Article
Plant Sciences
Luca Marcolungo, Leonardo Vincenzi, Matteo Ballottari, Michela Cecchin, Emanuela Cosentino, Thomas Mignani, Antonina Limongi, Irene Ferraris, Matteo Orlandi, Marzia Rossato, Massimo Delledonne
Summary: High-throughput chromosome conformation capture (Hi-C) is commonly used in de novo assembly for its ability to produce highly contiguous genomes. However, its statistical approach can introduce connection errors. We used optical mapping to evaluate the quality of Hi-C reconstructed scaffolds and found numerous inconsistencies. Manual inspection confirmed that some of these conflicts were caused by Hi-C joining errors. We conclude that integrating optical mapping data after Hi-C-based scaffolding improves the assembly quality by identifying and investigating misjoins.
Article
Genetics & Heredity
Gangcai Xie, Xu Zhang, Feng Lv, Mengmeng Sang, Hairong Hu, Jinqiu Wang, Dong Liu
Summary: In this study, a high-quality reference genome for Trachidermus fasciatus was successfully assembled, containing 19,147 protein-coding genes and 35,093 mRNA transcripts. Additionally, a novel gene-finding strategy was introduced, leading to the identification of 51 new genes.
Article
Biochemistry & Molecular Biology
Stephanie H. Chen, Maurizio Rossetto, Marlien van der Merwe, Patricia Lu-Irving, Jia-Yee S. Yap, Herve Sauquet, Greg Bourke, Timothy G. Amos, Jason G. Bragg, Richard J. Edwards
Summary: This study presents the first chromosome-level genome of Telopea speciosissima, providing valuable insights into the speciation, introgression, and adaptation processes. The genome assembly is of high quality and the annotation revealed important genetic information, such as the presence of CYCLOIDEA genes and potential gene duplications. The T. speciosissima reference genome will contribute to the conservation efforts of Proteaceae plants in Australia and beyond.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Biochemistry & Molecular Biology
Bingyan Li, Zhenyong Du, Li Tian, Limeng Zhang, Zhihua Huang, Shujun Wei, Fan Song, Wanzhi Cai, Yanbi Yu, Hailin Yang, Hu Li
Summary: The study constructed a high-quality reference genome of Aphidius gifuensis, revealing significantly expanded gene families involved in metabolic processes, cell signal communication, and other functions, along with contracted olfactory receptors. This provides a solid foundation for future research on the molecular mechanisms of population decline and host-parasitoid relationship for parasitoid wasps.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Microbiology
Ignat V. Sonets, Nikita V. Dovidchenko, Sergey V. Ulianov, Maria S. Yarina, Stanislav I. Koshechkin, Sergey V. Razin, Larissa M. Krasnopolskaya, Alexander V. Tyakht
Summary: The complete genome sequence of G. lucidum strain 5.1 was obtained using high-throughput shotgun sequencing. The improved assembly process resulted in 12 chromosome-level scaffolds. Comprehensive annotation of the genome identified genes likely involved in polysaccharide biosynthesis. This study is important for elucidating the medicinal potential of Ganoderma species, discovering novel pharmaceutically valuable compounds, and understanding fungal genomic organization.
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
Biochemical Research Methods
Pingjing Li, Hong Liu, Jialiang Sun, Jianguo Lu, Jian Liu
Summary: In this study, HiBrowser, a browser for visualizing and analyzing Hi-C data and their associated genetic and epigenetic annotations, is developed. It offers flexible multi-omics navigation, novel multidimensional synchronization comparisons, and dynamic interaction system.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biochemical Research Methods
Kun Liu, Hong-Dong Li, Yaohang Li, Jun Wang, Jianxin Wang
Summary: In this study, we conducted a systematic comparison of twenty-six TAD callers, evaluating their performance in terms of TAD continuity, quality, and assessment. By considering multiple criteria, we provided a concise, comprehensive, and systematic framework for the detection and evaluation of TADs.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2023)
Article
Biochemistry & Molecular Biology
Yongdong Peng, Hong Li, Zhengzhu Liu, Chuansheng Zhang, Keqiang Li, Yuanfang Gong, Liying Geng, Jingjing Su, Xuemin Guan, Lei Liu, Ruihong Zhou, Ziya Zhao, Jianxu Guo, Qiqi Liang, Xianglong Li
Summary: The study utilized PacBio sequencing and chromosome structure capture technique to assemble the first high-quality genome of Arctic fox. The genome assembly revealed a high percentage of repeat sequences and provided insights into the genetic adaptations of the Arctic fox to extreme climate conditions. This assembled genome will not only facilitate future studies on genetic diversity and evolution in foxes and other canids, but also serve as an important resource for conservation of Arctic species.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Multidisciplinary Sciences
