Review
Agricultural Engineering
Raya Bhattacharjya, Archana Tiwari, Thomas Kiran Marella, Hina Bansal, Shireesh Srivastava
Summary: Diatoms are a diverse group of eukaryotic plankton known for their role in regulating the earth's biogeochemical cycles and maintaining marine ecosystems. The advent of multidisciplinary omics approaches has transformed our understanding of their genetic toolkit, ecophysiology, and metabolic adaptability. Advanced bioinformatics tools and genome-scale mathematical modeling have been instrumental in overcoming genetic bottlenecks in microbial and diatom exploration.
BIORESOURCE TECHNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Jiankai Wei, Penghui Liu, Fuyun Liu, An Jiang, Jinghan Qiao, Zhongqi Pu, Bingrou Wang, Jin Zhang, Dongning Jia, Yuli Li, Shi Wang, Bo Dong
Summary: Evolutionary developmental biology (evo-devo) is an interdisciplinary field that aims to understand the origin and evolution of developmental processes in different animals. EDomics is a comparative multi-omics database that provides comprehensive genomic, transcriptomic, and single-cell data for 40 representative species. It offers valuable resources and customized datasets for evo-devo research, allowing researchers to decipher the history of developmental evolution across the tree of life.
NUCLEIC ACIDS RESEARCH
(2023)
Review
Plant Sciences
Milan Jockovic, Sinisa Jocic, Sandra Cvejic, Ana Marjanovic-Jeromela, Jelena Jockovic, Aleksandra Radanovic, Dragana Miladinovic
Summary: The review emphasizes the importance of systematic approaches to sunflower breeding, highlighting the lack of desirable genetic variation in the field. By integrating information from various omics technologies, a comprehensive understanding of the molecular mechanisms in sunflower can be achieved, leading to more efficient breeding strategies.
Article
Food Science & Technology
Kexue Chen, Xingya Zhou, Jianxin Zhao, R. Paul Ross, Catherine Stanton, Wei Chen, Bo Yang
Summary: This study explores the genetic diversity and functional gene features of L. johnsonii through comparative genomic analysis. The results show that L. johnsonii can be classified into two phylogenetic clusters, with differences in carbohydrate utilization genes, bacteriocin operon, extracellular polysaccharide gene cluster, and bile salt hydrolase encoding genes between the clusters.
Review
Plant Sciences
Zhou Zhou, Lei Zhang, Jing Shu, Mengyu Wang, Han Li, Huairui Shu, Xiaoyun Wang, Qinghua Sun, Shizhong Zhang
Summary: This paper describes the concepts and methods of breeding rootstocks with a high-quality dwarf-type root system in the apple industry. It aims to achieve precise breeding by combining existing resources and molecular breeding, and by utilizing wild resources. The paper also summarizes the challenges in the breeding process and elaborates on the genetic mechanisms regulating root diversity.
Review
Nutrition & Dietetics
Omar Ramos-Lopez, J. Alfredo Martinez, Fermin Milagro
Summary: The combination of multiple omics approaches provides a comprehensive view of human diseases and their underlying molecular and physiological events, aiding in the understanding of metabolic phenotypes and disease associations, guiding dietary treatments and prognosis. However, challenges include ethical and regulatory issues, lack of reliable and reproducible results, high cost and high-dimensional data analysis.
Article
Environmental Sciences
Maya E. Natnan, Chen-Fei Low, Chou-Min Chong, Hamidun Bunawan, Syarul N. Baharum
Summary: The increasing demand for fish protein has led to a rise in fish production through aquaculture and wild capture. Pathogen infections in hatcheries and grow-out ponds have resulted in reduced productivity and economic losses for farmers. Utilizing omics datasets and systems biology approaches can help scientists understand complex host-pathogen interactions and identify new targets for combating diseases in aquaculture. Various omics approaches such as genomics, transcriptomics, proteomics, and metabolomics are valuable tools in developing treatment and prevention strategies to address aquaculture diseases caused by microbial infections.
