Article
Genetics & Heredity
Cyrill John P. Godinez, Peter June D. Dadios, Dinah M. Espina, Megumi Matsunaga, Masahide Nishibori
Summary: The Philippines is a hotspot for animal genetic resources, with Philippine chickens showing high haplotypic diversity across Southeast Asia and Oceania. Maternal lineage haplogroup D predominates within the population, with evidence suggesting a Philippine origin of Pacific chickens. Philippine chickens also exhibit low genetic differentiation and high gene flow into the Pacific chicken population, with signals of expansion and population growth in Southeast Asia.
FRONTIERS IN GENETICS
(2021)
Article
Ecology
Shuichi Kitada, Hirohisa Kishino
Summary: Genetic stock identification (GSI) is an important management tool for Pacific salmon, providing rich genetic baseline data across the Pacific Rim. Analyzing data from chum salmon populations, it was observed that Japanese/Korean populations had the greatest impact and SNP selection was based on predicted structures.
ECOLOGY AND EVOLUTION
(2021)
Article
Agriculture, Dairy & Animal Science
Rong Li, Jianshu Sun, Yincheng Zhao, Heng Xiao, Shanyuan Chen
Summary: This study analyzed mitochondrial DNA control region sequences from Yunnan indigenous goat breeds, identifying two lineages A and B, with the B2 subclade possibly originating from Southwestern China. There was high gene flow and genetic admixture among Yunnan goat breeds, leading to no significant phylogeographic structuring.
JOURNAL OF ANIMAL BREEDING AND GENETICS
(2021)
Article
Biochemistry & Molecular Biology
Sarah J. du Plessis, Mark Blaxter, Klaus-Peter Koepfli, Elizabeth A. Chadwick, Frank Hailer
Summary: This study compared whole genome sequencing and microsatellite genotyping for the study of Eurasian otters. The results showed that whole genome sequencing provided more genetic information and higher resolution, revealing previously unknown genetic diversity and lineage differences. This study has important implications for understanding population structure and genetic diversity in otters.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Jie Qian, Min Zheng, Lingyu Wang, Yu Song, Jiawen Yan, Yi-Feng Hsu
Summary: Faithful DNA replication is crucial for living organisms. This study reveals the roles of SSB1 and SSB2 proteins in maintaining mitochondrial DNA stability through regulating DNA replication and homologous recombination. The findings provide new insights into plant mitochondrial DNA maintenance.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2022)
Article
Microbiology
Michel Tibayrenc
Summary: Genetic and genomic studies have identified at least eight genetic clusters within Giardia duodenalis, some of which have been designated as species. These clusters, referred to as assemblages, are considered near-clades that are discrete and stable in space and time despite occasional genetic exchange. The parallels between the subspecific genetic variability and clustering patterns of G. duodenalis and other parasitic species highlight the importance of a comparative population genomics approach enabled by the predominant clonal evolution model (PCE).
