Article
Plant Sciences
Samantha P. Setta, Sarah Lerch, Bethany D. Jenkins, Sonya T. Dyhrman, Tatiana A. Rynearson
Summary: Diatoms are important components of the marine food web, but little is known about their diversity and community composition in oligotrophic offshore regions. This study compared the diatom diversity and community composition between oligotrophic and eutrophic waters along a transect in the western North Atlantic. The results showed that oligotrophic waters harbor a diverse diatom community that is distinct from coastal regions, and their composition is influenced by temperature and phosphate levels.
JOURNAL OF PHYCOLOGY
(2023)
Article
Environmental Sciences
Michael W. Lomas, Steven E. Baer, Celine Mouginot, Kristina X. Terpis, Debra A. Lomas, Mark A. Altabet, Adam C. Martiny
Summary: The concentrations and elemental ratios of suspended particulate organic matter in the ocean influence various biogeochemical processes, with phytoplankton populations showing differences across ocean basins. While light and temperature were not consistent predictors, nutrient availability and taxonomic composition best predicted bulk particulate organic matter composition in different marine biomes. Plankton biodiversity and cellular acclimation to nutrient flux ratio play a central role in controlling the linkages between ocean nutrient and carbon cycles.
COMMUNICATIONS EARTH & ENVIRONMENT
(2021)
Article
Biochemistry & Molecular Biology
Emily. Dutrow, James A. Serpell, Elaine A. Ostrander
Summary: Selective breeding of domestic dogs has generated diverse breeds optimized for specialized tasks. This study develops a framework to understand the genetic drivers of canine behavior and identifies ten major genetic lineages and their behavioral correlates. The study also highlights the role of non-coding regulatory variation and identifies enrichment for interrelated axon guidance functions in sheepdogs.
Article
Ecology
Lanlan Cai, Yue Chen, Shiwei Xiao, Riyue Liu, Maoqiu He, Rui Zhang, Qinglu Zeng
Summary: Cyanopodoviruses play a significant role in the mortality and population dynamics of picocyanobacteria in the oceans. A new cyanopodovirus clade with smaller genomes and longer latent periods has been identified, showing different abundance patterns at different depths in the ocean. This discovery indicates that cyanophages with distinct genomic contents and infection kinetics can exhibit different distribution profiles in marine environments.
Article
Multidisciplinary Sciences
Shourong Shi, Dan Shao, Lingyun Yang, Qiqi Liang, Wei Han, Qian Xue, Liang Qu, Li Leng, Yishu Li, Xiaogang Zhao, Ping Dong, Muhammed Walugembe, Boniface B. Kayang, Amandus P. Muhairwa, Huaijun Zhou, Haibing Tong
Summary: Investigating the genetic footprints of historical temperature selection on chickens can provide insights into the effects of climate change on population dynamics. This study conducted whole genome resequencing of 119 domesticated chickens in China and found that genetic adaptation to tropical and frigid environments has occurred.
JOURNAL OF ADVANCED RESEARCH
(2023)
Article
Biology
Geoffrey C. Waldbieser, Shikai Liu, Zihao Yuan, Caitlin E. Older, Dongya Gao, Chenyu Shi, Brian G. Bosworth, Ning Li, Lisui Bao, Mona A. Kirby, Yulin Jin, Monica L. Wood, Brian Scheffler, Sheron Simpson, Ramey C. Youngblood, Mary V. Duke, Linda Ballard, Adam Phillippy, Sergey Koren, Zhanjiang Liu
Summary: This study generated high-quality chromosome level reference genome sequences for channel catfish and blue catfish in the US, and identified three major pericentric inversions on their chromosomes. These reference genome sequences, along with the contrasting chromosomal architecture, can provide guidance for interspecific breeding programs.
