Article
Agricultural Engineering
Raul E. Martinez-Herrera, O. Miriam Rutiaga-Quinones, Maria E. Aleman-Huerta
Summary: This review explores the incorporation of Agave plants derivatives into the production of polyhydroxybutyrate (PHB), highlighting the potential benefits and challenges associated with this biotechnological approach. The study focuses on enhancing PHB production, improving physical properties by blending with Agave fibers, and analyzing the possible advantages of implementing circular economy strategies in rural communities dedicated to Agave production.
INDUSTRIAL CROPS AND PRODUCTS
(2021)
Article
Biochemistry & Molecular Biology
Abdulqader Jighly
Summary: The optimal sequencing depth for genotyping autopolyploid populations remains controversial, as studies have varied in depth thresholds without clear guidance. While some suggest high depth values, recent reports have shown lower thresholds can achieve similar accuracy, reducing overall genotyping costs. The need for stringent depth thresholds and the use of relaxed ones depend on research goals and the probabilities of sampling different homologues at a given sequencing depth.
Article
Zoology
Bryan N. Macneill, Juan Pablo Ortiz-Brunel, Aaron Rodriguez, Eduardo Ruiz-Sanchez, Jesus Navarro-Moreno, Nathaniel P. Hofford, Michael R. Mckain
Summary: The genus Agave plays a crucial ecological role in American deserts and holds cultural and economic importance in Mexico. This large genus of about 250 species has adapted to desert environments and diversified through interactions with pollinators like hummingbirds and nocturnal moths. A study on Agave subgenus Manfreda reveals the evolution of floral form in response to specialization in pollinators, indicating the presence of hidden diversity in floral phenotypes. The study also highlights the need to consider the variation between herbarium and live specimens when combining data.
INTEGRATIVE AND COMPARATIVE BIOLOGY
(2023)
Article
Biology
Qiuwei Zhang, Kathryn L. Kingsley, James F. White
Summary: This study demonstrates the growth-promoting potential of endophytic bacteria isolated from Agave palmeri on different crops. The researchers found that these endophytic bacteria not only enter other plants' tissues and participate in the rhizophagy cycle but also may be transported through the plant's vascular bundle. These findings provide further insights into the mechanisms behind the way in which endophytes promote growth in plants.
Article
Biochemistry & Molecular Biology
Thomas A. Delomas, Stuart C. Willis, Blaine L. Parker, Donella Miller, Paul Anders, Andrea Schreier, Shawn Narum
Summary: This study presents a strategy for high-throughput genotyping of polyploid organisms, along with a method to infer individual ploidy from sequencing data that is applicable to any ploidy level without prior identification of heterozygous genotypes. By combining these techniques, researchers can infer ploidy and generate ploidy-aware genotypes simultaneously.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Plant Sciences
Anastasia Klimova, Karen Y. Ruiz Mondragon, Francisco Molina Freaner, Erika Aguirre-Planter, Luis E. Eguiarte
Summary: This study examined the genetic structure of Agave angustifolia var. pacifica used for bacanora production in northwestern Mexico, finding shallow genetic structure among wild samples, no differentiation between cultivated and wild populations, and evidence of clonality in cultivated plants.
Article
Biodiversity Conservation
Kristin Saltonstall, Graham D. Bonnett, Karen S. Aitken
Summary: Polyploidy may enhance the invasive ability of plants like Saccharum spontaneum, which is believed to have accidentally escaped from a historical sugarcane germplasm collection. The high genetic diversity due to polyploidy and possible pre-adaptation to local conditions may have facilitated its rapid spread and persistence in Panama. These findings have implications for the biosecurity of germplasm collections.
