Article
Biology
Nissanka P. De Silva, Christopher Lee, Paul Battlay, A. Fournier-Level, Joslin L. Moore, Kathryn A. Hodgins
Summary: This study presents the genome assembly and annotation of Bothriochloa decipiens, an Australian grass species with a complex history of hybridization and polyploidy. Comparative analysis reveals a recent whole-genome duplication event and differences in repeat activity and gene retention between subgenomes. Bothriochloa decipiens has ecological importance and potential for climate change-resilient restoration of Australian grasslands. The reference genome provides a valuable resource for future population genomic research on Australian grasses.
Article
Biochemistry & Molecular Biology
Hong Chen, Jamie E. Blum, Anna Thalacker-Mercer, Zhenglong Gu
Summary: The WGD event affected the sensitivity of PYK activity to FBP. Mutations in the FBP binding domain of PYK induce metabolic shifts that favor respiration and suppress fermentation.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
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
Zeng-Qiang Xia, Zuo-Ying Wei, Hui Shen, Jiang-Ping Shu, Ting Wang, Yu-Feng Gu, Amit Jaisi, Yue-Hong Yan
Summary: By analyzing the transcriptomes of 13 species of lycophytes, researchers identified multiple whole-genome duplication events in the lycophyte family Lycopodiaceae and revealed the evolutionary history of this family. They also found genetic discordance in the genus Phlegmariurus, indicating its complex evolutionary history.
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
Biochemistry & Molecular Biology
Matt Huff, Josiah Seaman, Wu Di, Tetyana Zhebentyayeva, Laura J. Kelly, Nurul Faridi, Charles D. Nelson, Endymion Cooper, Teodora Best, Kim Steiner, Jennifer Koch, Jeanne Romero Severson, John E. Carlson, Richard Buggs, Margaret Staton
Summary: Green ash, the most widely distributed ash tree in North America, has been threatened by the non-native invasive emerald ash borer. Some native green ash trees display partial resistance to the insect, indicating potential for breeding more resistant populations. The chromosome-level assembly and genetic variation studies provide valuable resources for research on ash breeding, ecology, and evolution.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Endocrinology & Metabolism
Daniel Ocampo Daza, Christina A. Bergqvist, Dan Larhammar
Summary: This study provides a parsimonious explanation for the origin of the OTR/VTR gene family, based on phylogenetic and chromosomal conserved synteny analyses. The findings suggest a chromosome quadruplication event associated with whole-genome duplications early in vertebrate evolution, prior to the radiation of jawed vertebrates. The evolution of the OTR/VTR gene family can be explained by two whole-genome duplications followed by differential gene losses of VTR2 genes in different lineages.
FRONTIERS IN ENDOCRINOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Dongna Ma, Shanshan Dong, Shengcheng Zhang, Xiuqing Wei, Qingjun Xie, Qiansu Ding, Rui Xia, Xingtan Zhang
Summary: By incorporating PacBio long HiFi reads and Hi-C technology, a chromosome-level genome assembly of passion fruit was achieved. The highly repetitive genome contains 39,309 protein-coding genes, with 93.48% functionally annotated. Genome evolution analysis revealed multiple duplication events, and rapidly expanded gene families were associated with the formation of featured flavors.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Biochemistry & Molecular Biology
Magdalena Bohutinska, Mark Alston, Patrick Monnahan, Terezie Mandakova, Sian Bray, Pirita Paajanen, Filip Kolar, Levi Yant
Summary: Two plant species exhibit different genomic responses to whole genome duplication, suggesting the presence of multiple evolutionary trajectories when adapting to the challenges of whole genome duplication.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Plant Sciences
Matthew Haas, Thomas Kono, Marissa Macchietto, Reneth Millas, Lillian McGilp, Mingqin Shao, Jacques Duquette, Candice N. Hirsch, Jennifer Kimball, Yinjie Qiu
Summary: The study conducted genomic research on Zizania palustris L. (NWR) revealed characteristics such as genome size, repetitive rate, and number of protein-coding genes. Comparative analysis indicated the conservation between NWR and O. sativa, and predicted seed-shattering genes. Estimates of divergence times showed the evolutionary history of the Zizania genus and the NWR-Z. latifolia speciation.