Zev N. Kronenberg, Arang Rhie, Sergey Koren, Gregory T. Concepcion, Paul Peluso, Katherine M. Munson, David Porubsky, Kristen Kuhn, Kathryn A. Mueller, Wai Yee Low, Stefan Hiendleder, Olivier Fedrigo, Ivan Liachko, Richard J. Hall, Adam M. Phillippy, Evan E. Eichler, John L. Williams, Timothy P. L. Smith, Erich D. Jarvis, Shawn T. Sullivan, Sarah B. Kingan
Summary: FALCON-Phase is a phasing tool that uses ultra-long-range Hi-C chromatin interaction data to extend phase blocks of partially-phased diploid assemblies to chromosome or scaffold scale. This method is accurate without parental data and performs better in samples with higher heterozygosity, achieving up to 97% accuracy for some species.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Dongna Ma, Zejun Guo, Qiansu Ding, Zhizhu Zhao, Zhijun Shen, Mingyue Wei, Changhao Gao, Ludan Zhang, Huan Li, Shan Zhang, Jing Li, Xueyi Zhu, Hai-Lei Zheng
Summary: In this study, a chromosome-level genome assembly of A. corniculatum was achieved by integrating PacBio long-read sequencing and Hi-C technology, revealing information on genome size, repetitive sequences, gene family evolution, expansion of genes related to metabolic pathways, and insights into the adaptation mechanisms of A. corniculatum in intertidal environments. The high-quality genome provides historical insights into genomic transformations supporting the survival of A. corniculatum in harsh intertidal habitats.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Genetics & Heredity
Chi Yang, Lu Ma, Donglai Xiao, Xiaoyu Liu, Xiaoling Jiang, Zhenghe Ying, Yanquan Lin
Summary: In this study, an improved draft genome sequence of S. latifolia was generated using Oxford Nanopore sequencing and Hi-C technique, providing a high coverage and quality assembly. The genome features, including repetitive sequences and protein-coding genes, were further analyzed, which will facilitate molecular elucidation, breeding, and evolutionary studies of S. latifolia.
G3-GENES GENOMES GENETICS
(2021)
Article
Genetics & Heredity
Jingjing Li, Haiyan Wang, Jianqing Zhu, Qi Yang, Yang Luan, Leming Shi, Jose Arturo Molina-Mora, Yuanting Zheng
Summary: This study successfully constructed a chromosome-level reference genome for S. montelus using Oxford Nanopore long-read sequencing, Illumina short-read sequencing, and Hi-C technology. The genome size was 581.44 Mb, with an expected size of 619.27 Mb, and approximately 90% of the bases could be mapped to 30 chromosomes. The study found that the ability of S. montelus to survive on toxic Aristolochia plants is associated with the expansion of the P450 gene family and positive selection on certain genes.
FRONTIERS IN GENETICS
(2023)
Article
Biodiversity Conservation
Euna Jo, Seung Jae Lee, Jeong-Hoon Kim, Steven J. Parker, Eunkyung Choi, Jinmu Kim, So-Ra Han, Tae-Jin Oh, Hyun Park
Summary: This study presents the chromosomal-level genome assembly of T. loennbergii, the first genome representative of the genus Trematomus. The genome assembly consists of 23 chromosomal-level scaffolds totaling 940 Mb, with 24,525 protein-coding genes annotated.
Article
Biochemical Research Methods
Chenxi Zhou, Shane A. McCarthy, Richard Durbin
Summary: YaHS is a user-friendly command-line tool that constructs chromosome-scale scaffolds from Hi-C data. It requires minimal input from users (an assembly file and an alignment file), can be run with a single-line command, and provides assembly results in multiple formats, enabling rapid and accurate construction of high-quality genome assemblies.
Article
Biology
Guoxin Cui, Yi Jin Liew, Migle K. Konciute, Ye Zhan, Shiou-Han Hung, Jana Thistle, Lucia Gastoldi, Sebastian Schmidt-Roach, Job Dekker, Manuel Aranda
Summary: This study investigates the effects of nitrogen limitation on symbiont cell proliferation and life stage transitions in coral-algal symbiosis, and identifies nitrogen availability as a major factor limiting symbiont density and life stage transitions.
Article
Evolutionary Biology
Lewis Stevens, Nicolas D. Moya, Robyn E. Tanny, Sophia B. Gibson, Alan Tracey, Huimin Na, Rojin Chitrakar, Job Dekker, Albertha J. M. Walhout, L. Ryan Baugh, Erik C. Andersen
Summary: This study constructed chromosome-level reference genomes for two strains of Caenorhabditis briggsae using high-coverage sequencing data. The comparison with the reference genome of C. elegans revealed substantial differences, including the presence of hyper-divergent haplotypes in the C. briggsae genome. The study also showed that selfing Caenorhabditis species have undergone more rearrangement, biasing previous estimates of rearrangement rate.