BIOLOGICAL INVASIONS
(2021)
Article
Plant Sciences
Mauricio Orantes-Bonilla, Manar Makhoul, HueyTyng Lee, Harmeet Singh Chawla, Paul Vollrath, Anna Langstroff, Fritz J. Sedlazeck, Jun Zou, Rod J. Snowdon
Summary: Novel structural genome variants from the synthetic parent cause immediate genome diversification among F1 offspring, leading to unexpected phenotypic variation. Natural genome restructuring can have a more drastic impact on genetic diversity in agricultural ecosystems than precise biotechnological genome modifications.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Mingzhu Sun, Erli Pang, Wei-Ning Bai, Da-Yong Zhang, Kui Lin
Summary: Polyploidy is common and its effects are complex and variable. Computational tools for ploidy estimation are urgently needed to avoid cumbersome experiments. We developed ploidyfrost, a method for estimating ploidy levels without a reference genome, and evaluated its performance using different samples.
MOLECULAR ECOLOGY RESOURCES
(2023)
Review
Biochemistry & Molecular Biology
Domenico Tierno, Gabriele Grassi, Serena Scomersi, Marina Bortul, Daniele Generali, Fabrizio Zanconati, Bruna Scaggiante
Summary: The poor survival of triple-negative breast cancer (TNBC) is attributed to its aggressive behavior, large heterogeneity, and high risk of recurrence. Next-generation sequencing (NGS) has been used to investigate the molecular characteristics of TNBC, revealing recurrent pathogenic alterations in TP53, immunocheckpoint response genes, and PIK3CA and DNA repair pathways. NGS has also identified potential personalized treatments and novel biomarkers such as AURKA, MYC, and JARID2 mutations. Additionally, NGS studies have identified ethnicity-specific alterations in African and African American TNBC, including EZH2 overexpression, BRCA1 alterations, and a BRCA2-delaAAGA mutation. The development of long-read sequencing methods and their combination with optimized short-read techniques hold promise for improving the efficiency of NGS approaches in future clinical use.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biotechnology & Applied Microbiology
Stefan Milosavljevic, Tony Kuo, Samuele Decarli, Lucas Mohn, Jun Sese, Kentaro K. Shimizu, Rie Shimizu-Inatsugi, Mark D. Robinson
Summary: ARPEGGIO is a workflow for analyzing epigenetic data in allopolyploids, utilizing the EAGLE-RC read classification algorithm to address sequence similarity challenges among parental genomes. This workflow offers automation and a complete set of analyses starting from raw WGBS data to outputting a list of genes showing differential methylation, ensuring reproducibility with simple set up and interpretation. ARPEGGIO stands out as the only workflow supporting polyploid data, as shown through its performance evaluation and agreement with published results.
Article
Biodiversity Conservation
Alexander A. Gnutikov, Nikolai N. Nosov, Igor G. Loskutov, Elena V. Blinova, Victoria S. Shneyer, Alexander V. Rodionov
Summary: In this article, the origin of wild polyploid oats was analyzed using NGS to obtain 18S rDNA and ITS1-5.8S rDNA. Comparing the sequences of polyploid oats with their putative diploid ancestors, 15 major ribotypes were identified in polyploid oats. The AB tetraploid oats possibly inherited their A-genome ribotypes from A. atlantica, while their B-genome ribotypes are specific and possibly derived from the A-genome family. The CD-genome set in A. magna, A. murphyi, and A. insularis was found to be AC-genome ribotype instead. The C-genome-related sequences could have come from A. ventricosa. Hexaploid oats showed a different ribotype pattern than tetraploid oats, with the main ribotypes of A. fatua, A. ludoviciana, and A. sterilis likely belonging to the D-genome and shared with A. clauda.
