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
Multidisciplinary Sciences
Jiashun Miao, Qi Feng, Yan Li, Qiang Zhao, Congcong Zhou, Hengyun Lu, Danlin Fan, Juan Yan, Yiqi Lu, Qilin Tian, Wenjun Li, Qijun Weng, Lei Zhang, Yan Zhao, Tao Huang, Laigeng Li, Xuehui Huang, Tao Sang, Bin Han
Summary: The genome assembly of Miscanthus lutarioriparius reveals its allotetraploid origin and an expanded number of genes in families related to stress resistance. This underscores the potential of the genus Miscanthus for bio-energy production.
NATURE COMMUNICATIONS
(2021)
Article
Genetics & Heredity
Luis J. Chueca, Tilman Schell, Markus Pfenninger
Summary: This study presents the draft genome assembly of the land snail Candidula unifasciata, providing a reference for further evolutionary, genomic, and population genetic studies. The genome size is approximately 1.29 Gb, with 22,464 protein-coding genes identified, of which 62.27% were functionally annotated.
G3-GENES GENOMES GENETICS
(2021)
Article
Multidisciplinary Sciences
Mengdi Zhang, Xinyue Cheng, Runmao Lin, Bingyan Xie, Ralf Nauen, Silvia I. Rondon, Jorge A. Zavala, Subba Reddy Palli, Suhua Li, Xingyao Xiong, Wenwu Zhou, Yulin Gao
Summary: This study reports the genome assembly of the potato tuberworm at the chromosomal level, providing a significant resource for understanding the genetic basis of this insect and promoting its integrative management in the future.
Article
Cell Biology
Hussain Bahbahani, Sanaa Al-Zoubi, Fatima Ali, Arwa Afana, Mohammed Dashti, Abdulaziz Al-Ateeqi, David Wragg, Suzanne Al-Bustan, Faisal Almathen
Summary: This study investigates the natural selection signatures in the mitochondrial DNA of different dromedary camel populations. The findings reveal adaptive divergence between Old World and New World camels, with evidence of purifying selection among Old World camel species. A total of 89 codons, known to impact the physiochemical properties of proteins, were found to be under positive selection in the Camelidae family.
Article
Multidisciplinary Sciences
Gaorui Gong, Wensi Ke, Qian Liao, Yang Xiong, Jingqi Hu, Jie Mei
Summary: This study presents a high-quality, chromosome-level genome assembly of the darkbarbel catfish using PacBio long-read sequencing and Hi-C technologies, which provides a critical resource for future hybrid catfish breeding, comparative genomics, and evolutionary studies.
Article
Ecology
Qingxia Ma, Fengping Li, Jiawen Zheng, Chunsheng Liu, Aimin Wang, Yi Yang, Zhifeng Gu
Summary: This study sequenced the complete mitochondrial genomes of 10 cowrie species, revealing two monophyletic clades and confirming the classification at the genus level. The results suggest that mitochondrial DNA can be used as a tool to improve the phylogenetic resolution of cowries and provide important information for species delimitation.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2023)
Article
Biology
Haoran Luo, Xinrui Jiang, Boping Li, Jiahong Wu, Jiexin Shen, Zaoxu Xu, Xiaoping Zhou, Minghao Hou, Zhen Huang, Xiaobin Ou, Luohao Xu
Summary: This study conducted multi-omic analyses on a well-preserved great bustard individual, resulting in a near-complete genome assembly and revealing the low genetic diversity of the species. The study also identified expanded gene families related to cardiac contraction and metabolism in great bustards, as well as a rare case of extremely young evolutionary stratum on the sex chromosome. Overall, this research provides insights into the conservation genomics, adaptation, and chromosome evolution of the great bustard.
COMMUNICATIONS BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Ka Ming Nip, Saber Hafezqorani, Kristina K. Gagalova, Readman Chiu, Chen Yang, Rene L. Warren, Inanc Birol
Summary: Long-read sequencing technologies have greatly improved, but there is little focus on reference-free transcriptome assembly methods. In this study, the authors introduce RNA-Bloom2, a reference-free method for long-read transcriptome sequencing data. They demonstrate its competitive assembly quality compared to reference-based methods, as well as its lower memory and runtime requirements. They also showcase its application in assembling a transcriptome sample of Sitka spruce, setting the groundwork for large-scale comparative transcriptomics without readily available genome assemblies.
NATURE COMMUNICATIONS
(2023)
Article
Genetics & Heredity
Hequan Sun, Wen-Biao Jiao, Jose A. Campoy, Kristin Krause, Manish Goel, Kat Folz-Donahue, Christian Kukat, Bruno Huettel, Korbinian Schneeberger
Summary: This study reports the reconstruction of the autotetraploid genome of potato based on high-quality long reads, single-cell sequencing, and Hi-C data, revealing the characteristics of genome similarity and structural rearrangements caused by recent inbreeding. Only a portion of the genes were present in all four haplotypes, and some genes may be regulated through allele-specific DNA methylation.
