Integrative taxonomic approach to the systematics of the genus Pampus

In capture fisheries management, fish populations play a critical role in deciding management units employed. Projects like FishPopTrace have been employed in Europe, facilitating use of genetic data and morphological markers, including otoliths for this purpose. Multispecies, multi-gear fisheries landing closely resembling species mixes found in a common ecosystem or fishing ground is widespread in the Indian EEZ. Pomfrets are a low -volume, high value marine fishery in India and an important targeted fishery resource in the Indian Ocean region. However, the taxonomy of the genus Pampus has remained complex till date, with literature indicating several cryptic species leading to misidentification and nomenclature issues. This has serious ramifications for traceability concerns in seafood trade and supply chains as well to address sustainability concerns while preparing species specific fisheries management plans. A recent study involving an integrative taxonomic approach with conventional taxonomy tools as well as genetic data and otolith structure, has helped to clarify the taxonomic status of the genus Pampus in the Indian EEZ and the new findings with a global outlook is summarized below

The Consensus Coding Sequence (Ccds) Project: Identifying a Common Protein-Coding Gene Set for the Human and Mouse Genomes

Effective use of the human and mouse genomes requires reliable identification of genes and their products. Although multiple public resources provide annotation, different methods are used that can result in similar but not identical representation of genes, transcripts, and proteins. The collaborative consensus coding sequence (CCDS) project tracks identical protein annotations on the reference mouse and human genomes with a stable identifier (CCDS ID), and ensures that they are consistently represented on the NCBI, Ensembl, and UCSC Genome Browsers. Importantly, the project coordinates on manually reviewing inconsistent protein annotations between sites, as well as annotations for which new evidence suggests a revision is needed, to progressively converge on a complete protein-coding set for the human and mouse reference genomes, while maintaining a high standard of reliability and biological accuracy. To date, the project has identified 20,159 human and 17,707 mouse consensus coding regions from 17,052 human and 16,893 mouse genes. Three evaluation methods indicate that the entries in the CCDS set are highly likely to represent real proteins, more so than annotations from contributing groups not included in CCDS. The CCDS database thus centralizes the function of identifying well-supported, identically-annotated, protein-coding regions.National Human Genome Research Institute (U.S.) (Grant number 1U54HG004555-01)Wellcome Trust (London, England) (Grant number WT062023)Wellcome Trust (London, England) (Grant number WT077198

The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics.

ABSTRACT: A global genome database of all of Earth’s species diversity could be a treasure trove of scientific discoveries. However, regardless of the major advances in genome sequencing technologies, only a tiny fraction of species have genomic information available. To contribute to a more complete planetary genomic database, scientists and institutions across the world have united under the Earth BioGenome Project (EBP), which plans to sequence and assemble high-quality reference genomes for all ∼1.5 million recognized eukaryotic species through a stepwise phased approach. As the initiative transitions into Phase II, where 150,000 species are to be sequenced in just four years, worldwide participation in the project will be fundamental to success. As the European node of the EBP, the European Reference Genome Atlas (ERGA) seeks to implement a new decentralised, accessible, equitable and inclusive model for producing high-quality reference genomes, which will inform EBP as it scales. To embark on this mission, ERGA launched a Pilot Project to establish a network across Europe to develop and test the first infrastructure of its kind for the coordinated and distributed reference genome production on 98 European eukaryotic species from sample providers across 33 European countries. Here we outline the process and challenges faced during the development of a pilot infrastructure for the production of reference genome resources, and explore the effectiveness of this approach in terms of high-quality reference genome production, considering also equity and inclusion. The outcomes and lessons learned during this pilot provide a solid foundation for ERGA while offering key learnings to other transnational and national genomic resource projects.info:eu-repo/semantics/publishedVersio

The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics

A genomic database of all Earth’s eukaryotic species could contribute to many scientific discoveries; however, only a tiny fraction of species have genomic information available. In 2018, scientists across the world united under the Earth BioGenome Project (EBP), aiming to produce a database of high-quality reference genomes containing all ~1.5 million recognized eukaryotic species. As the European node of the EBP, the European Reference Genome Atlas (ERGA) sought to implement a new decentralised, equitable and inclusive model for producing reference genomes. For this, ERGA launched a Pilot Project establishing the first distributed reference genome production infrastructure and testing it on 98 eukaryotic species from 33 European countries. Here we outline the infrastructure and explore its effectiveness for scaling high-quality reference genome production, whilst considering equity and inclusion. The outcomes and lessons learned provide a solid foundation for ERGA while offering key learnings to other transnational, national genomic resource projects and the EBP.info:eu-repo/semantics/publishedVersio

