Article
Forestry
Rainbow DeSilva, Richard S. Dodd
Summary: Patterns of dispersal play a crucial role in shaping genetic diversity within and among populations, especially in the face of environmental changes. Research on giant sequoia populations revealed predominantly outcrossing with moderate levels of inbreeding, low diversity in the pollen pool, and significant genetic structure at fine spatial scales. The findings suggest a potential for restoration planting to mitigate diversity loss in giant sequoia populations.
Article
Genetics & Heredity
Amanda R. De la Torre, Manoj K. Sekhwal, David B. Neale
Summary: The study investigated the genome-wide climate adaptation in giant sequoia and coast redwood, revealing a complex architecture of climate adaptation which may involve selective sweeps, polygenic adaptation, or a combination of both in response to moisture and temperature gradients. This suggests recent or ongoing climate adaptation in these tree species.
Article
Ecology
Lacey E. E. Hankin, Chad T. T. Anderson, Garrett J. J. Dickman, Parker Bevington, Scott L. L. Stephens
Summary: The Washburn fire, which started on July 7, 2022, in the lower Mariposa Grove in Yosemite National Park, posed immediate threats to iconic giant sequoias, Pacific fisher habitat, and the community of Wawona. The fire management efforts and roadside thinning in the Park played a crucial role in protecting key resources. The use of prescribed fire and fuels treatments can promote frequent-fire regimes, moderate extreme fire behavior, and increase human safety.
Article
Plant Sciences
Amanda R. De La Torre, Manoj K. Sekhwal, Daniela Puiu, Steven L. Salzberg, Alison D. Scott, Brian Allen, David B. Neale, Alana R. O. Chin, Thomas N. Buckley
Summary: This study utilized genome-wide association study methods to identify candidate genes related to drought tolerance in coast redwood and giant sequoia, contributing to a better understanding of the genomic basis of drought tolerance in long-generation conifers and guiding current and future conservation efforts.
Article
Ecology
Jingyao Ping, Jing Hao, Jinye Li, Yiqing Yang, Yingjuan Su, Ting Wang
Summary: In this study, evolutionary analysis was conducted on 78 gymnosperm species, revealing differences in selection pressure and evolutionary rates between conifers and non-conifers for certain genes. Despite the loss of typical IR regions in conifers, gene function, plant habitat, or newly acquired IRs did not significantly affect the substitution rate or selection pressure of most protein-coding genes.
ECOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Emile Gluck-Thaler, Timothy Ralston, Zachary Konkel, Cristhian Grabowski Ocampos, Veena Devi Ganeshan, Anne E. Dorrance, Terry L. Niblack, Corlett W. Wood, Jason C. Slot, Horacio D. Lopez-Nicora, Aaron A. Vogan
Summary: Accessory genes in a species can vary and act as a reservoir of adaptive functions. This study discovered a group of massive mobile elements called Starships in fungi that facilitate genome content variation. These Starships have shaped fungal genomes for millions of years and represent a new route for evolution in eukaryotes.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Genetics & Heredity
Guangwei Li, Lijian Wang, Jianping Yang, Hang He, Huaibing Jin, Xuming Li, Tianheng Ren, Zhenglong Ren, Feng Li, Xue Han, Xiaoge Zhao, Lingli Dong, Yiwen Li, Zhongping Song, Zehong Yan, Nannan Zheng, Cuilan Shi, Zhaohui Wang, Shuling Yang, Zijun Xiong, Menglan Zhang, Guanghua Sun, Xu Zheng, Mingyue Gou, Changmian Ji, Junkai Du, Hongkun Zheng, Jaroslav Dolezel, Xing Wang Deng, Nils Stein, Qinghua Yang, Kunpu Zhang, Daowen Wang
Summary: The study sequenced the genome of an elite Chinese rye variety, Weining rye, and found that the assembled contigs accounted for 98.47% of the estimated genome size. Further analysis revealed insights into gene duplications and their effects within rye.
Article
Ecology
Chun Fu, WenCong Long, ChaoBing Luo, Xiong Nong, XiMeng Xiao, Hong Liao, YuanQiu Li, Ying Chen, JiaXin Yu, SiXuan Cheng, Saira Baloch, YaoJun Yang
Summary: The study obtained a high-quality genome of the bamboo-snout beetle, revealing its special functions in degrading lignocellulose and detoxifying plant chemical components.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2021)
Article
Biology
F. Gozde Cilingir, Luke A'Bear, Dennis Hansen, Leyla R. Davis, Nancy Bunbury, Arpat Ozgul, Daniel Croll, Christine Grossen
Summary: This study presents the first chromosome-level de novo genome assembly of the Aldabra giant tortoise. It also provides insights into the population structure of the wild population and the origins of captive individuals. The high-quality genome assembly will contribute to conservation efforts and the understanding of the genetic basis of the species' longevity.
