Review
Biochemical Research Methods
Venket Raghavan, Louis Kraft, Fantin Mesny, Linda Rigerte
Summary: A transcriptome constructed from short-read RNA sequencing is a proxy catalog of protein-coding genes. De novo assembly and annotation of the transcriptome can be challenging due to the lack of standardized workflows and authoritative literature.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Ramon E. Rivera-Vicens, Catalina A. Garcia-Escudero, Nicola Conci, Michael Eitel, Gert Woerheide
Summary: The use of RNA sequencing and de novo transcriptome assembly is crucial for ecological and evolutionary studies, especially for nonmodel organisms lacking genome information. A multi-assembler approach, followed by a reduction step, is often employed to improve the assembly quality. TransPi is a comprehensive pipeline for de novo transcriptome assembly that achieves higher completeness percentages and reduces duplication rates compared to single assembler approaches. It is easy to configure and can be seamlessly deployed using Conda, Docker, and Singularity.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Genetics & Heredity
Mohammed Bakkali, Ruben Martin-Blazquez, Mercedes Ruiz-Estevez, Manuel A. Garrido-Ramos
Summary: The sporophyte transcriptome of Killarney fern was sequenced, revealing the species' genome characteristics and providing important data for evolutionary studies. The analysis offered insights into genes involved in key functions and genetic control of plant development, stress response, and transcription factors. Overall, this study represents a significant step towards understanding gene expression in ferns and land plants.
Article
Biochemical Research Methods
Timothy R. Fallon, Tereza Calounova, Martin Mokrejs, Jing-Ke Weng, Tomas Pluskal
Summary: transXpress is a tool that simplifies the processing of RNA-seq data for de novo transcriptome assembly and annotation of non-model organisms, supporting parallel computing and producing standardized output files.
BMC BIOINFORMATICS
(2023)
Article
Horticulture
Juan Pacheco, Santiago Vilanova, Ruben Grillo-Risco, Francisco Garcia-Garcia, Jaime Prohens, Pietro Gramazio
Summary: This study conducted genomic and transcriptomic analyses of purple-fruited and orange-fruited tree tomato varieties, identifying a wealth of genetic information and variations. The results provide valuable reference data for genetic improvement of the tree tomato.
Article
Agronomy
Tae-Heon Kim, Young-Mi Yoon, Jin-Cheon Park, Jong-Ho Park, Kyong-Ho Kim, Yang-Kil Kim, Jae-Han Son, Tae-Il Park
Summary: This study used transcriptome sequencing to investigate the seedling stage of oat and developed 30 dCAPS markers, which are important for oat genetic analysis, cultivar identification, and breeders' rights protection.
Article
Multidisciplinary Sciences
Andrea Chiocchio, Pietro Libro, Giuseppe Martino, Roberta Bisconti, Tiziana Castrignano, Daniele Canestrelli
Summary: This study reported the first de novo brain transcriptome of Apennine yellow-bellied toad, which will serve as a valuable resource for further research on the genomic underpinnings of behavioral variation in amphibians.
Article
Agriculture, Dairy & Animal Science
Ju Qiu, Rui Guo, Yidan Li, Yuyao Zhang, Kangsheng Jia, Yinghu Lei, Linsen Zan, Anning Li
Summary: The golden takin, an endemic ruminant species, has been listed as endangered and vulnerable. This study used RNA sequencing and microsatellite prediction to assess the transcriptome of its muscles, providing valuable genetic information for conservation efforts and further studies on takins.
Article
Plant Sciences
Wei Long, Xiaohua Yao, Kailiang Wang, Yu Sheng, Leyan Lv
Summary: In this study, the gene expression and global gene expression profiles during Camellia oleifera seed germination were analyzed using transcriptome sequencing. Differentially expressed genes were identified, indicating the role of cotyledons in seed germination and seedling growth. This study will contribute to the breeding and cultivation of C. oleifera.
Article
Multidisciplinary Sciences
Xu Shi, Xiao Wang, Andrew F. Neuwald, Leena Halakivi-Clarke, Robert Clarke, Jianhua Xuan
Summary: BayesDenovo addresses the challenge of de novo transcriptome assembly by accurately reconstructing splicing graphs using a read-guided and Bayesian strategy, achieving higher accuracy and reducing false positives, especially for alternatively spliced genes and highly/lowly expressed transcripts. Additionally, it is more robust on multiple replicates and can identify phenotype-specific transcripts associated with breast cancer recurrence.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Qiuyu Sun, Jie Liu, Keyu Zhang, Chong Huang, Leifu Li, Jiayu Dong, Yong Luo, Zhanhong Ma
Summary: In this study, high-quality cDNA sequence reads of Southern corn rust disease were obtained using Illumina sequencing technology, resulting in the identification of a large number of potential SSRs. Nine polymorphic SSR markers were developed to evaluate the genetic diversity and population structure of 96 isolates from Guangdong Province in China, showing dominant clonal reproduction of P. polysora. The results provide valuable information for molecular genetic analysis of P. polysora and related species.
