Review
Plant Sciences
Carl J. Rothfels
Summary: Polyploidy is a prominent feature in current plant diversity, with ongoing debates on whether it plays a crucial role in long-term evolution. The emerging field of 'polyploid phylogenetics' has provided researchers with opportunities to study the evolutionary history of polyploid lineages, laying the foundation for mechanistic models of ploidy change. This advancement also allows for a more comprehensive analysis of plant taxa in general.
Article
Biology
Zhenling Lv, Zijuan Li, Meiyue Wang, Fei Zhao, Wenjie Zhang, Changping Li, Lei Gong, Yijng Zhang, Annaliese S. Mason, Bao Liu
Summary: The majority of homoeologous triad genes in the A and B subgenomes of polyploid wheat showed highly conserved histone modification patterns during domestication and ploidy transitions, while a subset of functionally relevant genes were trans-regulated by the D genome in hexaploid wheat. The overall histone modification levels were stable in most genes, but certain genes displayed differential modification and enrichment for specific gene ontology terms, indicating a complex regulatory network during evolution and domestication.
Article
Evolutionary Biology
Zhi Yan, Zhen Cao, Yushu Liu, Huw A. Ogilvie, Luay Nakhleh
Summary: Phylogenetic networks are powerful tools for modeling and analyzing reticulate evolutionary histories. Recent developments have introduced statistical methods for handling specific types of polyploids, as well as parsimony methods that simplify polyploidy, implemented in the PhyloNet software package.
SYSTEMATIC BIOLOGY
(2022)
Article
Genetics & Heredity
Antoine Moinet, Flavia Schlichta, Stephan Peischl, Laurent Excoffier
Summary: This article investigates the shape of neutral valleys of diversity under a model of population size change and compares it to signals of a selective sweep. The results show that selective sweep valleys of diversity are wider than neutral valleys, but it is possible to find a neutral valley with the same width as a given selective valley by parameterizing the model.
Article
Plant Sciences
Venkata Suresh Bonthala, Benjamin Stich
Summary: Potato is the most important non-grain food crop, and tandem duplication plays a significant role in genome evolution. This study used multiple potato genotypes to investigate the abundance and distribution of tandemly duplicated genes, the bias in functional specificities, the relationship among coding sequence, promoter and expression divergences, and the role of tandem duplication in generating lineage-specific gene families. The results showed that tandemly duplicated genes are dispersed throughout the genome and exhibit different functional enrichments. There is a significant correlation among expression, promoter, and protein divergences in tandemly duplicated genes. The lineage-specific expansion of gene families by tandem duplication, coupled with functional bias, has contributed to potato's genotypic diversity and adaptation to environmental stimuli.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Nian Wang, Laura J. Kelly, Hugh A. McAllister, Jasmin Zohren, Richard J. A. Buggs
Summary: This study utilized RAD sequences to generate genome-wide sequence reads for 27 diploid and 36 polyploid Betula species, and reconstructed the evolutionary relationships among these species using supermatrix and species tree methods. The research identified the complex reticulate origins of the majority of polyploid taxa in the genus Betula, leading to the proposal of splitting Betula into two subgenera based on differences in seed-wing morphology.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2021)
Article
Plant Sciences
Jinping Cheng, Guiqian Zhang, Linhao Xu, Chang Liu, Hua Jiang
Summary: Polyploidization in Arabidopsis affects the trimethylation of histone H3 at lysine 27 in FLC, leading to variations in flowering time. Ecotype-dependent responses to tetraploidization result in significant changes in gene expression and epigenetic marks. These variations play a role in autopolyploid speciation in flowering plants.
JOURNAL OF EXPERIMENTAL BOTANY
(2022)
Article
Biochemistry & Molecular Biology
Gabriel Rodrigues Alves Margarido, Fernando Henrique Correr, Agnelo Furtado, Frederik C. Botha, Robert James Henry
Summary: This study examined the frequency and patterns of allele-specific expression (ASE) in the highly polyploid sugarcane genome. The analysis revealed that most genes were expressed in proportion to the frequency of the allele in the genome, with a lower level of ASE reflecting the recent origin of polyploid hybrid sugarcane. ASE was found to be more common in defense-response genes and processes related to cell wall biosynthesis.