Article
Multidisciplinary Sciences
Donald Davesne, Matt Friedman, Armin D. Schmitt, Vincent Fernandez, Giorgio Carnevale, Per E. Ahlberg, Sophie Sanchez, Roger B. J. Benson
Summary: Teleost fishes, which make up half of all vertebrate species, underwent a whole-genome duplication early in their evolutionary history, likely contributing to their exceptional radiation. By analyzing bone cell volumes, researchers have concluded that this duplication occurred in the stem lineage of teleosts, with all known extinct stem-group teleosts possessing duplicated genomes. This early event allowed for significant postduplication reorganization before the emergence of the teleost crown group, indicating a potentially indirect link between WGD and evolutionary success.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Kevin J. Peterson, Alan Beavan, Peter J. Chabot, Mark A. McPeek, Davide Pisani, Bastian Fromm, Oleg Simakov
Summary: WGDs do not result in the creation of miRNA novelty, nor do WGDs correlate to increases in complexity. Instead, it is the number of miRNA seed sequences in the genome itself that not only better correlate to instances in complexification, but also mechanistically explain why complexity increases when new miRNA families are established.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Plant Sciences
Lin Zhang, Diego F. Morales-Briones, Yujie Li, Guojin Zhang, Taikui Zhang, Chien-Hsun Huang, Peng Guo, Kaiming Zhang, Yihan Wang, Hongwei Wang, Fu-De Shang, Hong Ma
Summary: In this study, the researchers used nuclear genes to analyze 62 transcriptomes/genomes, reconstruct a well-supported phylogeny, and study the evolution of fruit and leaf morphology and the possible effect of whole genome duplication. The results showed that a whole genome duplication event occurred in the most recent common ancestor of Maleae, and innovations in fruit and leaf morphologies were observed during evolution. These findings provide important insights into the phylogeny, rapid diversification, and morphological and molecular evolution of Maleae.
Article
Biochemistry & Molecular Biology
Brett Trost, Bhooma Thiruvahindrapuram, Ada J. S. Chan, Worrawat Engchuan, Edward J. Higginbotham, Jennifer L. Howe, Livia O. Loureiro, Miriam S. Reuter, Delnaz Roshandel, Joe Whitney, Mehdi Zarrei, Matthew Bookman, Cherith Somerville, Rulan Shaath, Mona Abdi, Elbay Aliyev, Rohan Patel, Thomas Nalpathamkalam, Giovanna Pellecchia, Omar Hamdan, Gaganjot Kaur, Zhuozhi Wang, Jeffrey R. MacDonald, John Wei, Wilson W. L. Sung, Sylvia Lamoureux, Ny Hoang, Thanuja Selvanayagam, Nicole Deflaux, Melissa Geng, Siavash Ghaffari, John Bates, Edwin J. Young, Qiliang Ding, Carole Shum, Lia D'Abate, Clarrisa A. Bradley, Annabel Rutherford, Vernie Aguda, Beverly Apresto, Nan Chen, Sachin Desai, Xiaoyan Du, Matthew L. Y. Fong, Sanjeev Pullenayegum, Kozue Samler, Ting Wang, Karen Ho, Tara Paton, Sergio L. Pereira, Jo-Anne Herbrick, Richard F. Wintle, Jonathan Fuerth, Juti Noppornpitak, Heather Ward, Patrick Magee, Ayman Al Baz, Usanthan Kajendirarajah, Sharvari Kapadia, Jim Vlasblom, Monica Valluri, Joseph Green, Vicki Seifer, Morgan Quirbach, Olivia Rennie, Elizabeth Kelley, Nina Masjedi, Catherine Lord, Michael J. Szego, Ma'n H. Zawati, Michael Lang, Lisa J. Strug, Christian R. Marshall, Gregory Costain, Kristina Calli, Alana Iaboni, Afiqah Yusuf, Patricia Ambrozewicz, Louise Gallagher, David G. Amaral, Jessica Brian, Mayada Elsabbagh, Stelios Georgiades, Daniel S. Messinger, Sally Ozonoff, Jonathan Sebat, Calvin Sjaarda, Isabel M. Smith, Peter Szatmari, Lonnie Zwaigenbaum, Azadeh Kushki, Thomas W. Frazier, Jacob A. S. Vorstman, Khalid A. Fakhro, Bridget A. Fernandez, M. E. Suzanne Lewis, Rosanna Weksberg, Marc Fiume, Ryan K. C. Yuen, Evdokia Anagnostou, Neal Sondheimer, David Glazer, Dean M. Hartley, Stephen W. Scherer
Summary: This study identifies rare variants associated with autism spectrum disorder (ASD) through whole-genome sequencing (WGS) and provides a research guide to explore genotype-phenotype correlations in families carrying these rare variants.