GENOME BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Maria Akopyan, Anna Tigano, Arne Jacobs, Aryn P. Wilder, Hannes Baumann, Nina O. Therkildsen
Summary: The study compares the recombination landscape and genome collinearity between two populations of Atlantic silverside. It finds higher recombination rates in females than males and restricted recombination to only the terminal ends of male chromosomes. Additionally, massive chromosomal inversions suppress recombination and coincide with highly differentiated genomic regions between locally adapted populations. Furthermore, the study identifies significantly higher recombination rates on chromosomes in the northern population.
Article
Multidisciplinary Sciences
Jacob T. Sanders, Rosela Golloshi, Priyojit Das, Yang Xu, Peyton H. Terry, Darrian G. Nash, Job Dekker, Rachel Patton McCord
Summary: This study investigates the effects of chromatin extension during volume changes using low-salt swelling and genome-wide chromosome conformation capture technology. The results show that global genome structure remains stable despite significant nuclear volume swelling. Extension of the local chromatin fiber leads to changes in contact probabilities, but loops, TADs, active and inactive compartments, and chromosome territories are maintained. This suggests that genome topology is robust to chromatin fiber extension and shape changes.
SCIENTIFIC REPORTS
(2022)
Article
Evolutionary Biology
Aryn P. Wilder, Olga Dudchenko, Caitlin Curry, Marisa Korody, Sheela P. Turbek, Mark Daly, Ann Misuraca, Gaojianyong Wang, Ruqayya Khan, David Weisz, Julie Fronczek, Erez Lieberman Aiden, Marlys L. Houck, Debra M. Shier, Oliver A. Ryder, Cynthia C. Steiner
Summary: High-quality reference genomes are essential for understanding population history and conserving biodiversity. In this study, a new genome assembly was generated for the federally endangered Pacific pocket mouse (PPM) using PacBio HiFi long reads, Omni-C and Hi-C data. The assembly revealed interesting features, such as a long heterochromatic region and variable heterozygosity across the genome. The study suggests recent inbreeding in a formerly large population. This reference genome will be valuable for future studies on outbreeding depression, inbreeding depression, and genetic load.
GENOME BIOLOGY AND EVOLUTION
(2022)
Article
Multidisciplinary Sciences
Daniel J. Emerson, Peiyao A. Zhao, Ashley L. Cook, R. Jordan Barnett, Kyle N. Klein, Dalila Saulebekova, Chunmin Ge, Linda Zhou, Zoltan Simandi, Miriam K. Minsk, Katelyn R. Titus, Weitao Wang, Wanfeng Gong, Di Zhang, Liyan Yang, Sergey V. Venev, Johan H. Gibcus, Hongbo Yang, Takayo Sasaki, Masato T. Kanemaki, Feng Yue, Job Dekker, Chun-Long Chen, David M. Gilbert, Jennifer E. Phillips-Cremins
Summary: This article reveals the determinants of replication origin positioning in the human genome. The study found that topologically associating domains and loops play crucial roles in the localization of replication initiation zones. By disrupting cohesin-mediated loop extrusion, the positioning of replication origins can be altered. These findings contribute to a better understanding of the mechanism of DNA replication.
Review
Biochemistry & Molecular Biology
Bastiaan Dekker, Job Dekker
Summary: Significant progress has been made in identifying the molecular machines involved in chromosome folding, such as condensins and topoisomerases, in recent years. The discovery of condensins generating chromatin loops through loop extrusion has greatly impacted and energized the field. Current understanding suggests that these machines and factors are regulated through cell cycle dependent expression, chromatin localization, post-translational modifications, and associations with other factors and the chromatin template. Although there are still unanswered questions about the regulation of condensins and topoisomerases, it is likely that many of these will be addressed in the future, given the pace of progress in the field of chromosome folding.
BIOCHEMICAL JOURNAL
(2022)
Article
Cell Biology
Yu Liu, Job Dekker
Summary: The cohesin complex plays a crucial role in sister-chromatid cohesion and chromatin looping, but its mechanisms vary depending on the genomic context.
