Hu, Jing Zhang, Zhen Wang, Jiliang Xu, Hongyan Yao, Biao Wang, De Chen, Zhengwang Zhang, Yang Liu
Summary: This study investigates the genetic differentiation of the common pheasant across a longitudinal gradient in northern China using population genomics, geographical information, and environmental variables. The study finds that environmental heterogeneity is the most important driver explaining the genetic differentiation in this species.
JOURNAL OF AVIAN BIOLOGY
(2022)
Article
Ecology
Hui Wang, Shenghan Gao, Yu Liu, Pengcheng Wang, Zhengwang Zhang, De Chen
Summary: The study introduces a pipeline for the rapid development of polymorphic SSR markers from multi-sample genomic data. By genotyping multiple individuals using bioinformatic software based on resequencing data, highly polymorphic SSRs can be detected prior to experimental validation, significantly improving efficiency and reducing experimental effort. Overall, the pipeline demonstrates a successful application of NGS technology for mining and developing molecular markers for ecological and evolutionary studies.
ECOLOGY AND EVOLUTION
(2022)
Article
Biodiversity Conservation
Bing-Run Zhu, Mo A. Verhoeven, Nicolas Velasco, Lisa Sanchez-Aguilar, Zhengwang Zhang, Theunis Piersma
Summary: Habitat loss and climate change threaten global biodiversity, with high latitudes being the most affected. This study predicts the future distributions of two subspecies of Black-tailed Godwits in Asia, indicating that climate change will cause northward shifts and shrinking breeding ranges for both subspecies.
GLOBAL CHANGE BIOLOGY
(2022)
Article
Zoology
Keyi Tang, Yufeng Wang, Mengling Wu, Shufang Wang, Changkun Fu, Zhengwang Zhang, Yiqiang Fu
Summary: Understanding the diet and seasonal changes of the Sichuan partridge is crucial for species-specific conservation and habitat management, as well as the preservation of the plant species in its habitat.
Article
Ornithology
Yu Liu, Li Tian, Zhuoya Zhou, Kai Gao, De Chen, Donglai Li, Yong Wang, Zhengwang Zhang
Summary: In this study, the Barn Swallow population in East Asia used the tolerance strategy, rather than resistance, to defend against nest mites. We found that males with more extravagant sexually selected traits had weaker resistance to the parasites. Overall, the Barn Swallow population showed strong tolerance against the parasite and it did not significantly affect reproductive success.
Article
Multidisciplinary Sciences
Jin Liu, Ziwen Chai, Hui Wang, Anton Ivanov, Vojtech Kubelka, Robert Freckleton, Zhengwang Zhang, Tamas Szekely
Summary: In order to understand species' resilience to future changes, it is important to investigate alterations in their life histories. The size and shape of eggs are key life-history traits in Arctic shorebirds, and our study shows that these characteristics vary significantly longitudinally, with a greater variation in monogamous species compared to polygamous species. This supports the recent disperse-to-mate hypothesis, suggesting that polygamous species disperse further to find mates, leading to panmictic populations. Overall, Arctic shorebirds provide valuable insights into evolutionary patterns in life history traits.
Article
Zoology
Guocheng Shu, Ping Liu, Tian Zha, Cheng Li, Yinmeng Hou, Chunlin Zhao, Jie Wang, Xiaoxiao Shu, Jiang Chang, Jianping Jiang, Feng Xie
Summary: Research suggests that disordered translocation of Chinese giant salamanders may have negative impacts on native populations, as most released individuals are not from local populations and could reduce the genetic integrity of original populations. Therefore, it is recommended to suspend current translocation activities until more robust measures can be developed and implemented.
ASIAN HERPETOLOGICAL RESEARCH
(2021)
Article
Ornithology
Tianlong Cai, Guiyou Wu, Lu Sun, Yu Zhang, Zhaojie Peng, Yanqing Guo, Xinyue Liu, Tao Pan, Jiang Chang, Zhonglou Sun, Baowei Zhang
Summary: Through analyzing the phylogeny and diversification patterns of Emberizidae, it was found that their most recent common ancestor originated in the New World and later invaded the eastern Palearctic through the Bering Straits Bridge, splitting into two lineages in Africa and the Palearctic. The group began to diversify in the late Miocene, rapidly at first due to the expansion of open habitats, but the diversification rate decreased in arid habitats as available habitats were occupied. Shifts in habitat preference to open forests led to terminal radiations in the mountains of Central Asia and the eastern Palearctic.
JOURNAL OF AVIAN BIOLOGY
(2021)