Article
Biotechnology & Applied Microbiology
Madeleine E. Aase-Remedios, Clara Coll-Llado, David E. K. Ferrier
Summary: Research on muscle responses to feeding-fasting-refeeding experiments reveals the genetic mechanisms involved in muscle degradation and maintenance, providing insight into the regulatory pathways of muscle nutrient response.
Article
Ecology
Cynthia Webster, Laura Figueroa-Corona, Ivan David Mendez-Gonzalez, Lluvia Alvarez-Soto, David B. Neale, Juan Pablo Jaramillo-Correa, Jill L. Wegrzyn, Alejandra Vazquez-Lobo
Summary: This study compared leaf heteroblastic development in Juniperus flaccida and Pinus cembroides and found differences in gene regulation and pathways between the two species. Juvenile leaves of P. cembroides showed a focus on cell division and development, while adult leaves of J. flaccida exhibited differential expression and gene interaction patterns related to photosynthesis and chloroplast biogenesis.
ECOLOGY AND EVOLUTION
(2022)
Article
Plant Sciences
Ajith Ashokan, Jana Leong-Skornickova, Piyakaset Suksathan, Mark Newman, W. John Kress, Vinita Gowda
Summary: This study aims to understand the evolution of nocturnal and diurnal flowers in the genus Hedychium, as well as their association with lineage diversification. The results show that floral color and size are not associated with specific pollinators. White or pale flowers are more common in early branching clades, while bright-colored flowers are more widely represented in the most-derived clade. Several informative evolutionary patterns were identified. The study challenges the role of moth-specialization and bird-specialization as central factors in the diversification of Hedychium.
AMERICAN JOURNAL OF BOTANY
(2022)
Editorial Material
Biodiversity Conservation
W. John Kress, Morgan R. Gostel
Article
Plant Sciences
Zhi-Yuan Du, Qiu-Yun (Jenny) Xiang, Jin Cheng, Wenbin Zhou, Qing-Feng Wang, Douglas E. E. Soltis, Pamela S. S. Soltis
Summary: This study integrates three sets of genome-wide data to investigate the evolutionary history and classification of Cornaceae (containing Cornus s.l.). The results reveal the origin and rapid diversification of Cornus into four major clades in the Northern Hemisphere during the late Cretaceous, with an eastern Asian ancestor. The study also suggests that dispersal into Africa likely occurred during the Paleogene, while dispersal into South America likely occurred during the Neogene. Thirteen well-supported clades were named following the rules of the PhyloCode.
AMERICAN JOURNAL OF BOTANY
(2023)
Article
Multidisciplinary Sciences
Ricardo De La Pena, Hannah Hodgson, Jack Chun -Ting Liu, Michael J. Stephenson, Azahara C. Martin, Charlotte Owen, Alex Harkess, Jim Leebens-Mack, Luis E. Jimenez, Anne Osbourn, Elizabeth S. Sattely
Summary: Triterpenes with complex scaffold modifications are common in plants, and limonoids are a well-known family responsible for the bitter taste in citrus and the active constituents of neem oil. However, the complete biosynthetic route of limonoids has not been described. This study discovered 22 enzymes involved in the biosynthesis of important limonoids and provided a template for the discovery and reconstitution of triterpene biosynthetic pathways in plants.
Article
Plant Sciences
Fabian Bratzel, Juraj Paule, Jim Leebens-Mack, Elton M. C. Leme, Rafaela C. C. Forzza, Marcus A. A. Koch, Sascha Heller, Georg Zizka
Summary: A phylogenomic analysis of the Bromelioideae subfamily of the Bromeliaceae family was conducted to understand species relationships and provide a basis for taxonomic treatment and further evolutionary and biogeographical studies. The study used a target-enrichment approach and analyzed nuclear, plastome, and mitogenome data. The resulting phylogenetic framework identified 26 well-supported clades and revealed interesting patterns, such as polyphyletic genera. This research is important for future taxonomic revisions and better understanding the evolutionary processes in this subfamily.