The function and expansion of the Patched- and Hedgehog-related homologs in C. elegans

The Hedgehog (Hh) signaling pathway promotes pattern formation and cell proliferation in Drosophila and vertebrates. Hh is a ligand that binds and represses the Patched (Ptc) receptor and thereby releases the latent activity of the multipass membrane protein Smoothened (Smo), which is essential for transducing the Hh signal. In Caenorhabditis elegans, the Hh signaling pathway has undergone considerable divergence. Surprisingly, obvious Smo and Hh homologs are absent whereas PTC, PTC-related (PTR), and a large family of nematode Hh-related (Hh-r) proteins are present. We find that the number of PTC-related and Hh-r proteins has expanded in C. elegans, and that this expansion occurred early in Nematoda. Moreover, the function of these proteins appears to be conserved in Caenorhabditis briggsae. Given our present understanding of the Hh signaling pathway, the absence of Hh and Smo raises many questions about the evolution and the function of the PTC, PTR, and Hh-r proteins in C. elegans. To gain insights into their roles, we performed a global survey of the phenotypes produced by RNA-mediated interference (RNAi). Our study reveals that these genes do not require Smo for activity and that they function in multiple aspects of C. elegans development, including molting, cytokinesis, growth, and pattern formation. Moreover, a subset of the PTC, PTR, and Hh-r proteins have the same RNAi phenotypes, indicating that they have the potential to participate in the same processes

Postulating the Modality of Integrative Taxonomy in Describing the Cryptic Congener Pampus griseus (Cuvier) and Systematics of the Genus Pampus (Perciformes: Stromateidae)

Pomfrets (genus Pampus), a highly commercial fishery resource distributed in the Indo-Western Pacific that includes Lessepsian migrants, have witnessed a series of systematic reforms. In this study, based on comprehensive sampling spanning type localities and coevals in the Northern Indian Ocean, the cryptic and valid species Stromateus griseus is resurrected from the synonymy and re-described as Pampus griseus (New Combination) based on 35 specimens from the Bay of Bengal, corroborated by a molecular analysis, which indicated a confined distribution of the species. The Bayesian phylogeny of the genus was reconstructed, incorporating redressed barcodes (582 nucleotides) and concatenated mitochondrial gene sequence data (1,822 nucleotides) generated from the recorded species P. candidus, P. chinensis and the neophyte along with sequences from GenBank entrusting the latest literature. The phylograms differed in topology as for seven valid species, and the one predicated on the concatenated data erected a highly supported polytomous clade for the P. cinereus complex (P. griseus, P. cinereus, and P. candidus) which shares synapomorphies. Pampus argenteus and P. minor, together, formed a sister clade to the rest. Climate-driven vicariant events during glacial epochs and the Indo-Pacific Barrier effect can be the drivers behind the Indian and Pacific Ocean sister lineages in P. chinensis. A multivariate analysis isolated the cryptic species from its congeners. This article portrays the systematics revision of genus Pampus with an integrative taxonomic approach compiling distinctive molecular, morphological, and anatomical features, revised key for species identification, taxonomic archives of Indian stromateids, and winds up with specific remarks

First Report of the Banded Driftfish Psenes arafurensis (Gunther, 1889) from the Indian Coast

Driftfshes belonging to the family Nomeidae are distributed circumtropically. Among them, four species of the genus Psenes, namely Psenes arafurencis, P. cyanophrys, P. maculatus and P. pellucidus are reported from the Indian Ocean. A specimen of Psenes sp. collected from a multiday trawler, operated of the southwest coast of India was identifed as Psenes arafurensis based on morphometric and meristic characteristics which were further confrmed using DNA barcoding and phylogenetic analysis. The earlier doubtful report on the species extending distribution to the Arabian Sea was in 1939 by Norman without a morphological description of the species. The study claims to be the frst documentation of the species from the Arabian Sea as well as from Indian waters