Review
Plant Sciences
Cheng Song, Yan Wang, Muhammad Aamir Manzoor, Di Mao, Peipei Wei, Yunpeng Cao, Fucheng Zhu
Summary: High-throughput sequencing technology and gene editing technologies are of great significance in orchid genomics research, helping to identify trait-related genes, improve genetic transformation, and investigate gene function.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Parichart Ninwichian, Jareeporn Ruangsri, Nirandon Phuwan, Bavornlak Khamnamtong, Sirawut Klinbunga
Summary: The commercially important bivalve species, White scar oyster, in Thailand has been characterized with appropriate genetic markers to enhance production efficiency. Newly developed microsatellites are found to be useful for genetic diversity analysis, facilitating studies in population genetics, stock management, and genetic improvement of the species.
MOLECULAR BIOLOGY REPORTS
(2021)
Article
Microbiology
Valerio Vitali, Rebecca Rothering, Francesco Catania
Summary: This research investigates the biomedical and evolutionary significance of amitosis, focusing on the suitability of single-cell whole-genome sequencing in studying the consequences of amitosis in Paramecium tetraurelia. The study reveals that somatic assortment levels in P. tetraurelia suggest that IES retention levels are largely established during macronuclear development and remain stable during vegetative growth.
Article
Plant Sciences
Denise L. Lindsay, Joel F. Swift, Richard F. Lance, Christine E. Edwards
BOTANICAL JOURNAL OF THE LINNEAN SOCIETY
(2018)
Article
Evolutionary Biology
Oscar E. Gaggiotti, Anne Chao, Pedro Peres-Neto, Chun-Huo Chiu, Christine Edwards, Marie-Josee Fortin, Lou Jost, Christopher M. Richards, Kimberly A. Selkoe
EVOLUTIONARY APPLICATIONS
(2018)
Article
Evolutionary Biology
Joel F. Swift, Richard F. Lance, Xin Guan, Eric R. Britzke, Denise L. Lindsay, Christine E. Edwards
EVOLUTIONARY APPLICATIONS
(2018)
Article
Biodiversity Conservation
Christine E. Edwards, Matthew A. Albrecht, Burgund Bassuener, George A. Yatskievych
CONSERVATION GENETICS
(2019)
Editorial Material
Biochemistry & Molecular Biology
Matthew A. Albrecht, Christine E. Edwards
Article
Biochemistry & Molecular Biology
Alexander G. Linan, Porter P. Lowry, Allison J. Miller, George E. Schatz, Jean-Claude Sevathian, Christine E. Edwards
Summary: The tree species in the genus Diospyros on the Mascarene islands have significant genetic differences between them, with hybridization observed between closely related species in the same subclade. As diversification progressed, interspecific hybridization occurred among species, but became infrequent as lineages diverged and evolved reproductive barriers. This suggests that introgression has played a role in the adaptation and diversification of Mascarene Diospyros, with implications for conservation.
Article
Multidisciplinary Sciences
Christine E. Edwards, Brooke C. Tessier, Joel F. Swift, Burgund Bassuner, Alexander G. Linan, Matthew A. Albrecht, George A. Yatskievych
Summary: Understanding genetic diversity and structure in Physaria filiformis is crucial for conservation efforts. This study found high genetic diversity in most populations, but identified geographic factors influencing genetic structure and highlighted the need for targeted conservation efforts in certain locations.
Article
Plant Sciences
Rebekah A. Mohn, Nora H. Oleas, Adam B. Smith, Joel F. Swift, George A. Yatskievych, Christine E. Edwards
Summary: The Appalachian-Ozark disjunction is likely the result of northward dispersal of the lowland lineage as climate warmed during the Holocene.
AMERICAN JOURNAL OF BOTANY
(2021)
Article
Plant Sciences
Alexander G. Linan, Jonathan A. Myers, Christine E. Edwards, Amy E. Zanne, Stephen A. Smith, Gabriel Arellano, Leslie Cayola, William Farfan-Rios, Alfredo F. Fuentes, Karina Garcia-Cabrera, Sebastian Gonzalez-Caro, M. Isabel Loza, Manuel J. Macia, Yadvinder Malhi, Beatriz Nieto-Ariza, Norma Salinas, Miles Silman, J. Sebastian Tello
Summary: The study found that on the elevational gradient of the Andes, species turnover is primarily driven by the replacement of clades that originated before the uplift of the mountains, indicating that immigration and sorting of clades pre-adapted to montane habitats are the main mechanisms shaping tree communities across elevational gradients.