NATURE CELL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Jennifer Zagelbaum, Allana Schooley, Junfei Zhao, Benjamin R. Schrank, Elsa Callen, Shan Zha, Max E. Gottesman, Andre Nussenzweig, Raul Rabadan, Job Dekker, Jean Gautier
Summary: Research shows that nuclear actin movements are involved in clustering DNA double-strand breaks (DSBs) for homology-directed repair. This study explores the three-dimensional reorganization of the genome after DNA damage and examines the role of the nuclear WASP-ARP2/3-actin pathway in chromatin topology changes during pathological repair. The results indicate that DNA damage induces genome-wide chromatin compartment flips mediated by ARP2/3, leading to enrichment of open, A compartments. Additionally, DSB interactions promote aberrant actin-dependent rearrangements within and between chromosomes. This work demonstrates that nuclear actin assembly orchestrates DSB clustering for repair while also impacting genome architecture and translocation frequency.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Anne-Laure Valton, Sergey V. Venev, Barbara Mair, Eraj Shafiq Khokhar, Amy H. Y. Tong, Matej Usaj, Katherine Chan, Athma A. Pai, Jason Moffat, Job Dekker
Summary: Cohesin-mediated loop extrusion is blocked at specific cis-elements, resulting in patterns of loops and domain boundaries along chromosomes. Transcription termination sites of active genes form cohesin-dependent boundaries without accumulating cohesin, while start sites of transcriptionally active genes form cohesin-bound boundaries. Disrupting the traffic pattern of cohesin by removing CTCF renders cells sensitive to knockout of genes involved in transcription initiation.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
George Spracklin, Nezar Abdennur, Maxim Imakaev, Neil Chowdhury, Sriharsa Pradhan, Leonid A. A. Mirny, Job Dekker
Summary: In this study, the researchers profiled long-range contact frequencies in HCT116 colon cancer cells and identified three silent chromatin states. They found that heterochromatin marked by H3K9me3, HP1 alpha, and HP1 beta showed strong compartmentalization. Their findings also showed that disruption of DNA methyltransferase activity altered genome compartmentalization, leading to changes in chromatin state and chromosome organization.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2023)
Correction
Biochemistry & Molecular Biology
Jennifer Zagelbaum, Allana Schooley, Junfei Zhao, Benjamin R. Schrank, Elsa Callen, Shan Zha, Max E. Gottesman, Andre Nussenzweig, Raul Rabadan, Job Dekker, Jean Gautier
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2023)
Article
Biology
Coral Y. Zhou, Bastiaan Dekker, Ziyuan Liu, Hilda Cabrera, Joel Ryan, Job Dekker, Rebecca Heald
Summary: This study reveals that the size of mitotic chromosomes is controlled by spatially and temporally distinct developmental cues. The scaling of mitotic chromosomes involves mechanisms different from other subcellular structures such as spindles and nuclei. It is regulated by factors such as cell, spindle and nuclear size, as well as the nuclear-cytoplasmic ratio and importin alpha. Additionally, the shrinking of mitotic chromosomes during embryogenesis is attributed to decreased recruitment of condensin I and rearrangement of DNA loop architecture.
Article
Biochemistry & Molecular Biology
Job Dekker, Frank Alber, Sarah Aufmkolk, Brian J. Beliveau, Benoit G. Bruneau, Andrew S. Belmont, Lacramioara Bintu, Alistair Boettiger, Riccardo Calandrelli, Christine M. Disteche, David M. Gilbert, Thomas Gregor, Anders S. Hansen, Bo Huang, Danwei Huangfu, Reza Kalhor, Christina S. Leslie, Wenbo Li, Yun Li, Jian Ma, William S. Noble, Peter J. Park, Jennifer E. Phillips-Cremins, Katherine S. Pollard, Susanne M. Rafelski, Bing Ren, Yijun Ruan, Yaron Shav-Tal, Yin Shen, Jay Shendure, Xiaokun Shu, Caterina Strambio-De-Castillia, Anastassiia Vertii, Huaiying Zhang, Sheng Zhong
Summary: The four-dimensional nucleome (4DN) consortium investigates the structure and temporal-spatial characteristics of the genome and nucleus. The consortium has made significant progress in mapping genome folding, identifying nuclear components and bodies, and imaging nuclear organization. The generated datasets have been used to develop computational models that reveal connections between genome structure and function. Future aims include studying dynamics of nuclear architecture, understanding cis-determinants and trans-modulators of genome organization, exploring functional consequences of changes in regulators, and developing predictive models
Article
Evolutionary Biology
Asako Y. Chaille, Robert C. Lacy, Andrea S. Putnam, Jamie L. Toste, Aryn P. Wilder, Jamie A. Ivy
Summary: The integration of empirical kinships into the genetic management of ex situ populations can impact genetic summary statistics and highlights the importance of understanding the scale of molecular kinships. This study focuses on Baer's pochard and provides guidance on incorporating empirical kinships into population management.
JOURNAL OF HEREDITY
(2023)
