Transcript- and annotation-guided genome assembly of the European starling

First published: 28 June 2022The European starling, Sturnus vulgaris, is an ecologically significant, globally invasive avian species that is also suffering from a major decline in its native range. Here, we present the genome assembly and long- read transcriptome of an Australian-sourced European starling (S. vulgaris vAU), and a second, North American, short- read genome assembly (S. vulgaris vNA), as complementary reference genomes for population genetic and evolutionary characterization. S. vulgaris vAU combined 10× genomics linked- reads, low-coverage Nanopore sequencing, and PacBio Iso-Seq full- length transcript scaffolding to generate a 1050 Mb assembly on 6222 scaffolds (7.6 Mb scaffold N50, 94.6% busco completeness). Further scaffolding against the high-quality zebra finch (Taeniopygia guttata) genome assigned 98.6% of the assembly to 32 puta-tive nuclear chromosome scaffolds. Species-specific transcript mapping and gene an-notation revealed good gene- level assembly and high functional completeness. Using S. vulgaris vAU, we demonstrate how the multifunctional use of PacBio Iso-Seq tran-script data and complementary homology-based annotation of sequential assembly steps (assessed using a new tool, saaga) can be used to assess, inform, and validate assembly workflow decisions. We also highlight some counterintuitive behaviour in traditional busco metrics, and present buscomp, a complementary tool for assembly comparison designed to be robust to differences in assembly size and base-calling quality. This work expands our knowledge of avian genomes and the available toolkit for assessing and improving genome quality. The new genomic resources presented will facilitate further global genomic and transcriptomic analysis on this ecologically important species.Katarina C. Stuart, Richard J. Edwards, Yuanyuan Cheng, Wesley C. Warren, David W. Burt, William B. Sherwin, Natalie R. Hofmeister, Scott J. Werner, Gregory F. Ball, Melissa Bateson, Matthew C. Brandley, Katherine L. Buchanan, Phillip Cassey, David F. Clayton, Tim De Meyer, Simone L. Meddle, Lee A. Rollin

A Mechanistic Approach to Understanding Range Shifts in a Changing World: What Makes a Pioneer?

AbstractA species’ range can be thought of as a manifestation of the ecological niche in space. Within a niche, evolution has resulted in traits that maximize fitness. Across millennia, natural oscillations in temperature have caused shifts in the geographic location of appropriate habitat and with corresponding changes in species’ ranges. Contemporary climate change and human disturbance may lead to rapid range expansion or contractions with largely unknown consequences. Birds provide an excellent case study of this phenomenon with some taxa expanding range and others contracting even to the point of extinction. What leads some populations to expand while others contract? Are there physiological and behavioral attributes of “pioneers” at the forefront of a range shift/expansion?The concept of allostasis provides a framework with which to begin to evaluate when a species will be able to successfully expand into new habitat. This tool allows the integration of normal energetic demands (e.g. wear and tear of daily and seasonal routines) with novel challenges posed by unfamiliar and human altered environments. Allostasis is particularly attractive because it allows assessment of how individual phenotypes may respond differentially to changing environments. Here, we use allostasis to evaluate what characteristics of individuals and their environment permit successful range expansion. Understanding variation in the regulatory mechanisms that influence response to a novel environment will be fundamental for understanding the phenotypes of pioneers

Photoneuroendocrine control of reproduction in Japanese quail The use of immediate early genes (C-FOC) as a marker of cell activiation

SIGLEAvailable from British Library Document Supply Centre- DSC:DX186238 / BLDSC - British Library Document Supply CentreGBUnited Kingdo

Direct pathways to the supraoptic nucleus from the brainstem and the main olfactory bulb are activated at parturition in the rat

Sensory input from female reproductive structures is paramount for the co-ordination of neuroendocrine changes at parturition. Using a retrograde tracer (fluorescent latex microspheres) in combination with Fos (as an indicator of neuronal activation) and tyrosine hydroxylase (to identify catecholaminergic neurons) immunocytochemistry we identified cells within the brainstem and main olfactory bulb that project to the supraoptic nucleus, and which become significantly activated at parturition (compared to virgin rats and rats on the day of expected parturition). Within the A2/C2 region in the nucleus tractus solitarii, 60% of the projecting activated cells were catecholaminergic, as were 59% of such cells in the A1/C1 region of the ventrolateral medulla. This suggests that oxytocin and vasopressin neurons within the supraoptic nucleus are stimulated at parturition via afferent inputs from the brainstem, but the input is not exclusively noradrenergic. Within the mitral layer of the main olfactory bulb, cells that projected to the supraoptic nucleus were significantly activated, suggesting that the olfactory system may regulate supraoptic nucleus cell firing at parturition. The preoptic area, organum vasculosum of the lamina terminalis and medial amygdala contained cells that projected to the supraoptic nucleus but these projections were not significantly activated at parturition, although non-projecting cells in these regions were. On the expected day of parturition, but before birth, projections from the organum vasculosum of the lamina terminalis to the supraoptic nucleus became significantly activated. These findings provide evidence of direct afferent pathways to the supraoptic nucleus from the brain stem and olfactory bulbs that are activated at parturition.<p></p

Transcript- and annotation-guided genome assembly of the European starling

First published: 28 June 2022The European starling, Sturnus vulgaris, is an ecologically significant, globally invasive avian species that is also suffering from a major decline in its native range. Here, we present the genome assembly and long- read transcriptome of an Australian-sourced European starling (S. vulgaris vAU), and a second, North American, short- read genome assembly (S. vulgaris vNA), as complementary reference genomes for population genetic and evolutionary characterization. S. vulgaris vAU combined 10× genomics linked- reads, low-coverage Nanopore sequencing, and PacBio Iso-Seq full- length transcript scaffolding to generate a 1050 Mb assembly on 6222 scaffolds (7.6 Mb scaffold N50, 94.6% busco completeness). Further scaffolding against the high-quality zebra finch (Taeniopygia guttata) genome assigned 98.6% of the assembly to 32 puta-tive nuclear chromosome scaffolds. Species-specific transcript mapping and gene an-notation revealed good gene- level assembly and high functional completeness. Using S. vulgaris vAU, we demonstrate how the multifunctional use of PacBio Iso-Seq tran-script data and complementary homology-based annotation of sequential assembly steps (assessed using a new tool, saaga) can be used to assess, inform, and validate assembly workflow decisions. We also highlight some counterintuitive behaviour in traditional busco metrics, and present buscomp, a complementary tool for assembly comparison designed to be robust to differences in assembly size and base-calling quality. This work expands our knowledge of avian genomes and the available toolkit for assessing and improving genome quality. The new genomic resources presented will facilitate further global genomic and transcriptomic analysis on this ecologically important species.Katarina C. Stuart, Richard J. Edwards, Yuanyuan Cheng, Wesley C. Warren, David W. Burt, William B. Sherwin, Natalie R. Hofmeister, Scott J. Werner, Gregory F. Ball, Melissa Bateson, Matthew C. Brandley, Katherine L. Buchanan, Phillip Cassey, David F. Clayton, Tim De Meyer, Simone L. Meddle, Lee A. Rollin