The Planarian Anatomy Ontology: A resource to connect data within and across experimental platforms

As the planarian research community expands, the need for an interoperable data organization framework for tool building has become increasingly apparent. Such software would streamline data annotation and enhance cross-platform and cross-species searchability. We created the Planarian Anatomy Ontology (PLANA), an extendable relational framework of defined Schmidtea mediterranea (Smed) anatomical terms used in the field. At publication, PLANA contains over 850 terms describing Smed anatomy from subcellular to system-level across all life cycle stages, in intact animals, and regenerating body fragments. Terms from other anatomy ontologies were imported into PLANA to promote interoperability and comparative anatomy studies. To demonstrate the utility of PLANA as a tool for data curation, we created resources for planarian embryogenesis, including a staging series and molecular fate mapping atlas, and the Planarian Anatomy Gene Expression database, which allows retrieval of a variety of published transcript/gene expression data associated with PLANA terms. As an open-source tool built using FAIR (findable, accessible, interoperable, reproducible) principles, our strategy for continued curation and versioning of PLANA also provides a platform for community-led growth and evolution of this resource.

Genomic Tools to Accelerate Improvement in Okra (Abelmoschus esculentus)

Okra (Abelmoschus esculentus L. Moench), is an important vegetable crop with limited studies on genomics. It is considered as an essential constituent for balanced food due to its dietary fibers, amino-acid and vitamins. It is most widely cultivated for its pods throughout Asia and Africa. Most of the okra cultivation is done exclusively in the developing countries of Asia and Africa with very poor productivity. India ranks first in the world with a production of 6.3 million MT (72% of the total world production). Cultivated okra is mostly susceptible to a large number of begomoviruses. Yellow vein mosaic disease (YVMD) caused by Yellow vein mosaic virus (YVMV) of genus Begomovirus (family Geminiviridae) results in the serious losses in okra cultivation. Symptoms of YVMD are chlorosis and yellowing of veins and veinlets at various levels, small size leaves, lesser and smaller fruits, and stunting growth. The loss in yield, due to YVMD in okra was found ranging from 30 to 100% depending on the age of the plant at the time of infection. Exploitation of biotechnological tools in okra improvement programmes is often restricted, due to the non availability of abundant polymorphic molecular markers and defined genetic maps. Moreover, okra genome is allopolyploid in nature and possess a large number of chromosomes (2n = 56–196) which makes it more complicated. Genomics tools like RNA- seq. for transcriptome analysis has emerged as a powerful tool to identify novel transcript/gene sequences in non-model plants like okra.

Differential Gene Expression Pipeline for Whole Transcriptome RNA-Seq Data using Personal Computer

ABSTRACTAdvances in the next generation sequencing (NGS) technologies, their cost effectiveness and well-developed pipelines using computational tools/softwares has allowed researchers to reveal ground-breaking discoveries in multi-omics data analysis. However, there is still uncertainty due to massive upsurge in parallel tools and difficulty in choosing best practiced pipeline for expression profiling of RNA sequenced (RNA-seq) data. Here, we detail the optimized pipeline that works at a fast pace with enhanced accuracy on personal computer rather than using cloud or high-performance computing clusters (HPC). The steps include quality check, base filtration, quasi-mapping, quantification of samples, estimation and counting of transcript/gene expression abundances, identification and clustering of differentially expressed features and visualization of the data. The tools FastQC, Trimmomatic, Salmon and some other scripts in Trinity toolkit were applied on two paired-end datasets. An extension of this pipeline may also be formulated in future for the gene ontology enrichment analysis and functional annotation of the differential expression matrix to make this data biologically more significant.

DoubleRecViz: a web-based tool for visualizing transcript–gene–species tree reconciliation

Motivation A phylogenetic tree reconciliation is a mapping of one phylogenetic tree onto another which represents the co-evolution of two sets of taxa (e.g. parasite–host co-evolution, gene–species co-evolution). The reconciliation framework was extended to allow modeling the co-evolution of three sets of taxa such as transcript–gene–species co-evolutions. Several web-based tools have been developed for the display and manipulation of phylogenetic trees and co-phylogenetic trees involving two trees, but there currently exists no tool for visualizing the joint reconciliation between three phylogenetic trees. Results Here, we present DoubleRecViz, a web-based tool for visualizing double reconciliations between phylogenetic trees at three levels: transcript, gene and species. DoubleRecViz extends the RecPhyloXML model—developed for gene–species tree reconciliation—to represent joint transcript–gene and gene–species tree reconciliations. It is implemented using the Dash library, which is a toolbox that provides dynamic visualization functionalities for web data visualization in Python. Availability and implementation DoubleRecViz is available through a web server at https://doublerecviz.cobius.usherbrooke.ca. The source code and information about installation procedures are also available at https://github.com/UdeS-CoBIUS/DoubleRecViz. Supplementary information Supplementary data are available at Bioinformatics online.

Embryonic loss of human females with partial trisomy 19 identifies region critical for the single active X

To compensate for the sex difference in the number of X chromosomes, human females, like human males have only one active X. The other X chromosomes in cells of both sexes are silencedin uterobyXIST, theInactive X Specific Transcript gene, that is present on all X chromosomes. To investigate the means by which the human active X is protected from silencing byXIST, we updated the search for a key dosage sensitiveXISTrepressor using new cytogenetic data with more precise resolution. Here, based on a previously unknown sex bias in copy number variations, we identify a unique region in our genome, and propose candidate genes that lie within, as they could inactivateXIST. Unlike males, the females who duplicate this region of chromosome 19 (partial 19 trisomy) do not survive embryogenesis; this preimplantation loss of females may be one reason that more human males are born than females.