SCIENTIFIC REPORTS
(2021)
Article
Biotechnology & Applied Microbiology
Hongjie Wang, Yongqiang Wu, Yong He, Guoyu Li, Lichao Ma, Shuo Li, Jianwei Huang, Guofeng Yang
Summary: This study successfully generated a high-quality de novo assembly of the white clover genome at the chromosomal level using PacBio Hi-Fi sequencing. The annotated genome provides important resources for molecular breeding and evolution research of white clover and other forage crops.
Article
Cell Biology
Paul C. Marcogliese, Samantha L. Deal, Jonathan Andrews, J. Michael Harnish, V. Hemanjani Bhavana, Hillary K. Graves, Sharayu Jangam, Xi Luo, Ning Liu, Danqing Bei, Yu-Hsin Chao, Brooke Hull, Pei-Tseng Lee, Hongling Pan, Pradnya Bhadane, Mei-Chu Huang, Colleen M. Longley, Hsiao-Tuan Chao, Hyung-lok Chung, Nele A. Haelterman, Oguz Kanca, Sathiya N. Manivannan, Linda Z. Rossetti, Ryan J. German, Amanda Gerard, Eva Maria Christina Schwaibold, Sarah Fehr, Renzo Guerrini, Annalisa Vetro, Eleina England, Chaya N. Murali, Tahsin Stefan Barakat, Marieke F. van Dooren, Martina Wilke, Marjon van Slegtenhorst, Gaetan Lesca, Isabelle Sabatier, Nicolas Chatron, Catherine A. Brownstein, Jill A. Madden, Pankaj B. Agrawal, Boris Keren, Thomas Courtin, Laurence Perrin, Melanie Brugger, Timo Roser, Steffen Leiz, Frederic Tran Mau-Them, Julian Delanne, Elena Sukarova-Angelovska, Slavica Trajkova, Erik Rosenhahn, Vincent Strehlow, Konrad Platzer, Roberto Keller, Lisa Pavinato, Alfredo Brusco, Jill A. Rosenfeld, Ronit Marom, Michael F. Wangler, Shinya Yamamoto
Summary: This study functionally tested the effects of missense mutations in autism spectrum disorder (ASD) using fruit flies and found that 38% of the variants caused functional alterations. Additionally, GLRA2 was identified as the cause of neurodevelopmental phenotypes in 13 previously undiagnosed subjects, going beyond ASD. Functional characterization of variants in ASD candidate genes points to conserved neurobiological mechanisms and facilitates gene discovery for rare neurodevelopmental diseases.
Article
Biochemistry & Molecular Biology
Matin Miryeganeh, Hidetoshi Saze
Summary: Mangrove trees, with their high adaptability to difficult coastal conditions, serve as an interesting model system for understanding stress tolerance in plants. This study utilized RNA-Seq to characterize the leaf transcriptome of the Bruguiera gymnorhiza species and compared gene expression profiles between populations growing under different levels of stress, providing valuable insights into plant adaptations. Genes related to salt and osmotic stress showed elevated expression levels in trees growing in high salinity conditions, suggesting potential targets for future research on salt resistance in mangroves and other woody plants.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Genetics & Heredity
Javier Cordoba, Emilie Perez, Mick Van Vlierberghe, Amandine R. Bertrand, Valerian Lupo, Pierre Cardol, Denis Baurain
Summary: Euglena gracilis, a photosynthetic microeukaryote, has a complex gene ancestry and gene regulation in euglenozoans is not primarily controlled at the transcriptional level, as revealed in transcriptome analysis. The evolutionary history of E. gracilis involves a convoluted process with more than two partners, ruling out sequence contamination as a possible explanation for the mixed gene ancestry observed.
Article
Plant Sciences
Yazhini Velappan, Tinashe G. Chabikwa, John A. Considine, Patricia Agudelo-Romero, Christine H. Foyer, Santiago Signorelli, Michael J. Considine
Summary: There is a disconnect between the physiology and transcriptome of grapevine buds during dormancy, and ABA-related gene expression and photoperiod play important roles.
JOURNAL OF EXPERIMENTAL BOTANY
(2022)
Article
Plant Sciences
Suyash B. Patil, Francois F. Barbier, Jinfeng Zhao, Syed A. Zafar, Muhammad Uzair, Yinglu Sun, Jingjing Fang, Maria-Dolores Perez-Garcia, Jessica Bertheloot, Soulaiman Sakr, Franziska Fichtner, Tinashe G. Chabikwa, Shoujiang Yuan, Christine A. Beveridge, Xueyong Li
Summary: Sucrose promotes shoot branching by antagonizing the inhibitory effect of the plant hormone strigolactone (SL) through affecting key components of SL signaling pathway. This study reveals the central role played by SLs in regulating plant architecture in response to nutrients, with sucrose inhibiting SL response.