Article
Genetics & Heredity
Vera Marjorie Elauria Velasco, Alyssa Ferreira, Sumaira Zaman, Devin Noordermeer, Ingo Ensminger, Jill L. Wegrzyn
Summary: In this study, a highly accurate and complete reference transcriptome and genome annotation of Douglas-fir were generated. Deep sequencing of the transcriptome using long-read and short-read platforms was performed on Douglas-fir needles grown under nonstress control conditions or a combination of heat and drought stress conditions. Two computational approaches were used for transcriptome assembly, and the results showed that the de novo assembly approach identified more high-quality transcripts, complete genes, and functionally annotated genes compared to the genome-guided assembly approach. Additionally, a refined genome annotation was generated using an improved informatics approach.
G3-GENES GENOMES GENETICS
(2023)
Editorial Material
Plant Sciences
Douglas E. Soltis, Vassiliki Betty Smocovitis, Kasey K. Pham, Maria Beatriz S. Cortez, Annika L. Smith, Pamela S. Soltis
AMERICAN JOURNAL OF BOTANY
(2023)
Article
Plant Sciences
Ingrid E. Jordon-Thaden, Jonathan P. Spoelhof, Lyderson Facio Viccini, Joseph Combs, Francisco Gomez Jr, Imari Walker, Douglas E. Soltis, Pamela S. Soltis
Summary: A study on allopolyploids and their parental species in Tragopogon genus shows that allopolyploidy results in some phenotypic changes, such as larger physical traits and increased photosynthetic capacity. However, there is no significant reproductive advantage for polyploid species. Comparison between natural and synthetic allopolyploids revealed minimal differences in traits.
AMERICAN JOURNAL OF BOTANY
(2023)
Article
Plant Sciences
Douglas E. Soltis, Evgeny V. Mavrodiev, Vladimir Brukhin, Eric H. Roalson, Dirk C. Albach, Grant T. Godden, Yuri E. Alexeev, Matthew A. Gitzendanner, Craig C. Freeman, Victor N. Suarez-Santiago, Pamela S. Soltis
Summary: Tragopogon (Asteraceae) is a genus that includes two recently formed allopolyploids, T. mirus and T. miscellus, in western North America. The introduction of diploid parents, T. dubius and T. porrifolius from Europe, played a role in the formation of these allopolyploids. In this study, we focused on the introduction of the second diploid parent, T. pratensis, into North America. Our findings show that T. pratensis as currently defined is polyphyletic, with at least four major ITS types in its native range. Two of these ITS types have been introduced from Europe into North America and are widespread in Canada and the U.S.A. The formation of T. miscellus in the western North America involved only one of these ITS types. Our research suggests that not all genotypes of T. pratensis may be capable of participating in the formation of allopolyploids. Additionally, we found that there are genetically distinct entities within T. pratensis that may be considered separate species. Further research involving phylogenetic analyses, taxonomy, morphology, and cytology are needed to fully understand the complexities of T. pratensis.
Article
Plant Sciences
Myoungbo Kang, Andre Chanderbali, Seungyeon Lee, Douglas E. Soltis, Pamela S. Soltis, Sangtae Kim
Summary: This article presents an effective HMW DNA extraction method that combines nuclei extraction and CTAB extraction, resulting in longer and purer DNA fragments compared to a commercial kit. This protocol can be widely used in plant genomic research.
APPLICATIONS IN PLANT SCIENCES
(2023)
Editorial Material
Plant Sciences
Jonathan P. P. Spoelhof, Pamela S. S. Soltis, Douglas E. E. Soltis
Article
Multidisciplinary Sciences
Jun Zhang, Xiao-Qian Li, Huan-Wen Peng, Lisi Hai, Andrey S. S. Erst, Florian Jabbour, Rosa del C. Ortiz, Fu-Cai Xia, Pamela S. S. Soltis, Douglas E. E. Soltis, Wei Wang
Summary: The Arctic tundra is a relatively young and new biome that is highly susceptible to global warming. This study investigates the origin and evolutionary dynamics of the Arctic flora, finding that both long-term dispersal and in situ speciation may have contributed to its assembly, in association with landscape, climate, and sea-level changes.
NATURE COMMUNICATIONS
(2023)
Letter
Plant Sciences
Paul J. Kersey, Alexandre Antonelli
Article
Cell Biology
Douglas E. Soltis, Jennifer A. Tate, Pamela S. Soltis, V. Vaughan Symonds
Summary: Allopolyploidy is an important force in evolution. The compatibility hypothesis suggests that only a subset of genotypes can form viable hybrids, leading to allopolyploid formation. Evidence from natural allopolyploids in Tragopogon suggests that the compatibility model plays a significant role. The implications of this model for other allopolyploids are also discussed.