FRONTIERS IN MARINE SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Zhiquan Yang, Shengbo Wang, Lulu Wei, Yiming Huang, Dongxu Liu, Yupeng Jia, Chengfang Luo, Yuchen Lin, Congyuan Liang, Yue Hu, Cheng Dai, Liang Guo, Yongming Zhou, Qing-Yong Yang
Summary: In the post-genome-wide association study era, multi-omics techniques have great potential for candidate gene mining and functional genomics research. However, the lack of effective data integration and analysis platforms hinders the widespread application of these techniques in rapeseed. This study reports a comprehensive rapeseed multi-omics database (BnIR) that provides datasets of six omics, as well as variation-gene expression-phenotype associations and various search and analysis tools. Two case studies demonstrate the power of BnIR in mining candidate genes and analyzing their regulatory mechanisms.
Review
Biochemistry & Molecular Biology
Huan Li, Muhammad Tahir ul Qamar, Li Yang, Junchao Liang, Jun You, Linhai Wang
Summary: Sesame is an important traditional oil crop with high economic and nutritional value. Advances in high throughput sequencing techniques and bioinformatical methods have led to rapid developments in genomics, methylomics, transcriptomics, proteomics, and metabonomics studies of sesame.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Multidisciplinary Sciences
Marty Kardos, Ellie E. Armstrong, Sarah W. Fitzpatrick, Samantha Hauser, Philip W. Hedrick, Joshua M. Miller, David A. Tallmon, W. Chris Funk
Summary: Conserving genome-wide genetic variation is generally the best approach to prevent inbreeding depression and loss of adaptive potential, while focusing on functional genetic variation is not always feasible and can often lead to misleading and counterproductive outcomes.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Roman Martin, Hagen Dressler, Georges Hattab, Thomas Hackl, Matthias G. Fischer, Dominik Heider
Summary: MOSGA 2 is an accessible and easy-to-use analysis tool for eukaryotic genome annotations, developed with advanced analyses to improve annotation quality. By validating and ensuring genome data quality, integrating comparative genomics methods, and extending established applications, MOSGA 2 provides a broader genomic view and comprehensive genome analysis.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Biochemistry & Molecular Biology
Joao C. Sequeira, Miguel Rocha, M. Madalena Alves, Andreia F. Salvador
Summary: Omics and meta-omics technologies provide powerful approaches to explore microbial functions. However, the analysis of large and complex datasets is often challenging. In this study, three novel bioinformatics tools were developed to facilitate functional annotation and metabolic pathway analysis. These tools are user-friendly and valuable resources for interpreting microbial activities in nature and biotechnological processes.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Public, Environmental & Occupational Health
Giovanna Elisa Calabro, Francesco Andrea Causio, Denise Pires Marafon, Michele Sassano, Francesca Moccia, Roberta Pastorino, Stefania Boccia
Summary: Advancements in genomics have implications for public health and citizens' education is crucial for informed decision-making. Our survey found a widespread interest in genetic testing among Italian citizens, but also a lack of knowledge and uncertainties about associated risks. There is an urgent need for educational tools to improve literacy and engagement in this field.
EUROPEAN JOURNAL OF PUBLIC HEALTH
(2023)
Review
Biochemistry & Molecular Biology
Muhammad Naeem, Zeeshan Ali, Anzal Khan, Sami-Ul-Allah, Hassan Javed Chaudhary, Javeria Ashraf, Faheem Shahzad Baloch
Summary: Rice, as a crucial food crop for half of the world population, has a small genome size and its whole sequenced genome has proven to be valuable for genome research. The sequenced rice genome provides insights into molecular biology, transcriptomics, and genetic variability, which are essential for improving yield, quality, and stress resistance in rice crop.