Review
Plant Sciences
Lucky Paudel, Stephanie Kerr, Peter Prentis, Milos Tanurdzic, Alexie Papanicolaou, Jonathan M. Plett, Christopher Cazzonelli
Summary: Multipartite viral vectors are a simple, inexpensive, and effective biotechnological tool for transiently manipulating gene expression in plants. By manipulating carotenoid biosynthesis, these vectors have advanced our understanding of carotenoid regulation and accumulation. This technology is important for characterizing gene function, accelerating fruit tree breeding programs, and developing carotenoid-enriched plant products.
HORTICULTURE RESEARCH
(2022)
Review
Biochemistry & Molecular Biology
Yan Zhang, Haylie Andrews, Judith Eglitis-Sexton, Ian Godwin, Milos Tanurdzic, Peter A. Crisp
Summary: Epigenomics is a broad field of study that investigates the impact of chromatin states, chromatin modifications, and epigenetic inheritance on gene regulation. It plays a crucial role in improving crop performance by enhancing our understanding of complex crop genomes and identifying heritable epialleles that control crop traits independent of genotype.
EMERGING TOPICS IN LIFE SCIENCES
(2022)
Article
Plant Sciences
Marcos H. Vinde, Da Cao, Rebecca J. Chesterfield, Kaori Yoneyama, Yosephine Gumulya, Raine E. S. Thomson, Tebogo Matila, Birgitta E. Ebert, Christine A. Beveridge, Claudia E. Vickers, Elizabeth M. J. Gillam
Summary: This study explores the functional evolution of the highly conserved CYP711A P450 family and reveals their role in the diversification of the phytohormone strigolactone.
Article
Plant Sciences
Da Cao, Tinashe Chabikwa, Francois Barbier, Elizabeth A. Dun, Franziska Fichtner, Lili Dong, Stephanie C. Kerr, Christine A. Beveridge
Summary: Apical dominance, the inhibition of shoot branching by the growing shoot tip of plants, was originally believed to be mediated by auxin. Recent studies have shown the importance of shoot tip sink strength and the role of sugars in promoting branching. This study explores the relative roles of auxin and sugars in apical dominance, suggesting a model that integrates auxin, sucrose, strigolactones, cytokinins, and gibberellins in regulating bud growth.
Review
Plant Sciences
Christine A. Beveridge, Catherine Rameau, Akila Wijerathna-Yapa
Summary: The importance of multidisciplinary and multispecies approaches is demonstrated through the review of apical dominance and shoot branching research. Different research methods have revealed the physiological process of apical dominance and the discovery of novel plant hormones. Further exploration of the whole network is needed to address challenges like sustainable food supply and climate change.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Article
Plant Sciences
Muhammad Umair Ahsan, Francois Barbier, Alice Hayward, Rosanna Powell, Helen Hofman, Siegrid Carola Parfitt, John Wilkie, Christine Anne Beveridge, Neena Mitter
Summary: This study investigated the potential molecular cues regulating the yearly flowering cycle in avocado for two consecutive crop cycles. Homologues of flowering-related genes were identified and assessed for their expression profiles. The study found that avocado homologues of known floral genes were upregulated at the typical time of floral induction.
Article
Plant Sciences
Alicia M. Hellens, Tinashe G. Chabikwa, Franziska Fichtner, Philip B. Brewer, Christine A. Beveridge
Summary: The study reveals a specific regulation of glucosinolate biosynthesis genes by strigolactones in Arabidopsis, suggesting their involvement in stress and shoot branching responses. It also provides evidence for non-auxin-mediated feedback on strigolactone biosynthesis and discusses its link to sugar signaling.
Article
Multidisciplinary Sciences
Alicia M. M. Hellens, Jazmine L. L. Humphreys, Franziska Fichtner, Milos Tanurdzic, Christine A. A. Beveridge, Francois F. Barbier
Summary: bZIP11 is a transcription factor in plants that is activated under low energy conditions and plays a crucial role in adaptability to starvation. Through ATAC-seq analysis, it was found that chromatin patterning changes induced by bZIP11 involve approximately 10,000 differentially accessible regions, corresponding to over 8,420 genes. This study provides insight into how bZIP11 regulates the genome at the chromatin level and demonstrates the impact of a single transcription factor on the entire plant genome.
Review
Plant Sciences
Francois Barbier, Franziska Fichtner, Christine Beveridge
Summary: This review summarizes recent progress in understanding the mechanisms by which the strigolactone pathway integrates sugar, metabolite, and nutrient signals. The study demonstrates that strigolactones and MAX2-dependent signaling play pivotal roles in mediating the effects of nutritional and metabolic cues on plant development and metabolism. Additionally, the authors discuss the implications of these interactions for plant evolution and adaptation to the environment. Overall, this review provides new insights into the role of strigolactone signaling in integrating nutritional and metabolic status and its consequences for plant development and architecture.