Article
Biochemistry & Molecular Biology
Christopher James O'Grady, Vignesh Dhandapani, John K. Colbourne, Dagmar Frisch
Summary: Whole genome sequencing is crucial for studying genome variation in natural populations, and large dormant eggbanks of aquatic invertebrates provide valuable information on genomic processes over centuries. An optimized workflow for whole genome amplification (WGA) has been developed to address limited DNA amounts in single eggs, allowing successful downstream whole genome sequencing of historical eggs. Comparison of two WGA kits showed high genome coverage breadth in samples, with high recovery of genomic positions with single nucleotide polymorphisms for genotyping, and even obtaining 100% coverage of mitochondrial genomes from the oldest isolates. Mitochondrial DNA serves as an additional source for evolutionary studies of these populations.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Biochemistry & Molecular Biology
Zhiqiang Han, Manhong Liu, Qi Liu, Hao Zhai, Shijun Xiao, Tianxiang Gao
Summary: The burbot, adapted solely to freshwater, has the widest longitudinal range among freshwater fish worldwide. A high-quality chromosome-level genome of burbot was constructed using PacBio long sequencing and Hi-C technology, providing valuable insights for ecological and evolutionary studies within the order Gadiformes.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Plant Sciences
Benzhong Fu, Yingyan Zhai, Mark Gleason, Gwyn A. Beattie
Summary: FBB1, a bacteriophage isolated from spotted cucumber beetles, can infect strains of Erwinia tracheiphila and some nonpathogenic bacteria, making it a promising candidate for biocontrol of E. tracheiphila.
Article
Biology
Elisa Maritan, Marialaura Gallo, Dagmar Srutkova, Anna Jelinkova, Oldrich Benada, Olga Kofronova, Nuno F. Silva-Soares, Tomas Hudcovic, Isaac Gifford, Jeffrey E. Barrick, Martin Schwarzer, Maria Elena Martino
Summary: The evolution of gut microbes in insects and mammals differs due to the influence of host diet and intrinsic factors in mammals. The symbiotic relationship between fruit flies and L. plantarum is mainly determined by the host diet, while the host's intrinsic factors play a critical role in the selection and evolution of gut microbes in mammals.
Article
Plant Sciences
Phougeishangbam Rolish Singh, Bart T. L. H. van de Vossenberg, Katarzyna Rybarczyk-Mydlowska, Magdalena Kowalewska-Groszkowska, Wim Bert, Gerrit Karssen
Summary: This study carried out a morphological and molecular analysis of three populations of Rotylenchus goodeyi, revealing important character variations within this species and suggesting the synonymization of R. rhomboides with R. goodeyi. The study also identified high nucleotide variation within cox1 gene sequences in these populations.
Article
Agriculture, Dairy & Animal Science
Sun-Hee Kim, Seung-Jae Lee, Euna Jo, Jangyeon Kim, Jong-U Kim, Jeong-Hoon Kim, Hyun Park, Young-Min Chi
Summary: The genome of the southern giant petrel Macronectes giganteus, with a size of 1.248 Gb and containing 14,993 predicted protein-coding genes, underwent a severe reduction in effective population size during the early Pleistocene. The genomic expansion related to maintenance of energy homeostasis was identified in M. giganteus, which is crucial for survival in cold environments.
Article
Microbiology
Savanah Senn, Sharmodeep Bhattacharyya, Gerald Presley, Anne E. Taylor, Bruce Nash, Ray A. Enke, Karen B. Barnard-Kubow, Jillian Ford, Brandon Jasinski, Yekaterina Badalova
Summary: This study investigated microbial soil communities in different wildfire areas in Southern California and found significant differences in fungal and bacterial taxa among the areas. Seasonal shifts in bacterial community diversity were also observed. The analysis revealed a strong association between longitude, elevation, and specific clusters of Amplicon Sequence Variants (ASVs). These findings suggest important traits for post-wildfire resilience.
Review
Plant Sciences
Sariel Huebner
Summary: Graph-based pangenomes can provide a comprehensive platform to study diversity in populations or species, but still face challenges in species with large complex genomes. However, with advancing technology, the graph-pangenome is expected to become a central platform in genomics studies and applications.
CURRENT OPINION IN PLANT BIOLOGY
(2022)
Article
Genetics & Heredity
Xiaoyang Wu, Qinguo Wei, Xibao Wang, Yongquan Shang, Honghai Zhang
Summary: This study compared the gut microbiome of 16 rare wild mammals and found that Firmicutes and Bacteroidetes were the most predominant phyla in all mammals, with Proteobacteria specifically dominant in carnivores and omnivores. Host impact on the microbiome composition was most evident in conspecific and congeneric relationships, highlighting the influence of phylogenetic relationships and diet on gut microbiome community composition. These results provide valuable data for future efforts in animal conservation and health.