Mitogenomic recognition of incognito lineages in the mud spiny lobster Panulirus polyphagus (Herbst, 1793): A tale of unique genetic structuring and diversification

This study provides the first documentation of three deep conspecific lineages within Panulirus polyphagus in the Indian Ocean, bridging the gap in genetic research. Comparative mitogenomics between lineages (L) at both species and family levels, evolutionary relationships and heterogeneity of sequence divergence within Decapoda, and divergence time estimation were performed. The characterized mitogenomes ranged from 15,685–15,705 bp in size and exhibited a typical pancrustacean pattern. Among the three lineages, L1 predominated the Bay of Bengal, L2 the Arabian Sea, and L2.a, a less common lineage genetically closer to L2, was restricted to the latter region. A minor lineage L1.a, was observed in the Coral Triangle area. All PCGs displayed evidence of purifying selection across species and family levels. The largest genetic distance (K2P) between lineages was 9 %, notably between L1.a and L2.a. The phylogenetic tree subdivided the Achelates into Palinuridae and Scyllaridae, and the topology demonstrated a distinct pattern of lineage diversification within P. polyphagus. AliGROOVE analysis revealed no discernible divergence in Decapoda. The diversification of P. polyphagus appears to have occurred during Miocene, with further diversification in Pliocene. Furthermore, genetic stocks and population connectivity recognized here will provide valuable insight for spatial management planning of this dwindling resource

COPO - Managing sample metadata for biodiversity: considerations from the Darwin Tree of Life project [version 3; peer review: 2 approved, 1 approved with reservations]

Large-scale reference genome sequencing projects for all of biodiversity are underway and common standards have been in place for some years to enable the understanding and sharing of sequence data. However, the metadata that describes the collection, processing and management of samples, and link to the associated sequencing and genome data, are not yet adequately developed and standardised for these projects. At the time of writing, the Darwin Tree of Life (DToL) Project is over two years into its ten-year ambition to sequence all described eukaryotic species in Britain and Ireland. We have sought consensus from a wide range of scientists across taxonomic domains to determine the minimal set of metadata that we collectively deem as critically important to accompany each sequenced specimen. These metadata are made available throughout the subsequent laboratory processes, and once collected, need to be adequately managed to fulfil the requirements of good data management practice. Due to the size and scale of management required, software tools are needed. These tools need to implement rigorous development pathways and change management procedures to ensure that effective research data management of key project and sample metadata is maintained. Tracking of sample properties through the sequencing process is handled by Lab Information Management Systems (LIMS), so publication of the sequenced data is achieved via technical integration of LIMS and data management tools. Discussions with community members on how metadata standards need to be managed within large-scale programmes is a priority in the planning process. Here we report on the standards we developed with respect to a robust and reusable mechanism of metadata collection, in the hopes that other projects forthcoming or underway will adopt these practices for metadata

Public Knowledge and Belief Regarding Antibiotic Use and Antimicrobial Resistance in Qatar

Background: Antibiotics act as a therapeutic weapon in eradicating pathogens. Antibiotics are the most common group of drugs misused for self-medication. This is a global public health concern and is one of the major contributing factors to antibiotic resistance (ABR). Objective: This study aimed to assess the knowledge and beliefs of the public in Qatar regarding appropriate antibiotic use and antimicrobial resistance. Methods: A cross-sectional research design was used to collect the information from the participants based on an adapted questionnaire from the Centers for Disease Control and Prevention (CDC) and the World Health Organization (WHO) between September – November 2018. The study enrolled 1000 participants who visited two large emergency departments (ED) of public hospitals in Qatar. Results: The mean knowledge and belief scores were 55.07±15.87 and 66.57±23.13 respectively. 42% of the participants had moderate knowledge regarding antibiotic and antimicrobial resistance. The majority of the participants (64.8%) believed that antibiotics fight against bacteria and viruses. The educational level significantly influences the belief of the participants. Graduates possess a higher belief score of 11.75±12.5 (P=0.001) compared to others. Conclusion: The key findings of this study highlighted the existing gap in knowledge among the public. A community-based health education program should be launched to raise citizen responsibility to use antibiotics judiciously