Article
Evolutionary Biology
Alexander G. Linan, Porter P. Lowry, Allison J. Miller, George E. Schatz, Jean Claude Sevathian, Christine E. Edwards
Summary: This study conducted a comparative population genomics analysis of Diospyros species endemic to the Mascarene Islands. The researchers assessed the relative importance of colonization history, rarity, and distribution in shaping genetic diversity of island-endemic trees. The results showed that species co-occurring with others on the same island had greater genetic diversity, likely due to interspecific hybridization and processes related to time since island colonization.
JOURNAL OF HEREDITY
(2022)
Article
Evolutionary Biology
Richard F. Lance, Xin Guan, Joel F. Swift, Christine E. Edwards, Denise L. Lindsay, Eric R. Britzke
Summary: DNA contained in animal scat can provide valuable information about the animal, and DNA metabarcoding is an efficient method for extracting this information. In this study, DNA metabarcoding was used to identify bat species, determine sex ratios, analyze diet, and detect pathogens and parasites in bat guano samples. The results were generally consistent with previous census data, but some unexpected findings were also observed. This study highlights the usefulness of noninvasive sampling and DNA metabarcoding for obtaining diverse data.
EVOLUTIONARY APPLICATIONS
(2022)
Review
Ecology
Rachel Ann Lyman, Christine E. Edwards
Summary: This study analyzed 184 phylogeographical studies of eastern North American taxa published between 2007 and 2019 to evaluate the taxonomic focus of the studies, the adoption of genotyping technologies and analytical approaches, and the support for hypothesized biogeographic discontinuities. The findings showed little change in taxonomic focus, slow uptake of technological and analytical advances, variable support for previously identified discontinuities, and the identification of a new recurrent discontinuity. The study highlights the need to broaden the taxonomic focus, improve genetic resolution, and use analytical approaches to better understand the forces shaping the phylogeography of eastern North America.
ECOLOGY AND EVOLUTION
(2022)
Article
Plant Sciences
Megan Philpott, Valerie C. Pence, Burgund Bassuner, Ashley S. Clayton, Emily E. D. Coffey, Jason L. Downing, Christine E. Edwards, Raquel Folgado, Jason J. Ligon, Christy Powell, Joseph Francis Ree, Alexandra E. Seglias, Nellie Sugii, Peter J. Zale, Jacob Zeldin
Summary: The article discusses the resources and strategies required for the conservation of exceptional plants. It suggests that both large and small projects can contribute to exceptional plant conservation for similar costs, and prioritizing species with lower costs can help advance the field.
APPLICATIONS IN PLANT SCIENCES
(2022)
Article
Evolutionary Biology
Brock Mashburn, Reshad Jhangeer-Khan, Alfred Begue, Vikash Tatayah, Kenneth M. Olsen, Christine E. Edwards
Summary: Hibiscus liliiflorus, an endemic species to Rodrigues island, is critically endangered with only 2 wild individuals remaining. The study found that the MWF nursery only has 3 of the 4 original wild genotypes, and no unique genotypes were found in ex situ botanic garden collections. Seeds produced in the MWF nursery were a result of both self-fertilization and crossing between genotypes.
JOURNAL OF HEREDITY
(2023)
Article
Biodiversity Conservation
Christine E. E. Edwards, Burgund Bassuener, Brigette R. R. Williams
Summary: Leavenworthia exigua var. laciniata is a plant species with low genetic diversity and potential for asexual reproduction. It should be recognized as an evolutionarily significant unit for conservation due to its geographical, morphological, and genetic distinctiveness.
FRONTIERS IN CONSERVATION SCIENCE
(2022)
