Pangolins are scale-covered mammals, containing eight endangered species. Maintaining pangolins in captivity is a significant challenge, in part because little is known about their genetics. Here we provide the first large-scale sequencing of the critically endangered Manis javanica transcriptomes from eight different organs using Illumina HiSeq technology, yielding ~75 Giga bases and 89,754 unigenes. We found some unigenes involved in the insect hormone biosynthesis pathway and also 747 lipids metabolism-related unigenes that may be insightful to understand the lipid metabolism system in pangolins. Comparative analysis between M. javanica and other mammals revealed many pangolin-specific genes significantly over-represented in stress-related processes, cell proliferation and external stimulus, probably reflecting the traits and adaptations of the analyzed pregnant female M. javanica. Our study provides an invaluable resource for future functional works that may be highly relevant for the conservation of pangolins.
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http://dx.doi.org/10.1038/srep28199 | DOI Listing |
BMC Res Notes
January 2025
Bioinformatics Center, North-Eastern Hill University, Shillong, 793022, India.
Objectives: Nepenthes, sometimes known as tropical pitcher plants or monkey cups, is a carnivorous plant genus that contains more than 160 species. Nepenthes khasiana, India's sole representative of the genus, is a rare and endangered dioecious plant endemic to North-east India. Despite the fact that it is a prominent insectivorous plant in the Nepenthaceae family, genomic resources for the species are limited, making genomic breeding and understanding the genetic basis of botanical carnivory difficult.
View Article and Find Full Text PDFCell Genom
January 2025
The Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Cell Biology and Pathology, Harvard Medical School, Boston, MA 02215, USA; The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Electronic address:
Sequence-based deep learning models have emerged as powerful tools for deciphering the cis-regulatory grammar of the human genome but cannot generalize to unobserved cellular contexts. Here, we present EpiBERT, a multi-modal transformer that learns generalizable representations of genomic sequence and cell type-specific chromatin accessibility through a masked accessibility-based pre-training objective. Following pre-training, EpiBERT can be fine-tuned for gene expression prediction, achieving accuracy comparable to the sequence-only Enformer model, while also being able to generalize to unobserved cell states.
View Article and Find Full Text PDFPlant Dis
January 2025
Guizhou University, Jiaxiu South Street, Huaxi District, Guiyang, China, 550025;
Passion fruit (Passiflora edulis) is a commercially important crop known for its nutritional value, high antioxidant content, and use in beverages and desserts. Gulupa baciliform virus A (GBVA), tentatively named Badnavirus in the family Caulimoviridae, is a cryptic circular double-stranded DNA (dsDNA, ≈6,951 bps) virus recently reported in Colombia with asymptomatic infection of passion fruit (Sepúlveda et al. 2022).
View Article and Find Full Text PDFGastric Cancer
January 2025
Department of Biochemistry and Molecular Biology, Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China.
Background: Gastroesophageal junction adenocarcinoma (GEJAC) exhibits distinct molecular characteristics due to its unique anatomical location. We sought to investigate effective and reliable molecular classification of GEJAC to guide personalized treatment.
Methods: We analyzed the whole genomic, transcriptomic, T-cell receptor repertoires, and immunohistochemical data in 92 GEJAC patients and delineated the landscape of genetic and immune alterations.
Microbiol Resour Announc
January 2025
Department of Livestock Infectiology and Environmental Hygiene, University of Hohenheim, Stuttgart, Germany.
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