MOLECULAR BIOLOGY REPORTS
(2022)
Article
Biochemistry & Molecular Biology
Rui-Sen Lu, Ke Hu, Feng-Jiao Zhang, Xiao-Qin Sun, Min Chen, Yan-Mei Zhang
Summary: China is an important domestication center of Dioscorea alata. However, the genetic variations among Chinese accessions and the genomic resources available for molecular breeding are limited. In this study, the first pan-plastome of D. alata was generated based on Chinese and African accessions, revealing the genetic variations, plastome evolution, and phylogenetic relationships. This study not only identified the genetic variations among Chinese D. alata accessions, but also provided the necessary groundwork for molecular-assisted breeding and industrial utilization of this species.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Plant Sciences
Satish Kumar, Chris Kirk, Cecilia Hong Deng, Claudia Wiedow, Mengfan Qin, Richard Espley, Jun Wu, Lester Brewer
HORTICULTURE RESEARCH
(2019)
Article
Forestry
Vincent G. M. Bus, Reiny W. A. Scheper, Monika Walter, Rebecca E. Campbell, Biff Kitson, Lauren Turner, Brent M. Fisher, Sarah L. Johnston, Chen Wu, Cecilia H. Deng, Gagandeep Singla, Deepa Bowatte, Linley K. Jesson, Duncan I. Hedderley, Richard K. Volz, David Chagne, Susan E. Gardiner
TREE GENETICS & GENOMES
(2019)
Article
Plant Sciences
David Chagne, Stijn Vanderzande, Chris Kirk, Natalie Profitt, Rosemary Weskett, Susan E. Gardiner, Cameron P. Peace, Richard K. Volz, Nahla Bassil
HORTICULTURE RESEARCH
(2019)
Article
Plant Sciences
S. M. Pilkington, J. Tahir, E. Hilario, S. E. Gardiner, D. Chagne, A. Catanach, J. McCallum, L. Jesson, L. G. Fraser, M. A. McNeilage, C. Deng, R. N. Crowhurst, P. M. Datson, Q. Zhang
Review
Plant Sciences
Cameron P. Peace, Luca Bianco, Michela Troggio, Eric van de Weg, Nicholas P. Howard, Amandine Cornille, Charles-Eric Durel, Sean Myles, Zoe Migicovsky, Robert J. Schaffer, Evelyne Costes, Gennaro Fazio, Hisayo Yamane, Steve van Nocker, Chris Gottschalk, Fabrizio Costa, David Chagne, Xinzhong Zhang, Andrea Patocchi, Susan E. Gardiner, Craig Hardner, Satish Kumar, Francois Laurens, Etienne Bucher, Dorrie Main, Sook Jung, Stijn Vanderzande
HORTICULTURE RESEARCH
(2019)
Article
Multidisciplinary Sciences
Satish Kumar, Chris Kirk, Cecilia Hong Deng, Angela Shirtliff, Claudia Wiedow, Mengfan Qin, Jun Wu, Lester Brewer
SCIENTIFIC REPORTS
(2019)
Article
Plant Sciences
Jibran Tahir, Stephen Hoyte, Heather Bassett, Cyril Brendolise, Abhishek Chatterjee, Kerry Templeton, Cecilia Deng, Ross Crowhurst, Mirco Montefiori, Ed Morgan, Andrew Wotton, Keith Funnell, Claudia Wiedow, Mareike Knaebel, Duncan Hedderley, Joel Vanneste, John McCallum, Kirsten Hoeata, Amardeep Nath, David Chagne, Luis Gea, Susan E. Gardiner
HORTICULTURE RESEARCH
(2019)
Article
Plant Sciences
Satish Kumar, Cecilia Hong Deng, Martin Hunt, Chris Kirk, Claudia Wiedow, Daryl Rowan, Jun Wu, Lester Brewer
Summary: ROH analysis of different varieties of pear materials revealed genomic regions associated with fruit traits and self-incompatibility traits, suggesting that systematic breeding of European pears may have started earlier than Asian pears. ROH analysis provides a new tool for managing hybrids in gene-banks of self-incompatible plant species and offers a complementary strategy to unravel the genetic architecture of complex traits.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Genetics & Heredity
Elizabeth Popowski, Susan J. Thomson, Mareika Knabel, Jibran Tahir, Ross N. Crowhurst, Marcus Davy, Toshi M. Foster, Robert J. Schaffer, D. Stuart Tustin, Andrew C. Allan, John McCallum, David Chagne
Summary: Commercially grown kiwifruit have different genomes, and using molecular resources can speed up breeding for green kiwifruit, through methods like marker-assisted selection. Additionally, a high-density linkage map constructed through genotyping-by-sequence successfully identified quantitative trait loci in hexaploid kiwifruit.
