Environmental DNA (eDNA) dataset of foraminiferal diversity and distribution from the mining-impacted estuaries of Goa, west coast of India.

The foraminiferal environmental DNA (eDNA) metabarcoding based on high-throughput sequencing (HTS) is a powerful tool to unravel the hidden genetic diversity and environmental lineages. Results from the eDNA approach provided valuable insight into an unplumbed diversity of soft-bodied monothalamous foraminifers [1]. Micropaleontologists overlooked monothalamids due to their soft organic and/or finely agglutinated test, which often gets destroyed during routine morphological investigations [2]. On the other hand, some foraminifera taxonomists or studies included monothalamids (soft-shelled species) in ecological and diversity investigations ranging from deep-sea locations to coastal marine habitats [1], [3], [4]. Here, we document our metabarcoding analysis of foraminiferal diversity and abundance from the mining-affected estuaries of the Indian state of Goa. High-throughput sequencing using the Illumina platform indicated the overwhelming abundance of monothalamous foraminifers in the studied estuarine sediments. For the first time, such detailed data of the foraminiferal diversity utilizing sedimentary environmental DNA (eDNA) methods was carried out in India. The raw sequence data used for analysis is available in NCBI under the Sequence Read Archive (SRA) with the BioProjects and SRA accession number: PRJNA1040471. The presented data may be used as baseline information for eDNA-based biomonitoring and biodiversity assessment surveys from Indian marine habitats across time and space.

Morphology and molecular phylogeny of two new species of Psammophaga (Rhizaria, Foraminifera) from the west coast of India.

Benthic foraminifera are unicellular eukaryotic protists that construct an organic, agglutinated, or calcareous test wall. Although single-chambered (monothalamous) foraminifera are ubiquitous in marine habitats worldwide, they are poorly known compared to their multi-chambered relatives, notably from the tropical marine environments of India. In this study, we describe two new species of marine monothalamid genus Psammophaga Arnold, 1982, from the Rajapuri Creek, coastal Maharashtra, India (Arabian Sea). Psammophaga holzmannae sp. nov. is ovoid to spherical shaped, 103-246 µm in length, single aperture, translucent to orange color cytoplasm, outer surface is composed of agglutinated fine clay particles, and ingested mineral grains are concentrated near its aperture. Psammophaga sinhai sp. nov. is oblong, elliptical, or droplet-shaped, 279-448 µm in length, single aperture, yellow olive color cytoplasm, the exterior surface formed of agglutinated fine clay particles, and the ingested mineral grains are dispersed throughout the body. Phylogenetic analyses based on partial small subunit rRNA gene sequences position new species within the Clade E of monothalamids and are genetically distinct from other Psammophaga. Elemental (SEM-EDS) analysis of engulfed mineral grains revealed preferential selection and uptake of heavy opaque titaniferous minerals from the ambient environment in the cytoplasm.

Pattern recognition in the landscape of seemingly random chimeric transcripts.

The molecular and functional diversity generated by chimeric transcripts (CTs) that are derived from two genes is indicated to contribute to tumor cell survival. Several gaps yet exist. The present research is a systematic study of the spectrum of CTs identified in RNA sequencing datasets of 160 ovarian cancer samples in the The Cancer Genome Atlas (TCGA) (https://portal.gdc.cancer.gov). Structural annotation revealed complexities emerging from chromosomal localization of partner genes, differential splicing and inclusion of regulatory, untranslated regions. Identification of phenotype-specific associations further resolved a dynamically modulated mesenchymal signature during transformation. On an evolutionary background, protein-coding CTs were indicated to be highly conserved, while non-coding CTs may have evolved more recently. We also realized that the current premise postulating structural alterations or neighbouring gene readthrough generating CTs is not valid in instances wherein the parental genes are genomically distanced. In addressing this lacuna, we identified the essentiality of specific spatiotemporal arrangements mediated gene proximities in 3D space for the generation of CTs. All these features together suggest non-random mechanisms towards increasing the molecular diversity in a cell through chimera formation either in parallel or with cross-talks with the indigenous regulatory network.