Article
Environmental Sciences
Lei Jin, Hongning Wu, Guo Li, Shengzhi Yang, Rongping Wei, Yan Huang, Petri Penttinen, Wenwen Deng, Jianbin Chen, Xinfeng Han, Caiwu Li, Lan Hu, Ti Li, Hemin Zhang, Ke Zhao, Likou Zou
Summary: This study investigated the composition and function of the gastrointestinal microbiome and resistance genes in wild giant pandas, and found that the microbiome plays a crucial role in lignocellulose degradation from bamboo. The study also highlighted the importance of monitoring metal levels in soil and bamboo due to their influence on the microbiome and resistance genes.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Biotechnology & Applied Microbiology
Ehren J. Bentz, Alexander G. Ophir
Summary: The Southern giant pouched rat is a large rodent with the ability to detect landmines using its impressive sense of smell. It has powerful chemosensory abilities and shows unique reproductive physiology, possibly mediated by pheromonal mechanisms. The chromosome-scale genomic sequence of the pouched rat reveals genetic expansions related to olfactory specialization. This reference-quality genomic sequence will be useful for future molecular research on the pouched rat.
Article
Multidisciplinary Sciences
Ingmar Janse, Rick Beeloo, Arno Swart, Michael Visser, Leo Schouls, Engeline van Duijkeren, Mark W. J. van Passel
Summary: Genome sequences provide valuable information on genetic elements in organisms. By analyzing bacterial genome databases, patterns of antibiotic resistance gene distribution can be mined, shedding light on the evolution and transmission mechanisms of bacterial resistance. This study utilized a public database to investigate the dissemination of carbapenemase-encoding genes in various species, revealing a large and widespread presence of these genes in bacterial genomes.
Article
Biochemistry & Molecular Biology
Jing-Ge Kuang, Zhi-Tong Han, Ming-Hui Kang, Tsam Ju, Sonam Tso, Xiao-Xiao Chen, Jia-Liang Li, Zhong-Ping Xiong, Tao Ma, Kang-Shan Mao
Summary: In this study, chromosome-level genome assemblies for two oligophagous conifer parasitoid species of Megastigmus were provided, representing the first two chromosome-level genomes of the genus. The expanded genomes of these species were larger than most hymenopterans due to the expansion of transposable elements. The study found differences in sensory-related genes between the two species, reflecting the difference in their hosts. The study also found that these two species have fewer family members but more single-gene duplications in certain gene families compared to polyphagous congeners.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Biochemistry & Molecular Biology
Martin Mascher, Thomas Wicker, Jerry Jenkins, Christopher Plott, Thomas Lux, Chu Shin Koh, Jennifer Ens, Heidrun Gundlach, Lori B. Boston, Zuzana Tulpova, Samuel Holden, Inmaculada Hernandez-Pinzon, Uwe Scholz, Klaus F. X. Mayer, Manuel Spannagl, Curtis J. Pozniak, Andrew G. Sharpe, Hana Simkova, Matthew J. Moscou, Jane Grimwood, Jeremy Schmutz, Nils Stein
Summary: Comparing different long-read sequencing platforms in barley pan-genome studies, accurate long-read assemblies excel in most metrics, with CCS approach being the most cost-effective strategy.
Article
Biochemistry & Molecular Biology
Tianle Tang, Yu Huang, Chao Peng, Yanling Liao, Yunyun Lv, Qiong Shi, Bingmiao Gao
Summary: This study successfully constructed a genome assembly for the reef stonefish and conducted comparative analysis of its toxin genes. It was found that sntx genes had higher transcription levels, especially those clustered on chromosome 2. Furthermore, comparative genomic analysis revealed independent duplication events of toxin genes in Scorpaenoidei species, marking the origin of authentic toxic stonustoxins.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Biochemical Research Methods
Christopher Pockrandt, Martin Steinegger, Steven L. Salzberg
Summary: PhyloCSF++ is an efficient and parallelized C++ implementation of the PhyloCSF method, which uses multiple sequence alignments to distinguish protein-coding and non-coding regions in a genome. It can score alignments, generate browser tracks, and annotate coding sequences in various file formats.
Article
Plant Sciences
Susan L. McEvoy, U. Uzay Sezen, Alexander Trouern-Trend, Sean M. McMahon, Paul G. Schaberg, Jie Yang, Jill L. Wegrzyn, Nathan G. Swenson
Summary: The first chromosome-scale assemblies for sugar maple and boxelder, as well as transcriptomic evaluation of the abiotic stress response in sugar maple, were reported in this study. The integrated research provides insights into the contribution of different factors to tolerance in each species and utilizes knowledge from various areas of plant genome biology and Acer physiology to understand the genomic complexities underlying tolerance in broadleaf tree species.