Editorial Material
Multidisciplinary Sciences
Heidi Ledford
Summary: The article tells the story of a human genome scientist who sequenced the genes of the ocean, set up a health-screening company after checking his own genes, and explains why he has no plans to stop.
Article
Environmental Sciences
Miguel Baltazar-Soares, Andre R. A. Lima, Goncalo Silva, Elie Gaget
Summary: The introduction of genomic resources in fisheries management has enhanced our understanding of stock dynamics by adding a temporal point of view. By integrating genomic information with temporal projections from Species Distribution Models (SDMs), we can inform about potential future range expansions, contractions, and suitable habitats for fish stocks based on their evolutionary potential. This framework combines the advantages of SDMs and genomic data to improve forecasting ability in fisheries management.
FRONTIERS IN MARINE SCIENCE
(2023)
Article
Genetics & Heredity
Larissa R. Carvalho, Rhewter Nunes, Mariane B. Sobreiro, Renata O. Dias, Leonardo C. J. Corvalan, Ramilla S. Braga-Ferreira, Cintia P. Targueta, Mariana P. C. Telles
Summary: This study assembled and annotated the chloroplast genome of Eugenia klotzschiana O. Berg and compared it with other 13 species from the Myrteae tribe. The E. klotzschiana plastome showed a conserved structure and gene composition. Mutational hotspots, repetitive sequences, SSR repeats, and RNA editing sites were identified. Furthermore, the study reconstructed a plastome-based Myrtales phylogenetic tree, including E. klotzschiana, and revealed its sister relationship with other Eugenia species.
Article
Multidisciplinary Sciences
Matthew J. Christmas, Irene M. Kaplow, Diane P. Genereux, Michael X. Dong, Graham M. Hughes, Xue Li, Patrick F. Sullivan, Allyson G. Hindle, Gregory Andrews, Joel C. Armstrong, Matteo Bianchi, Ana M. Breit, Mark Diekhans, Cornelia Fanter, Nicole M. Foley, Daniel B. Goodman, Linda Goodman, Kathleen C. Keough, Bogdan Kirilenko, Amanda Kowalczyk, Colleen Lawless, Abigail L. Lind, Jennifer R. S. Meadows, Lucas R. Moreira, Ruby W. Redlich, Louise Ryan, Ross Swofford, Alejandro Valenzuela, Franziska Wagner, Ola Wallerman, Ashley R. Brown, Joana Damas, Kaili Fan, John Gatesy, Jenna Grimshaw, Jeremy Johnson, Sergey V. Kozyrev, Alyssa J. Lawler, Voichita D. Marinescu, Kathleen M. Morrill, Austin Osmanski, Nicole S. Paulat, BaDoi N. Phan, Steven K. Reilly, Daniel E. Schaeffer, Cynthia Steiner, Megan A. Supple, Aryn P. Wilder, Morgan E. Wirthlin, James R. Xue, Bruce W. Birren, Steven Gazal, Robert M. Hubley, Klaus-Peter Koepfli, Tomas Marques-Bonet, Wynn K. Meyer, Martin Nweela, Pardis C. Sabeti, Beth Shapiro, Arian F. A. Smit, Mark S. Springer, Emma C. Teeling, Zhiping Weng, Michael Hiller, Danielle L. Levesque, Harris A. Lewin, William J. Murphy, Arcadi Navarro, Benedict Paten, Katherine S. Pollard, David A. Ray, Irina Ruf, Oliver A. Ryder, Andreas R. Pfenning, Kerstin Lindblad-Toh, Elinor K. Karlsson
Summary: Zoonomia is a comprehensive genomics resource for mammals, which aligns genomes for 240 species to identify mutations that affect fitness and disease risk. It reveals that a considerable portion of the human genome is evolutionarily constrained and contains highly conserved elements. Many of these constrained bases have no known function, presenting opportunities for therapeutic research. The vast biodiversity on Earth offers great potential in identifying genetic variants that influence genome function and organismal traits.
Article
Biochemistry & Molecular Biology
Jinfeng Chen, Jingfei Cheng, Xiufei Chen, Masato Inoue, Yibin Liu, Chun-Xiao Song
Summary: Long-read sequencing provides valuable information on difficult-to-map genomic regions and can improve genome assembly when combined with short-read sequencing. This study presents a method called whole-genome long-read TAPS (wglrTAPS), which combines TET-assisted pyridine borane sequencing with PacBio single-molecule real-time sequencing. Application of wglrTAPS to mouse embryonic stem cells showed the ability to detect previously uncovered CpG sites in problematic genomic regions. This method enhances the use of third-generation sequencing technologies for DNA epigenetics.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Plant Sciences
Xuejin Cui, Kehong Liu, Sagheer Atta, Chunhua Zeng, Changyong Zhou, Xuefeng Wang
Summary: Two unique prophages, designated as P-PA19-1 and P-PA19-2, were identified in the CLas strain PA19 from Pakistan, with P-PA19-2 integrated into the PA19 chromosome, indicating the genomic diversity and evolution of CLas prophages.