Article
Cell Biology
Garrison Buss, Miranda B. Stratton, Ljiljana Milenkovic, Tim Stearns
Summary: This study examines the centriole state and properties in trophoblast giant cells (TGCs) of the placenta. The results reveal that centrioles in TGC endocycles can disengage and convert to centrosomes, increasing the number of centrosomes.
MOLECULAR BIOLOGY OF THE CELL
(2022)
Article
Biochemistry & Molecular Biology
Lei Yang, Gavin J. P. Naylor, Richard L. Mayden
Summary: Despite the rarity of polyploidy in animals, the subfamily Cyprininae fishes present a complex and interesting pattern of reticulate evolution. Thirteen independent polyploidization events are hypothesized to have occurred during the evolution of Cyprininae, leading to a complicated post-polyploidization dynamics. The evolutionary history of Cyprinine can be divided into three stages, with the second stage witnessing all tetraploidization events and the last stage hosting hexaploidization events as well as species-specific polyploidization events.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2022)
Article
Plant Sciences
Mert Dogan, Milan Pouch, Terezie Mandakova, Petra Hlouskova, Xinyi Guo, Pieter Winter, Zuzana Chumova, Adriaan Van Niekerk, Klaus Mummenhoff, Ihsan A. Al-Shehbaz, Ladislav Mucina, Martin A. Lysak
Summary: The unigeneric tribe Heliophileae, which includes more than 100 Heliophila species, is morphologically diverse and endemic to southern Africa. Their evolution involves whole-genome duplication, diploidization, species radiations, and different ecological life histories. Despite the shared phylogenetic relationship between Chamira and Heliophila, they do not share tandem repeat sequences.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Plant Sciences
Grant W. de Jong, Keith L. Adams
Summary: Polyploidy has had a significant impact on the evolution of flowering plants. Allopolyploids, particularly Brassica napus, show extensive changes in gene expression and alternative splicing patterns when infected with the fungal pathogen Sclerotinia sclerotiorum. RNA-sequencing analyses reveal these differences and their role in enhancing the defense response against the pathogen.
Article
Fisheries
Shang Geng, Tianjun Xu, Yuena Sun
Summary: In this study, we identified 27 ChemR genes in miiuy croaker and analyzed their characteristics, including gene structure, evolutionary mechanism, and expression levels upon bacterial infection. The results showed that these genes underwent tandem and segmental duplication events during evolution, and teleost fishes' ChemRs may have a higher evolutionary dynamic compared to vertebrates. Additionally, 21 positively selected codons were detected in vertebrate ChemRs under Model 8, and certain genes were significantly up-regulated upon Vibrio harveyi infection, providing valuable information for further functional analysis.
FISH & SHELLFISH IMMUNOLOGY
(2021)
Review
Plant Sciences
Kentaro K. Shimizu
Summary: The prevalence of polyploidy in wild and crop species has sparked debates over its evolutionary advantages and disadvantages. Recent advancements in bioinformatics and empirical studies have allowed for a better understanding of the functional evolutionary study of polyploid species. Polyploid species can enhance their adaptability through inheriting parental stress responses and mutational robustness, and can even become generalists in nature. Identifying key genes responsible for gradual adaptive evolution will pave the way for synthetic biological approaches to transfer the advantages of polyploidy to other species.
CURRENT OPINION IN PLANT BIOLOGY
(2022)
Article
Physics, Fluids & Plasmas
Kota Ishida, Beata Oborny, Michael T. Gastner
Summary: Competition between alternative states is crucial in both social and biological networks, and neutral competition can be represented by an unbiased random drift process. Real-world processes introduce three limiting factors that affect the direction and rate of spread. The effectiveness of a heterogeneous mean-field theory allows for quantitative predictions of consensus even without a complete reconstruction of network edges from empirical data.