Article
Biochemistry & Molecular Biology
Swapnil Tichkule, Simone M. Caccio, Guy Robinson, Rachel M. Chalmers, Ivo Mueller, Samantha J. Emery-Corbin, Daniel Eibach, Kevin M. Tyler, Cock van Oosterhout, Aaron R. Jex
Summary: This study presents a whole-genome study of Cryptosporidium hominis, a major cause of diarrhea in low- and middle-income countries. The study identifies two distinct lineages of C. hominis, with one lineage predominantly found in low-income countries in Africa and Asia, and another lineage found in high-income countries in Europe, North America, and Oceania. The study also detects genomic regions of introgression between the lineages, leading to high diversity and divergence in potential virulence genes.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Multidisciplinary Sciences
Mark Lipson, Elizabeth A. Sawchuk, Jessica C. Thompson, Jonas Oppenheimer, Christian A. Tryon, Kathryn L. Ranhorn, Kathryn M. de Luna, Kendra A. Sirak, Inigo Olalde, Stanley H. Ambrose, John W. Arthur, Kathryn J. W. Arthur, George Ayodo, Alex Bertacchi, Jessica Cerezo-Roman, Brendan J. Culleton, Matthew C. Curtis, Jacob Davis, Agness O. Gidna, Annalys Hanson, Potiphar Kaliba, Maggie Katongo, Amandus Kwekason, Myra F. Laird, Jason Lewis, Audax Z. P. Mabulla, Fredrick Mapemba, Alan Morris, George Mudenda, Raphael Mwafulirwa, Daudi Mwangomba, Emmanuel Ndiema, Christine Ogola, Flora Schilt, Pamela R. Willoughby, David K. Wright, Andrew Zipkin, Ron Pinhasi, Douglas J. Kennett, Fredrick Kyalo Manthi, Nadin Rohland, Nick Patterson, David Reich, Mary E. Prendergast
Summary: Genetic and archaeological evidence suggest major demographic changes in sub-Saharan Africa during the Late Pleistocene and early Holocene. This study presents ancient DNA data from eastern and south-central Africa, revealing a geographically structured mixture of three highly divergent source populations.
Article
Multidisciplinary Sciences
Viengneesee P. Thao, Emily E. J. Sharpe, Ruchita C. Dholakia, Hannah H. N. Ahn, James P. Moriarty, Bijan J. Borah, Margaret C. Gill, Regan N. Theiler
Summary: True penicillin allergy is rare and commonly incorrectly reported. Testing shows that less than 5% of patients who report a penicillin allergy will have an active hypersensitivity when appropriately tested. Penicillin allergy testing is safe and cost-effective, and inaccurate penicillin allergy status may lead to inappropriate antibiotic use.
Article
Multidisciplinary Sciences
Silu Wang, Madelyn J. Ore, Else K. Mikkelsen, Julie Lee-Yaw, David P. L. Toews, Sievert Rohwer, Darren Irwin
Summary: Research on two hybridizing species of warblers in western North America found that populations with different mitochondrial DNA haplotypes and nuclear DNA regions may exhibit divergent mitonuclear coadaptation, especially in relation to genes associated with fatty acid oxidation and energy-related signaling transduction. The study suggests that spatial variation in mitonuclear ancestries is correlated with climatic conditions and may underpin cryptic differentiation in this species complex. Little is known about how mitonuclear interactions influence genomic divergence among hybrid and parental lineages.
NATURE COMMUNICATIONS
(2021)
Article
Agriculture, Dairy & Animal Science
Tijana Vucic, Ana Ivanovic, Maja Ajdukovic, Nikola Bajler, Milena Cvijanovic
Summary: Two large-bodied newt species, Triturus ivanbureschi and T. macedonicus, hybridize in nature across the Balkan Peninsula. This study examines the reproductive success and genetic composition of the first generation of hybrids. The results suggest that incompatibilities between mitochondrial and nuclear genomes may occur in later stages of development or subsequent hybrid generations.
Review
Genetics & Heredity
Giacomo Francesco Ena, Julen Aizpurua-Iraola, Neus Font-Porterias, Francesc Calafell, David Comas
Summary: This review presents the latest developments in the genetic background research of the Roma, including studies on their ancestral components and migrations. It is important for both the public and scholars to understand the genetic characteristics and origins of the Roma.
Article
Plant Sciences
Tam Minh Nguyen, Duy Dinh Vu, Hien Phan Dang, Xuan Thi Tuyet Bui, Hong Phan Lan Nguyen, Duc Minh Nguyen
Summary: Moderate levels of genetic diversity and differentiation were found in Anisoptera costata. Population divergence during the Younger Dryas was detected. The anthropogenic disturbance significantly impacted the genetic diversity of the species in low tropical forests.