Article
Multidisciplinary Sciences
W. John Kress, Douglas E. Soltis, Paul J. Kersey, Jill L. Wegrzyn, James H. Leebens-Mack, Morgan R. Gostel, Xin Liu, Pamela S. Soltis
Summary: Green plants are essential to ecosystems, human health, and agriculture, but generating and storing their genomes is a major challenge. Currently, there are fewer than 300 complete chromosome-scale genome assemblies for green plants, representing less than 900 species. Many species, especially those from extreme environments, still lack suitable tissue samples for genomic sequencing. The annotation of plant genomes also needs improvement.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Agronomy
Marlene Lachaux, Emilie Thomas, Adam J. Bogdanove, Boris Szurek, Mathilde Hutin
Summary: We identified and characterized TalD and TalI as two African Xoo TALEs with avirulence activity on IR64 and CT13432 respectively. Resistance of CT13432 against African Xoo results from the combination of two mechanisms, one relying on the TalI-mediated induction of an unknown executor gene and the other on an Xa1-like gene or allele.
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
Genetics & Heredity
Daniel Ence, Katherine E. Smith, Shenghua Fan, Leandro Gomide Neves, Robin Paul, Jill Wegrzyn, Gary F. Peter, Matias Kirst, Jeremy Brawner, C. Dana Nelson, John M. Davis
Summary: This study investigates the diversity of NLR genes in loblolly pine and identifies SNPs associated with resistance, providing a resource to enhance breeding and deployment of resistant pine seedlings.
G3-GENES GENOMES GENETICS
(2022)
Article
Biochemical Research Methods
Aleksey V. Zimin, Steven L. Salzberg
Summary: Third-generation sequencing technologies generate long reads, which are valuable for resolving complex repeats. An upgrade strategy for existing assemblies is to use long-read data to fill gaps and improve contiguity.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Genetics & Heredity
Aleksey Zimin, Alaina Shumate, Ida Shinder, Jakob Heinz, Daniela Puiu, Mihaela Pertea, Steven L. Salzberg
Summary: Until 2019, there was only one fully annotated version of the human genome. In 2019, a second individual genome was successfully assembled and annotated, which was from an individual of African descent. The new genome is more complete and contiguous than previous genomes.
Article
Microbiology
Matthew A. Tancos, Zoe E. Dubrow, Sara C. D. Carpenter, Adam J. Bogdanove
Summary: Xanthomonas campestris strain FDWSRU 18048, which is closely related to X. campestris pv. incanae strain CFBP2527, has been reported to infect nonnative, invasive garlic mustard populations in the eastern United States.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2022)
Article
Plant Sciences
Andrew Read, Trevor Weiss, Peter A. Crisp, Zhikai Liang, Jaclyn Noshay, Claire C. Menard, Chunfang Wang, Meredith Song, Candice N. Hirsch, Nathan M. Springer, Feng Zhang
Summary: The study revealed the importance of DOMAIN REARRANGED METHYLTRANSFERASEs (DRMs) in RNA-directed DNA methylation (RdDM) in plants. By using CRISPR-based genome editing, loss-of-function alleles for two putative functional DRM genes in S. viridis were created, showing the loss of methylation, altered gene expression, and activation of transposons in drm1ab mutants. These findings highlight the significance of RdDM in gene expression regulation and transposon repression.
Article
Biochemical Research Methods
Jennifer Lu, Natalia Rincon, Derrick E. Wood, Florian P. Breitwieser, Christopher Pockrandt, Ben Langmead, Steven L. Salzberg, Martin Steinegger
Summary: This article introduces a step-by-step protocol for the computational analysis of high-throughput DNA sequencing data using the Kraken suite. The protocol includes classification, quantification, and visualization, and can be used for quantifying species in a microbial community and identifying pathogens in clinical samples.
Article
Ecology
Laura Figueroa-Corona, Alejandra Moreno-Letelier, Diego Ortega-Del Vecchyo, Pablo Pelaez, David S. Gernandt, Luis E. Eguiarte, Jill Wegrzyn, Daniel Pinero
Summary: Climate changes and geographical barriers have influenced genetic diversity and distribution patterns of species in northern Mexico. The study on the genetic diversity of Pinus pinceana reveals that it diverged into two lineages and colonized the Sierra Madre Oriental and the Chihuahuan Desert.
ECOLOGY AND EVOLUTION
(2022)
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)
Article
Computer Science, Interdisciplinary Applications
Ales Varabyou, Beril Erdogdu, Steven L. Salzberg, Mihaela Pertea
Summary: ORFanage is a system that analyzes RNA-seq data to discover novel protein variants and enhance gene annotations. It is fast, scalable, and effectively filters out noise to improve the quality of transcriptome assemblies.
NATURE COMPUTATIONAL SCIENCE
(2023)
Article
Medicine, Research & Experimental
Caroline R. Wensel, Jennifer L. Pluznick, Steven L. Salzberg, Cynthia L. Sears
Summary: This Review discusses the advancements in NGS technology for studying the human microbiome, including the pros and cons of different NGS methodologies and important concepts in data variability and study design. Examples of NGS studies on the human microbiome in diverse clinical contexts are provided, as well as insights into the future integration and advancement of NGS in microbiome research and clinical care.
JOURNAL OF CLINICAL INVESTIGATION
(2022)