Article
Biology
Joanna L. Rifkin, Solomiya Hnatovska, Meng Yuan, Bianca M. Sacchi, Baharul Choudhury, Yunchen Gong, Pasi Rastas, Spencer C. H. Barrett, Stephen Wright
Summary: There is growing evidence for sex differences in the genomic landscape of recombination, but the causes and consequences of these differences are still poorly understood. This study provides evidence and characterization of sex differences in recombination landscape in a dioecious plant, suggesting that pre-existing differences in recombination may have contributed to sex chromosome formation and divergence.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Plant Sciences
Amandine Cornille, Mathieu Tiret, Adriana Salcedo, Huirun R. Huang, Marion Orsucci, Pascal Milesi, Dmytro Kryvokhyzha, Karl Holm, Xue-Jun Ge, John R. Stinchcombe, Sylvain Glemin, Stephen Wright, Martin Lascoux
Summary: The respective role of demography, plasticity and adaptation in the colonization success of plant species was investigated. It was found that both demography and high phenotypic plasticity contribute to the success of the tetraploid and self-fertilizing species, Capsella bursa-pastoris. The study provides insights into the ecological success of a plant species during range expansion.
Article
Biology
Liscely Tumi, Xue-Jun Ge, Gerson E. Prado, Andrea Cosacov, Victor H. Garcia, Monica Arakaki, Mery L. Suni
Summary: This study evaluated the genetic diversity and structure of Puya raimondii populations in Peru using specific microsatellite markers. The results showed moderate to high genetic diversity and high genetic differentiation among populations. The study suggests the need to establish an additional conservation area in southern Peru for the protection of this species.
REVISTA PERUANA DE BIOLOGIA
(2022)
Article
Biotechnology & Applied Microbiology
Tian-Wen Xiao, Xue-Jun Ge
Summary: This study reports the first case of drastic IR expansion in tribe Cinnamomeae, indicating that plastomes have sufficient parsimony-informative sites for molecular dating. Additionally, dating analyses provide preliminary insights into the divergence time within tribe Cinnamomeae and can facilitate future studies on its historical biogeography.
Article
Biochemistry & Molecular Biology
Nicolay Leme da Cunha, Haoran Xue, Stephen Wright, Spencer C. H. Barrett
Summary: This study compares the genetic diversity of two related water hyacinth species, E. crassipes and E. azurea, and finds that the highly clonal E. crassipes exhibits lower clonal diversity and weaker genetic structure compared to the moderately clonal E. azurea.
Article
Biology
Gang Yao, Yu-Qu Zhang, Craig Barrett, Bine Xue, Sidonie Bellot, William J. Baker, Xue-Jun Ge
Summary: By sequencing plastomes of 182 palm species and combining them with previously published data, researchers have obtained a robust phylogenetic hypothesis for the palm family. This comprehensive dataset enhances our understanding of plastid-based relationships and provides a solid framework for future comparative biological studies.
Article
Biochemistry & Molecular Biology
Feng Song, Ting Li, Hai-Fei Yan, Ying Feng, Lu Jin, Kevin S. S. Burgess, Xue-Jun Ge
Summary: DNA barcoding is a useful tool for species identification and biodiversity monitoring. However, a comprehensive DNA barcode reference library is lacking for the arid region in northwestern China. This study developed and evaluated a large DNA barcode library for native flowering plants in this region.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Dentistry, Oral Surgery & Medicine
Cuicui Fu, Xiaoyun Qin, Wenlong Shao, Jin Zhang, Ting Zhang, Jiaqi Yang, Chong Ding, Yeqing Song, Xuejun Ge, Gang Wu, Floris J. J. Bikker, Nan Jiang
Summary: The therapeutic effects of carbon quantum dots (CQDs) in immunomodulation on non-obese diabetic (NOD) mice, a model for Sjogren's syndrome (SS), were evaluated. CQDs generated from Setaria viridis showed no cytotoxicity and alleviated inflammation in the submandibular glands of NOD mice. CQDs also reduced the levels of anti-SSA and anti-SSB, increased saliva flow rates, decreased CD3(+) and CD4(+) T cells, and increased the percentage of Foxp3(+) cells in NOD mice.