Article
Genetics & Heredity
Quinn Langdon, Daniel Powell, Bernard Kim, Shreya Banerjee, Cheyenne Payne, Tristram Dodge, Ben Moran, Paola Fascinetto-Zago, Molly Schumer
Summary: This study analyzes the drivers of variation in local ancestry across the genome in hybridization events between two species pairs of swordtail fish and finds unexpectedly high levels of repeatability. The analysis also identifies regions of the genome where minor parent ancestry is unusually low or high across species pairs, indicating shared selection sites and mechanisms.
Letter
Biochemistry & Molecular Biology
Benjamin Davies, Anjali Gupta Hinch, Alberto Cebrian-Serrano, Samy Alghadban, Philipp W. Becker, Daniel Biggs, Polinka Hernandez-Pliego, Chris Preece, Daniela Moralli, Gang Zhang, Simon Myers, Peter Donnelly
Summary: Male hybrid offspring often exhibit sterility or subfertility, primarily due to improper chromosome pairing during male meiosis. In subspecies of the house mouse, the histone methyltransferase PRDM9 plays a crucial role in improving the likelihood of successful chromosome synapsis. Genetic manipulation altering PRDM9 binding can rescue chromosome pairing defects and restore fertility in hybrids between Mus musculus and Mus spretus, highlighting additional mechanisms that contribute to reproductive isolation between species.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Plant Sciences
Kai-Hua Jia, Hui Liu, Ren-Gang Zhang, Jie Xu, Shan-Shan Zhou, Si-Qian Jiao, Xue-Mei Yan, Xue-Chan Tian, Tian-Le Shi, Hang Luo, Zhi-Chao Li, Yu-Tao Bao, Shuai Nie, Jing-Fang Guo, Ilga Porth, Yousry A. El-Kassaby, Xiao-Ru Wang, Charles Chen, Yves Van de Peer, Wei Zhao, Jian-Feng Mao
Summary: The study on the tetraploid scarlet sage genome assembly revealed multiple whole-genome duplication (WGD) events and showed expression asymmetries among homoeologs in the most recent WGD, which may indicate the first step towards sub- and neofunctionalization.
HORTICULTURE RESEARCH
(2021)
Article
Plant Sciences
Shi-Ping Cheng, Kai-Hua Jia, Hui Liu, Ren-Gang Zhang, Zhi-Chao Li, Shan-Shan Zhou, Tian-Le Shi, Ai-Chu Ma, Cong-Wen Yu, Chan Gao, Guang-Lei Cao, Wei Zhao, Shuai Nie, Jing-Fang Guo, Si-Qian Jiao, Xue-Chan Tian, Xue-Mei Yan, Yu-Tao Bao, Quan-Zheng Yun, Xin-Zhu Wang, Ilga Porth, Yousry A. El-Kassaby, Xiao-Ru Wang, Zhen Li, Yves Van de Peer, Jian-Feng Mao
Summary: Ginger is a highly valued spice plant with important economic and cultural significance. Research has identified significant structural variations between haplotypes in ginger, with inversions potentially linked to infertility. Analysis also revealed that most alleles in ginger are coordinately expressed.
HORTICULTURE RESEARCH
(2021)
Article
Plant Sciences
Jing-Fang Guo, Baosheng Wang, Zhan-Lin Liu, Jian-Feng Mao, Xiao-Ru Wang, Wei Zhao
Summary: This study investigated the biogeographic history of a relict conifer species, Pinus bungeana, in central China. The species exhibited extremely low genetic diversity and strong population structure, indicating long-term isolation in small populations. The species experienced severe bottlenecks in the early Pliocene and continued to decline in the Pleistocene in the western distribution, while expanding in the east. Local adaptation played a small but significant role in population diversity. Fragmented populations with low genetic diversity make the species highly vulnerable to climate change.