Article
Ecology
Elaina D. Graham, Benjamin J. Tully
Summary: The marine Dadabacteria have the potential to degrade microbial dissolved organic matter, with the presence of distinct ecological niches in global metagenomic data.
Editorial Material
Biochemistry & Molecular Biology
Jenn Coughlan
Summary: As hybridization is found to be common in nature, understanding how natural selection affects hybrids is now more important for speciation. A study in PLOS Biology uses threespine stickleback to identify a genomic marker of ecological incompatibilities.
Article
Biotechnology & Applied Microbiology
Fan Jiang, Yaoxin Jiang, Wenxuan Wang, Changyi Xiao, Ruiyi Lin, Tanghui Xie, Wing-Kin Sung, Shijun Li, Ivan Jakovlic, Jianhai Chen, Xiaoyong Du
Summary: This study conducted chromosome-level genome assembly of the Muscovy duck and comparative genomic analysis, revealing unique gene families in Muscovy duck compared to other bird species, with adaptive evolution signals in immune defence pathways. The results provide valuable resources for future molecular ecology studies and the evolutionary arms race between hosts and influenza viruses.
Article
Biochemistry & Molecular Biology
Anwesha Saha, Sudeshna Chakraborty, G. Ravikanth, K. Praveen Karanth, N. A. Aravind
Summary: This study examines the species relationships and monophyly of Cremnoconchus and uncovers potential cryptic diversity. Cremnoconchus separated from its marine ancestors around 90.40 million years ago, possibly due to factors such as the break-up of Gondwana or fluctuating sea levels. The distribution of species in this group shows distinct geographic patterns, which may have been influenced by the patchiness of suitable habitats and low mobility.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2022)
Article
Multidisciplinary Sciences
Jianfeng Jin, Yuxin Zhao, Guoqiang Zhang, Zhixiang Pan, Feng Zhang
Summary: This study presents the first chromosome-level genome of Entomobrya proxima, the largest superfamily of Collembola, using PacBio long reads, Illumina short reads, and Hi-C data. The genome has a size of 362.37 Mb, with a scaffold N50 size of 57.67 Mb, and 97.12% (351.95 Mb) of the assembly is located on six chromosomes. The analysis revealed important expansions in gene families associated with detoxification and metabolism in E. proxima, as well as strong chromosomal synteny between E. proxima and Sinella curviseta. This research provides valuable genomic information for understanding the evolution and ecology of Collembola.
Article
Evolutionary Biology
Kerstin Johannesson, Erica H. Leder, Carl Andre, Sam Dupont, Susanne P. Eriksson, Karin Harding, Jonathan N. Havenhand, Marlene Jahnke, Per R. Jonsson, Charlotta Kvarnemo, Henrik Pavia, Marina Rafajlovic, Eva Marie Rodstrom, Michael Thorndyke, Anders Blomberg
Summary: The Centre for Marine Evolutionary Biology (CeMEB) at the University of Gothenburg, Sweden, was founded in 2008 with a 10-year research grant of 8.7 million euros. Over the past decade, CeMEB has made significant contributions to scientific publications, PhD theses, and organized various meetings and courses. This article reviews CeMEB's achievements, compares the initial goals with the actual achievements, and discusses future prospects for marine evolutionary biology.
EVOLUTIONARY APPLICATIONS
(2023)
Article
Evolutionary Biology
Aurelien De Jode, Alan Le Moan, Kerstin Johannesson, Rui Faria, Sean Stankowski, Anja Marie Westram, Roger K. Butlin, Marina Rafajlovic, Christelle Fraisse
Summary: Understanding population divergence and speciation is crucial for evolutionary biology. High species diversity in the sea is considered a paradox due to the lack of geographical barriers. However, combining genome-wide data with demographic modelling has provided new insights. Studies show that barriers to gene flow exist in the sea but divergence can also occur without strict isolation.
EVOLUTIONARY APPLICATIONS
(2023)
Article
Evolutionary Biology
Josefin Sefbom, Anke Kremp, Per Juel Hansen, Kerstin Johannesson, Anna Godhe, Karin Rengefors
Summary: This study examined whether multiple strains of the diatom Skeletonema marinoi from two genetically distinct Baltic Sea populations showed evidence of local adaptation to their respective environments. The results suggest that both estuarine and marine strains exhibit local adaptation strategies, with estuarine strains growing faster in high-salinity environments and marine strains outperforming estuarine strains in the marine environment.
EVOLUTIONARY APPLICATIONS
(2023)
Article
Evolutionary Biology
Marina A. Z. Panova, Marina A. Varfolomeeva, Elizaveta R. Gafarova, Arina L. Maltseva, Natalia A. Mikhailova, Andrei Granovitch
Summary: Microbes play a prominent role in the evolution of their hosts, facilitating ecological divergence. This study found differences in gut microbiome composition and biofilm composition between different Littorina snail ecotypes and their habitats, providing a promising marine system to study co-evolution of microbes and hosts.