Article
Plant Sciences
Marinoli Rivas-Chamorro, Richard Cadenillas, Xue-Jun Ge, Lu Jin, Betty Millan, Julissa Roncal
Summary: This study examined the variation within the hyperdominant tree species Astrocaryum murumuru in the Amazon rainforest. The results showed that this species is actually composed of three separate lineages, suggesting that the previously recognized 15 morphology-based species may be an overestimate. The findings highlight the importance of using genomic data for species delimitation analysis to understand the intraspecific variation of hyperdominant species in the Amazon rainforest.
Article
Chemistry, Multidisciplinary
Xuejun Ge, Gang Xue, Yan Ding, Ran Li, Kaining Hu, Tengjiao Xu, Ming Sun, Wang Liao, Bin Zhao, Chuangyu Wen, Jie Du
Summary: The nuclear N-6-methyladenosine (m(6)A)) reader YT521-B homology-domain-containing protein 1 (YTHDC1) plays a crucial role in maintaining embryonic stem cell identity. However, its functions in intestinal-resident macrophages and inflammatory bowel disease (IBD) are not well understood. This study shows that depletion or insufficiency of YTHDC1 in macrophages accelerates IBD development, with YTHDC1 reduction attributed to ZFP36-induced mRNA degradation. Mechanistically, YTHDC1 regulates RHOH to suppress inflammatory responses and fine-tunes NME1 to enhance colonic epithelial barrier integrity. Overall, this study identifies YTHDC1 as an important factor in resolving inflammatory responses and restoring colonic epithelial barrier in IBD.
Article
Clinical Neurology
Zhen-Ni Zhao, Zi-Qian Zhang, Qian-Qian Wang, Bao-Ling Zhao, He Wang, Xue-Jun Ge, Fei-Yan Yu
Summary: This study used genetic tools and found no causal relationship between periodontitis and migraines, or migraines and periodontitis.
NEUROLOGY AND THERAPY
(2023)
Article
Plant Sciences
Tong-Jian Liu, Shu-Yan Zhang, Lei Wei, Wei Lin, Hai-Fei Yan, Gang Hao, Xue-Jun Ge
Summary: This study analyzed 50 complete plastomes of 46 Lysimachia species to identify their structure features and hypervariable loci. Thirteen highly variable regions were identified and certain plastid markers were found to be under positive selection. The genomic data provided new insights into the interspecific relationships of Lysimachia, establishing a basis for further exploration of its taxonomy, phylogeny, and evolutionary history.
Article
Evolutionary Biology
George Sandler, Aneil F. Agrawal, Stephen Wright
Summary: This study examines the genetic diversity of the facultatively sexual liverwort Marchantia polymorpha and finds no evidence of strictly clonal descent or isolation by distance. Instead, evidence of recent recombination and gene flow between geographically distant isolates suggests a modest frequency of sexual reproduction. However, the genome of M. polymorpha has low levels of nucleotide diversity and signs of inefficient selection, indicating possible linked selection and a small effective population size due to asexual propagation. Overall, the genome reveals a complex history of both sexual and asexual reproduction in M. polymorpha.
GENOME BIOLOGY AND EVOLUTION
(2023)
Article
Biology
Zheng-Feng Wang, Mathieu Rouard, Gaetan Droc, Pat (J S) Heslop-Harrison, Xue-Jun Ge
Summary: This study generated a high-quality chromosome-scale genome assembly of M. beccarii and revealed its genome features and evolution, providing an important genetic resource for studying the genetics of Musaceae plants.
Article
Biology
Ziwei Wang, Mathieu Rouard, Manosh Kumar Biswas, Gaetan Droc, Dongli Cui, Nicolas Roux, Franc-Christophe Baurens, Xue-Jun Ge, Trude Schwarzacher, Pat J. S. Heslop-Harrison, Qing Liu
Summary: We have successfully assembled a high-quality genome of Ensete glaucum and characterized the chromosomal rearrangements between E. glaucum and Musa species. This genome assembly provides a valuable resource for crop breeding and understanding environmental responses.