Article
Microbiology
Qian Wang, Lei Zhang, Yiju Zhang, Huamin Chen, Jianghua Song, Mingjie Lyu, Rui Chen, Lixin Zhang
Summary: This study reveals the genome sequence of B. pumilus strain HM-7 and identifies its potential pathogenic mechanisms. The findings provide a foundation for developing effective prevention and control strategies against this pathogen in the future.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Shamam Waldman, Daniel Backenroth, Eadaoin Harney, Stefan Flohr, Nadia C. Neff, Gina M. Buckley, Hila Fridman, Ali Akbari, Nadin Rohland, Swapan Mallick, Inigo Olalde, Leo Cooper, Ariel Lomes, Joshua Lipson, Jorge Cano Nistal, Jin Yu, Nir Barzilai, Inga Peter, Gil Atzmon, Harry Ostrer, Todd Lencz, Yosef E. Maruvka, Maike Lammerhirt, Alexander Beider, Leonard Rutgers, Virginie Renson, Keith M. Prufer, Stephan Schiffels, Harald Ringbauer, Karin Sczech, Shai Carmi, David Reich
Summary: We obtained genome-wide data from 33 Ashkenazi Jews dating back to the 14th century, and found that they are genetically similar to modern Ashkenazi Jews but show more variability in their Eastern European-related ancestry. The study also reveals that the ancient Ashkenazi Jewish community had already experienced a significant reduction in size, indicating substructure in medieval Ashkenazi Jews.
Article
Microbiology
Kajal Mandal, Subhajeet Dutta, Aditya Upadhyay, Arijit Panda, Sucheta Tripathy
Summary: This study investigates the genomes of 128 Phytophthora species and reveals that their simple sequence repeats follow isolate-specific patterns, with TG/CA dinucleotide repeats being the most abundant. The telomeric repeats and RxLR effectors in Phytophthora show rapid divergence. The analysis also identifies a large number of other virulence genes present in repeat-rich compartments. Whole genome duplication studies suggest a geographic location-specific pattern. Overall, this study sheds light on the adaptive evolution of Phytophthora driven by localized host-mediated selection pressure.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Multidisciplinary Sciences
Eckart Stolle, Rodrigo Pracana, Federico Lopez-Osorio, Marian K. Priebe, Gabriel Luis Hernandez, Claudia Castillo-Carrillo, Maria Cristina Arias, Carolina Ivon Paris, Martin Bollazzi, Anurag Priyam, Yannick Wurm
Summary: The study investigates the role of supergene regions in Solenopsis fire ants, which determine whether colonies have multiple queens or not. By analyzing genomes, the researchers find that the supergene variant responsible for multiple-queen colonies evolved in one species and spread to other species through introgressive hybridization.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Qiang Li, Peng Wu, Lijiao Li, Huiyu Feng, Wenying Tu, Zhijie Bao, Chuan Xiong, Mingying Gui, Wenli Huang
Summary: The present study assembled and compared eleven novel complete mitogenomes of Boletus, revealing differences in gene arrangement and evolution rates among Boletus species. The study also found a close relationship between Boletus species and Paxillus in the phylogenetic tree of 72 Agaricomycetes.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Plant Sciences
Jinxin Liu, Mengmeng Shi, Zhaolei Zhang, Hongbo Xie, Weijun Kong, Qiuling Wang, Xinlei Zhao, Chunying Zhao, Yulin Lin, Xiaoxia Zhang, Linchun Shi
Summary: This study reveals the extensive discordance and complexity of the relationships across the members of the Atractylodes lancea complex according to cytonuclear genomic data, which may be caused by interspecific hybridization or gene introgression.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Genetics & Heredity
Sylvan C. Baca, Cassandra Singler, Soumya Zacharia, Ji-Heui Seo, Tunc Morova, Faraz Hach, Yi Ding, Tommer Schwarz, Chia-Chi Flora Huang, Jacob Anderson, Andre P. Fay, Cynthia Kalita, Stefan Groha, Mark M. Pomerantz, Victoria Wang, Simon Linder, Christopher J. Sweeney, Wilbert Zwart, Nathan A. Lack, Bogdan Pasaniuc, David Y. Takeda, Alexander Gusev, Matthew L. Freedman
Summary: Many genetic variants affect disease risk by altering context-dependent gene regulation. The cistrome-wide association study (CWAS) is a powerful framework for identifying variants that influence traits through effects on chromatin state.