G3-GENES GENOMES GENETICS
(2021)
Article
Plant Sciences
Hilary S. Ireland, Chen Wu, Cecilia H. Deng, Elena Hilario, Ali Saei, Sylvia Erasmuson, Ross N. Crowhurst, Karine M. David, Robert J. Schaffer, David Chagne
Summary: Gillenia, a species within the Rosaceae family, exhibits ancestral features and can be used as a 'rosetta stone' for translational science within the family. Analysis of its genome has led to improved understanding of the ancestral genome of Rosaceae and dynamics related to growth and reproduction. Gillenia can serve as a negative control for studying fleshy fruit development within the Rosaceae family.
HORTICULTURE RESEARCH
(2021)
Article
Plant Sciences
Giulia Pasqualetto, Luisa Palmieri, Stefan Martens, Vincent G. M. Bus, David Chagne, Claudia Wiedow, Mickael A. Malnoy, Susan E. Gardiner
Summary: Apple and pear are economically important fruit crops known for their unique qualities. This research utilized comparative genomic approaches to identify genetic differences and metabolite patterns, validating the effectiveness of three marker types in detecting hybridity between apple and pear. The findings will enhance breeding of new tree fruit crops, benefiting producers and consumers through marker assisted selection of desired traits between pear and apple.
HORTICULTURE RESEARCH
(2023)
Article
Plant Sciences
Simon Miranda, Stefano Piazza, Floriana Nuzzo, Mingai Li, Jorge Lagreze, Axel Mithoefer, Alessandro Cestaro, Danuse Tarkowska, Richard Espley, Andrew Dare, Mickael Malnoy, Stefan Martens
Summary: The effects of targeting the key gene MdPGT1 involved in phloridzin biosynthesis in apple using conventional transgenesis and CRISPR/Cas9-mediated genome editing were simultaneously assessed. Knockdown lines showed impaired growth and leaf morphology, while genome-edited lines exhibited normal growth despite reduced phloridzin levels. Transcriptomic and metabolic analyses revealed regulated genes involved in phenylpropanoid and flavonoid pathways. Phytohormone profiling demonstrated differential modulation, with increased salicylic and jasmonic acid levels in dwarf lines and no correlation between auxin and ABA with growth phenotype.
Article
Plant Sciences
Ling Hu, Jennifer A. Tate, Susan E. Gardiner, Marion MacKay
Summary: Polyploidy is common in Rhododendron genus, posing challenges to taxon recognition and conservation assessments. This study investigated the distribution of polyploidy in different subgenera of Rhododendron based on literature review and flow cytometry analysis. Specifically, the ploidy levels of 47 taxa in subsection Maddenia were estimated, revealing a predominantly diploid state with some taxa exhibiting high ploidy variation. This research sheds light on taxonomic complexity, ploidy variation, and their relevance to biodiversity conservation.
Article
Plant Sciences
Davide Bianchi, Valentina Ricciardi, Carola Pozzoli, Daniele Grossi, Leila Caramanico, Massimo Pindo, Erika Stefani, Alessandro Cestaro, Lucio Brancadoro, Gabriella De Lorenzis
Summary: The response of grapevines to drought is influenced by the interaction between the scion variety and the rootstock genotype. Under severe water deficit conditions, the rootstock genotype has a greater impact on gas exchange and stem water potential. The 1103P shows avoidance behavior, while the 101-14MGt exhibits a tolerance strategy. Transcriptomic analysis reveals that most differentially expressed genes are detected in roots, with a core set of genes related to the root response to drought being unaffected by genotype or grafting.
