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
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
Biology
Huapu Chen, Xiaomeng Li, Yaorong Wang, Chunhua Zhu, Hai Huang, Wei Yang, Guangli Li
Summary: Transcriptomic analysis was performed on Betta splendens to generate genetic data for developing polymorphic SSR markers and identifying functional genes. The data obtained not only enriched genetic information but also effectively facilitated the development of SSR markers, accelerating further studies on genetic variation, evolution, comparative genomics, linkage mapping, and molecular breeding in B. splendens.
Article
Multidisciplinary Sciences
Puspendu Sardar, Vladimir Sustr, Alica Chronakova, Frantisek Lorenc, Lucie Faktorova
Summary: In this study, the transcriptome of a tropical millipede was analyzed to explore the composition and function of its gut microbiota. It was found that the microbiota played a crucial role in essential amino acid biosynthesis, short-chain fatty acid metabolism, and fermentation in the millipede holobiont.
SCIENTIFIC REPORTS
(2022)
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
Hitomi Takei, Kenta Shirasawa, Kosuke Kuwabara, Atsushi Toyoda, Yuma Matsuzawa, Shinji Iioka, Tohru Ariizumi
Summary: This research successfully constructed high-quality genome assemblies of two ancestral tomato species, 'LA1670' and 'LA1673', predict a large number of protein-coding genes and validated them using transcriptome data, providing valuable resources for studying tomato domestication and breeding at a genome-scale level.
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
Virology
Zhuozhuang Lu, Yongjin Wang, Xiaohui Zou, Tao Hung
Summary: In this study, the transcriptome of fowl adenovirus 4 (FAdV-4) was analyzed using deep sequencing. 39 novel open reading frames (ORFs) and 18 viral promoters and 15 polyadenylation signals were identified. These findings provide a foundation for studying viral gene function, virulence, and evolution.
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
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
Biotechnology & Applied Microbiology
Mary Luz Yaya Lancheros, Krishan Mohan Rai, Vimal Kumar Balasubramanian, Lavanya Dampanaboina, Venugopal Mendu, Wilson Teran
Summary: This study presents the first de novo transcriptome of xylem-related genes in a commercially important tropical timber species, providing a valuable resource for both basic and breeding studies.
Article
Biochemistry & Molecular Biology
Dongshunyi Li, Jun Ding, Ziv Bar-Joseph
Summary: UNIFAN is a neural network method that simultaneously clusters and annotates cells using known gene sets, improving the cell type classification of single-cell RNA sequencing data. By leveraging knowledge about gene sets, UNIFAN provides strong evidence for annotations of the clustering results.
Article
Biotechnology & Applied Microbiology
Forough Joudaki, Ahmad Ismaili, Seyed Sajad Sohrabi, Seyedeh Zahra Hosseini, Danial Kahrizi, Hadi Ahmadi
Summary: The current research achieved de novo transcriptome assembly of Gall oak using RNA sequencing technique, generating 89,335 unigenes, among which 6,928 unigenes showed significant differential expression between leaves and root tissues. Gene ontology examination revealed enrichment in cellular processes and enzyme activity. KEGG enrichment analysis displayed a high proportion of unigenes related to metabolic pathways and biosynthesis of secondary metabolites. Additionally, 39 families of transcription factors were identified, with C2H2, bZIP, bHLH, and ERF having the highest frequency. This transcriptome study provides a valuable reference for future functional and comparative studies in the absence of a reference genome and serves as a scientific resource for Q.infectoria.
Article
Biochemistry & Molecular Biology
Shaymaviswanathan Karnaneedi, Roger Huerlimann, Elecia B. Johnston, Roni Nugraha, Thimo Ruethers, Aya C. Taki, Sandip D. Kamath, Nicholas M. Wade, Dean R. Jerry, Andreas L. Lopata
Summary: This study successfully identified seven known crustacean allergens and up to 39 unreported allergens in different shrimp species through mining complete transcriptomes. Multiple sequence alignment revealed high homology of these shrimp allergens with allergens from other invertebrates such as mites and cockroaches. This first transcriptomic analyses of allergens in a major food source provides a valuable resource for investigating shellfish allergens, comparing invertebrate allergens and future development of improved diagnostics for food allergy.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)