Article
Multidisciplinary Sciences
Poonam Singh, Kunal Mukhopadhyay
Summary: This study identified 23 novel TIFY genes in the wheat genome, revealing their important roles in phytohormone signaling and defense responses in plants. The distribution of TIFY genes in wheat was found to be arbitrary, with various cis-acting elements and corresponding microRNA targets. Predicted tertiary structures of TIFY proteins indicated critical active sites for DNA binding.
SCIENTIFIC REPORTS
(2021)
Article
Plant Sciences
Raz Avni, Thomas Lux, Anna Minz-Dub, Eitan Millet, Hanan Sela, Assaf Distelfeld, Jasline Deek, Guotai Yu, Burkhard Steuernagel, Curtis Pozniak, Jennifer Ens, Heidrun Gundlach, Klaus F. X. Mayer, Axel Himmelbach, Nils Stein, Martin Mascher, Manuel Spannagl, Brande B. H. Wulff, Amir Sharon
Summary: Aegilops species, particularly Aegilops longissima and Aegilops speltoides, offer genetic diversity for wheat improvement. Comparative analysis of whole-genome assemblies revealed the close relationship between Ae. longissima and the wheat D subgenome, while Ae. speltoides showed a closer relationship to the B subgenome. The presence of species-specific and lineage-specific nucleotide-binding leucine-rich repeat (NLR) genes in Aegilops genomes highlights their potential for wheat improvement.
Article
Microbiology
Kristen M. DeAngelis, Grace Pold, Beguem D. Topcuoglu, Linda T. A. van Diepen, Rebecca M. Varney, Jeffrey L. Blanchard, Jerry Melillo, Serita D. Frey
FRONTIERS IN MICROBIOLOGY
(2015)
Article
Biotechnology & Applied Microbiology
Grace Pold, Andrew F. Billings, Jeff L. Blanchard, Daniel B. Burkhardt, Serita D. Frey, Jerry M. Melillo, Julia Schnabel, Linda T. A. van Diepen, Kristen M. DeAngelis
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2016)
Article
Multidisciplinary Sciences
Olivier Tenaillon, Jeffrey E. Barrick, Noah Ribeck, Daniel E. Deatherage, Jeffrey L. Blanchard, Aurko Dasgupta, Gabriel C. Wu, Sebastien Wielgoss, Stephane Cruveiller, Claudine Medigue, Dominique Schneider, Richard E. Lenski
Article
Microbiology
Kelly Nicole Haas, Jeffrey L. Blanchard
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2017)
Article
Multidisciplinary Sciences
Elsa Petit, Maddalena V. Coppi, James C. Hayes, Andrew C. Tolonen, Thomas Warnick, William G. Latouf, Danielle Amisano, Amy Biddle, Supratim Mukherjee, Natalia Ivanova, Athanassios Lykidis, Miriam Land, Loren Hauser, Nikos Kyrpides, Bernard Henrissat, Joanne Lau, Danny J. Schnell, George M. Church, Susan B. Leschine, Jeffrey L. Blanchard
Article
Soil Science
Emily J. Cole, Omid R. Zandvakili, Jeffrey Blanchard, Baoshan Xing, Masoud Hashemi, Fatemeh Etemadi
APPLIED SOIL ECOLOGY
(2019)
Article
Multidisciplinary Sciences
Frederik Schulz, Lauren Alteio, Danielle Goudeau, Elizabeth M. Ryan, Feiqiao B. Yu, Rex R. Malmstrom, Jeffrey Blanchard, Tanja Woyke
NATURE COMMUNICATIONS
(2018)
Article
Microbiology
Kelly N. Haas, Jeffrey L. Blanchard
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2020)
Article
Microbiology
L. Alteio, F. Schulz, R. Seshadri, N. Varghese, W. Rodriguez-Reillo, E. Ryan, D. Goudeau, S. A. Eichorst, R. R. Malmstrom, R. M. Bowers, L. A. Katz, J. L. Blanchard, T. Woyke
Article
Microbiology
Jason P. Andras, William G. Rodriguez-Reillo, Alexander Truchon, Jeffery L. Blanchard, Erin A. Pierce, Katherine A. Ballantine
FEMS MICROBIOLOGY ECOLOGY
(2020)
Article
Engineering, Environmental
Rachelle E. LaCroix, Nicolas Walpen, Michael Sander, Malak M. Tfaily, Jeffrey L. Blanchard, Marco Keiluweit
Summary: Global warming accelerates microbial decomposition of soil organic matter, leading to a decrease in the redox capacity of water-extractable organic matter in soil. This decline may negatively impact critical biogeochemical processes such as microbial respiration, nutrient cycling, and contaminant degradation.