EVOLUTIONARY APPLICATIONS
(2023)
Article
Evolutionary Biology
Alan Le Moan, Marina Panova, Aurelien De Jode, Olga Ortega-Martinez, Marten Duvetorp, Rui Faria, Roger Butlin, Kerstin Johannesson
Summary: Understanding the genetic targets of natural selection is a challenging goal in population genetics. Using the marine snail as an example, this study explores the genomic architecture and adaptive significance of a candidate gene.
EVOLUTIONARY APPLICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Ricardo T. Pereyra, Marina Rafajlovic, Pierre De Wit, Matthew Pinder, Alexandra Kinnby, Mats Topel, Kerstin Johannesson
Summary: This study investigates the origin and evolution of large clones formed in a macroalgal species during range expansion. It found that large dominant clonal lineages repeatedly evolved from different sexual populations at range margins, while low but persistent clonality was observed in core populations. The study concludes that clones favored by uniparental reproductive assurance can play an important role in range expansion, resulting in a complex spatiotemporal mosaic of clonal and sexual lineages.
Article
Plant Sciences
Ahmed S. S. Alenazi, Matheus E. E. Bianconi, Ella Middlemiss, Vanja Milenkovic, Emma V. V. Curran, Graciela Sotelo, Marjorie R. R. Lundgren, Florence Nyirenda, Lara Pereira, Pascal-Antoine Christin, Luke T. T. Dunning, Colin P. P. Osborne
Summary: C-4 photosynthesis is a complex trait that increases productivity in warm conditions by concentrating CO2 around Rubisco. The strengthening of the C-4 pathway within species remains largely unexplored, but anatomical variation has been found to be linked to C-4 activity in Alloteropsis semialata populations.
PLANT CELL AND ENVIRONMENT
(2023)
Article
Genetics & Heredity
Felix Mittermayer, Cecilia Helmerson, Marten Duvetorp, Kerstin Johannesson, Marina Panova
Summary: This study reveals that the AAT gene in intertidal snails from Central and Southern Europe have different protein sequences, indicating the important role of AAT in adaptation to desiccation. Furthermore, the study shows that the genetic polymorphism of AAT is an ancient trait, and the AAT120 allele in Southern snails is derived from AAT100. The study also provides insights into the location and structure of the AAT gene in the L. saxatilis genome, as well as the presence of additional non-functional gene copies.
Article
Biochemistry & Molecular Biology
Bjorn Andersson, Olof Berglund, Helena L. Filipsson, Olga Kourtchenko, Anna Godhe, Kerstin Johannesson, Mats Topel, Matthew I. M. Pinder, Lara Hoepfner, Karin Rengefors
Summary: Phytoplankton have the ability to rapidly evolve and adapt to selection pressures. In a study of a diatom population in the Baltic Sea, it was found that copper tolerance did not differ between a mining-exposed population and a non-exposed population, but there was greater variation within the mining-exposed population. Through an artificial evolution experiment, it was observed that the mining-exposed population rapidly evolved copper tolerance due to the presence of hyper-tolerant strains.
Article
Biochemistry & Molecular Biology
James Reeve, Roger K. Butlin, Eva L. Koch, Sean Stankowski, Rui Faria
Summary: Inversions play a key role in adaptation and speciation, and the intertidal snail Littorina saxatilis exhibits strong associations between inversions and phenotypic differences. Inversion polymorphisms are widespread across the species range.
Article
Biochemistry & Molecular Biology
Joao Carvalho, Hernan E. Morales, Rui Faria, Roger K. Butlin, Vitor C. Sousa
Summary: In this study, a new Approximate Bayesian Computation (ABC) method was developed to infer the demographic history using pool-seq data. The results showed that pool-seq data can distinguish between general scenarios of ecotype formation and infer relevant demographic parameters.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Ecology
Joao Carvalho, Rui Faria, Roger K. K. Butlin, Vitor C. C. Sousa
Summary: Pool-seq is a valuable tool in population genomics and molecular ecology, but it has challenges in accurately estimating allele frequencies. Researchers have developed poolHelper, an R package that simulates SNP data, taking into account unequal individual contributions and sequencing errors. This tool allows users to optimize sampling schemes for Pool-seq studies.
METHODS IN ECOLOGY AND EVOLUTION
(2023)
Review
Ecology
Emma L. Berdan, Nicholas H. Barton, Roger Butlin, Brian Charlesworth, Rui Faria, Ines Fragata, Kimberly J. Gilbert, Paul Jay, Martin Kapun, Katie E. Lotterhos, Claire Merot, Esra Durmaz Mitchell, Marta Pascual, Catherine L. Peichel, Marina Rafajlovic, Anja M. Westram, Stephen W. Schaeffer, Kerstin Johannesson, Thomas Flatt
Summary: Inversions are structural mutations that have a significant impact on adaptation and speciation. However, their study has been challenging due to reduced recombination and the effects of drift and hitchhiking. This review examines the different mechanisms of selection that affect the evolution of inversions, emphasizing the complexity of analyzing the causes underlying their evolution.
JOURNAL OF EVOLUTIONARY BIOLOGY
(2023)