JOURNAL OF SYSTEMATICS AND EVOLUTION
(2023)
Article
Genetics & Heredity
Hui Liu, Wei Zhao, Ren-Gang Zhang, Jian-Feng Mao, Xiao-Ru Wang
Summary: This study reports the complete mitogenome sequence of Cupressaceae and compares it with other gymnosperm mitogenomes. The results show significant differences in genome size, repetitive content, and substitution rate among mitogenomes. Dispersed repeats are closely associated with mitogenome expansion and most of them accumulate in recent duplication events. Syntenic blocks and shared sequences between mitogenomes decay with divergence time, except in Ginkgo and Cycads. Phylogenetic analysis supports a sister group relationship between Cupressophytes and Gnetophytes, which have lost several protein-coding genes that are likely transferred to the nucleus. These clades also exhibit accelerated and highly variable substitution rates compared to other gymnosperms.
FRONTIERS IN GENETICS
(2022)
Article
Forestry
Jenjira Fungjanthuek, Man-Juan Huang, Alice C. Hughes, Jian-Feng Huang, Huan-Huan Chen, Jie Gao, Yan-Qiong Peng
Summary: This study used the ecological niche model MAXENT to evaluate habitat suitability and predict potential habitats for two fig species in the Xishuangbanna region of China. The results showed that key variables influencing habitat suitability differ for the two species, and suitable distribution areas may decrease in the future. Specific actions are needed to conserve these species.
Article
Plant Sciences
Jie Gao, Kyle W. W. Tomlinson, Wei Zhao, Baosheng Wang, Ralph Sedricke Lapuz, Jing-Xin Liu, Bonifacio O. O. Pasion, Bach T. T. Hai, Souvick Chanthayod, Jin Chen, Xiao-Ru Wang
Summary: Through studying the population genetic structure and diversity of two pine species, it is found that tropical pine species and subtropical pine species have different evolutionary processes and distribution ranges under the influence of past climate change in SEA. The subtropical Pinus yunnanensis shows significant gene flow, while the tropical Pinus kesiya exhibits strong population structure. There is a wide hybrid zone between the two species in southern Yunnan. Predictions indicate that the range of Pinus kesiya will decrease under future climate change. This study highlights the different evolutionary trajectories of pine species in SEA compared to high latitude species, emphasizing the urgent need for conservation efforts in this fragmented landscape.
JOURNAL OF SYSTEMATICS AND EVOLUTION
(2023)
Review
Entomology
Yiyi Dong, Jie Gao, Jiri Hulcr
Summary: Invasive wood borers pose a threat to global forests and tree-related industries. Reports of damages caused by wood borers on plants planted overseas can help identify potential invaders and speed up risk assessment. However, language barriers, lack of digitization, and limited circulation of literature hinder the availability of this information to the international plant protection community.
ENVIRONMENTAL ENTOMOLOGY
(2023)
Article
Plant Sciences
Chang Qu, Hong-Na Kao, Hui Xu, Bao-Sheng Wang, Zhi-Ling Yang, Qi Yang, Gui-Feng Liu, Xiao-Ru Wang, Yan-Jing Liu, Qing-Yin Zeng
Summary: This study investigates the diversity of the glutathione S-transferase (GST) gene family in a hybrid pine and its parent species, and explores the functional significance of sequence variations in conifer genomes. The results show that there are significant differences in gene expression and enzymatic activities towards different substrates among the GST orthologous groups. The hybrid pine prefers to retain GST genes similar to one of its parent species, and amino acid changes in key sites of GSTs can significantly affect their enzyme functions.
JOURNAL OF SYSTEMATICS AND EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Li He, Fei-Yi Guo, Xin-Jie Cai, Hong-Pu Chen, Chun-Lan Lian, Yuan Wang, Ce Shang, Yue Zhang, Natascha Dorothea Wagner, Zhi-Xiang Zhang, Elvira Hoerandl, Xiao-Ru Wang
Summary: We tested the role of stable sex-determination system and spatial/ecological isolation in the establishment of polyploid dioecious plants. Our study focused on the dioecious species Salix polyclona and revealed that 52% of individuals were tetraploids with an autopolyploid origin. Phylogenetic analysis showed that tetraploids had a distinct geographic distribution in western and central China. The inheritance of the sex-determining system from diploid progenitors as an intrinsic factor and spatial isolation as an extrinsic factor may have facilitated the preservation and establishment of polyploid dioecious populations.