ENVIRONMENTAL SCIENCE & TECHNOLOGY LETTERS
(2021)
Correction
Biotechnology & Applied Microbiology
Stephen Nayfach, Simon Roux, Rekha Seshadri, Daniel Udwary, Neha Varghese, Frederik Schulz, Dongying Wu, David Paez-Espino, I- Min Chen, Marcel Huntemann, Krishna Palaniappan, Joshua Ladau, Supratim Mukherjee, T. B. K. Reddy, Torben Nielsen, Edward Kirton, Jose P. Faria, Janaka N. Edirisinghe, Christopher S. Henry, Sean P. Jungbluth, Dylan Chivian, Paramvir Dehal, Elisha M. Wood-Charlson, Adam P. Arkin, Susannah G. Tringe, Axel Visel, Tanja Woyke, Nigel J. Mouncey, Natalia N. Ivanova, Nikos C. Kyrpides, Emiley A. Eloe-Fadrosh
NATURE BIOTECHNOLOGY
(2021)
Article
Ecology
Gregory J. Pec, Linda T. A. van Diepen, Melissa Knorr, A. Stuart Grandy, Jerry M. Melillo, Kristen M. DeAngelis, Jeffrey L. Blanchard, Serita D. Frey
Summary: A study conducted at Harvard Forest found that long-term soil warming led to compositional shifts in soil fungal communities, particularly in the saprotrophic and unknown components, while short-term warming did not have a significant impact. Soil warming resulted in declines in soil C concentrations and total C stored in the organic horizon. Furthermore, after long-term warming, changes in fungal guild relative abundances were associated with substantial alterations in soil organic matter chemistry, particularly the abundance of lignin.
Article
Microbiology
Priyanka Roy Chowdhury, Stefan M. Golas, Lauren Alteio, Joshua T. E. Stevens, Andrew F. Billings, Jeffrey L. Blanchard, Jerry M. Melillo, Kristen M. DeAngelis
Summary: The study indicates that long-term climate warming has a significant impact on microbial degradation of carbon in the soil, potentially accelerating the carbon cycle in heated plots. Furthermore, it was found that heating leads to increased expression of specific enzymes in soil, particularly those related to carbohydrate and lipid metabolism.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Stephen Nayfach, Simon Roux, Rekha Seshadri, Daniel Udwary, Neha Varghese, Frederik Schulz, Dongying Wu, David Paez-Espino, I-Min Chen, Marcel Huntemann, Krishna Palaniappan, Joshua Ladau, Supratim Mukherjee, T. B. K. Reddy, Torben Nielsen, Edward Kirton, Jose P. Faria, Janaka N. Edirisinghe, Christopher S. Henry, Sean P. Jungbluth, Dylan Chivian, Paramvir Dehal, Elisha M. Wood-Charlson, Adam P. Arkin, Susannah G. Tringe, Axel Visel, Tanja Woyke, Nigel J. Mouncey, Natalia N. Ivanova, Nikos C. Kyrpides, Emiley A. Eloe-Fadrosh
Summary: Reconstructing bacterial and archaeal genomes from shotgun metagenomes has led to the creation of a comprehensive catalog representing a significant expansion of the known phylogenetic diversity of bacteria and archaea. This resource is available for streamlined comparative analyses, interactive exploration, metabolic modeling, and bulk download, demonstrating the utility of genome-centric approaches for understanding genomic properties of uncultivated microorganisms.
NATURE BIOTECHNOLOGY
(2021)