Article
Multidisciplinary Sciences
Tianquan Yang, Rengang Zhang, Xiaoling Tian, Gang Yao, Yuanting Shen, Sihai Wang, Jianfeng Mao, Guangyuan Li, Aizhong Liu, Weibang Sun, Yongpeng Ma
Summary: By using PacBio long-read, short-read Illumina, and Hi-C sequencing data, we generated a high-quality chromosome-scale assembly of the M. oleifera genome, which provides important references for studying the genome evolution and nervonic acid biosynthesis of this plant.
Article
Biochemistry & Molecular Biology
Jing-Fang Guo, Wei Zhao, Bea Andersson, Jian-Feng Mao, Xiao-Ru Wang
Summary: This study investigated the genetic structure and clines in Pinus densata to gain an understanding of the contemporary dynamics of species barriers. It found four distinct genetic groups within P. densata that reflect its migration history and major gene-flow barriers across the landscape. Ecological selection played an important role in generating genomic heterogeneity and a genetic barrier across a zone of species transition.
PLANT COMMUNICATIONS
(2023)
Article
Forestry
David Hall, Wei Zhao, Alisa Heuchel, Jie Gao, Ulfstand Wennstro, Xiao-Ru Wang
Summary: A study found that external pollination and fecundity variation can influence the genetic composition and autumn frost hardiness of seed orchards. The study also observed that the origin of parental genotypes affects the freeze damage levels of the seedlings. Therefore, the origin of orchard parents, mating composition, and orchard environment all play a role in the quality and climate adaptation of seed crops.
FOREST ECOLOGY AND MANAGEMENT
(2023)
Article
Forestry
Jie Xu, Hang Luo, Shan-Shan Zhou, S. Qian Jiao, Kai-Hua Jia, Shuai Nie, Hui Liu, Wei Zhao, Xiao-Ru Wang, Yousry A. El-Kassaby, Ilga Porth, Jian-Feng Mao
Summary: This study evaluated the physiological and transcriptomic responses of Pinus tabuliformis Carr. to high-irradiance UV-B and UV-C waves, revealing both communalities and differences in the plant's responses to the two types of UV radiation. The research found that both UV-B and UV-C significantly inhibited photosynthesis while enhancing antioxidant capacity, flavonoid production, and stress resistance pathways in pine, indicating a shift towards enhanced defensive metabolism. The study isolated distinct subnetworks related to photoreceptor-mediated signal transduction, Fv/Fm regulation, and flavonoid biosynthesis in response to UV-B and UV-C radiation.
Article
Biochemistry & Molecular Biology
David Hall, Jenny Olsson, Wei Zhao, Johan Kroon, Ulfstand Wennstrom, Xiao-Ru Wang
Summary: This study revealed significant adaptation in frost hardiness among Scots pine populations through freezing tests and genotyping. Despite weak genetic differentiation among populations, the associations between climate variables and genotypes in this trait indicate a certain level of genetic basis.
PLANT COMMUNICATIONS
(2021)
Article
Forestry
Jie Xu, Shuai Nie, Chao-Qun Xu, Hui Liu, Kai-Hua Jia, Shan-Shan Zhou, Wei Zhao, Xian-Qing Zhou, Yousry A. El-Kassaby, Xiao-Ru Wang, Ilga Porth, Jian-Feng Mao
Summary: The study revealed that UV-B radiation inhibits photosynthesis and biosynthesis of photosynthetic pigments, while enhancing antioxidant processes such as the biosynthesis of flavonoids. Additionally, stress-related phytohormones and signal transduction pathways are activated in response to UV-B stress.