Lepomis macrochirus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA287763 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR2144000_1.fastq.gz | Fastqsanger.gz | |||
| SRR2144000_2.fastq.gz | Fastqsanger.gz | |||
| SRR2144230_1.fastq.gz | Fastqsanger.gz | |||
| SRR2144230_2.fastq.gz | Fastqsanger.gz | |||
| SRR2144360_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 80 |
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Project description:Heat Shock Proteins and Invasive Potential of Lepomis macrochirus (Bluegill Sunfish)
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Project description:North American sunfishes (Family Centrarchidae) are among the most popular sportfish throughout the United States and Canada. Despite the popularity of sunfishes, their ecological importance, and their extensive stocking and aquacultural history, few molecular studies have examined the evolutionary relationships and species boundaries among members of this group, many of which are known to hybridize. Here, we describe a chromosome-scale genome assembly representing Bluegill (Lepomis macrochirus), one of the most widespread centrarchid species. By combining long-read, Oxford Nanopore sequencing data with short-insert, whole-genome and HiC sequence reads, we produced an assembly (Lm_LA_1.1) having a total length of 889 Mb including 1,841 scaffolds and having a scaffold N50 of 36 Mb, L50 of 12, N90 of 29 Mb, and L90 of 22. We detected 99% (eukaryota_odb10) and 98% (actinopterygii_odb10) universal single-copy orthologs (BUSCOs), and ab initio gene prediction performed using this new assembly identified a set of 17,233 genes that were supported by external (OrthoDB v10) data. This new assembly provides an important addition to the growing set of assemblies already available for spiny-rayed fishes (Acanthomorpha), and it will serve as a resource for future studies that focus on the complex evolutionary history of centrarchids.
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Project description:In their natural habitat, fish rarely swim steadily. Instead they frequently accelerate and decelerate. Relatively little is known about how fish produce extra force for acceleration in routine swimming behavior. In this study, we examined the flow around bluegill sunfish Lepomis macrochirus during steady swimming and during forward acceleration, starting at a range of initial swimming speeds. We found that bluegill produce vortices with higher circulation during acceleration, indicating a higher force per tail beat, but they do not substantially redirect the force. We quantified the flow patterns using high speed video and particle image velocimetry and measured acceleration with small inertial measurement units attached to each fish. Even in steady tail beats, the fish accelerates slightly during each tail beat, and the magnitude of the acceleration varies. In steady tail beats, however, a high acceleration is followed by a lower acceleration or a deceleration, so that the swimming speed is maintained; in unsteady tail beats, the fish maintains the acceleration over several tail beats, so that the swimming speed increases. We can thus compare the wake and kinematics during single steady and unsteady tail beats that have the same peak acceleration. During unsteady tail beats when the fish accelerates forward for several tail beats, the wake vortex forces are much higher than those at the same acceleration during single tail beats in steady swimming. The fish also undulates its body at higher amplitude and frequency during unsteady tail beats. These kinematic changes likely increase the fluid dynamic added mass of the body, increasing the forces required to sustain acceleration over several tail beats. The high amplitude and high frequency movements are also likely required to generate the higher forces needed for acceleration. Thus, it appears that bluegill sunfish face a trade-off during acceleration: the body movements required for acceleration also make it harder to accelerate.
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Project description:Escape responses of fishes are one of the best characterized vertebrate behaviors, with extensive previous research on both the neural control and biomechanics of startle response performance. However, very little is known about the hydrodynamics of escape responses, despite the fact that understanding fluid flow patterns during the escape is critical for evaluating how body movement transfers power to the fluid, for defining the time course of power generation, and for characterizing the wake signature left by escaping fishes, which may provide information to predators. In this paper, we present an experimental hydrodynamic analysis of the C-start escape response in bluegill sunfish (Lepomis macrochirus). We used time-resolved digital particle image velocimetry at 1000 frames s(-1) (fps) to image flow patterns during the escape response. We analyzed flow patterns generated by the body separately from those generated by the dorsal and anal fins to assess the contribution of these median fins to escape momentum. Each escape response produced three distinct jets of fluid. Summing the components of fluid momentum in the jets provided an estimate of fish momentum that did not differ significantly from momentum measured from the escaping fish body. In contrast to conclusions drawn from previous kinematic analyses and theoretical models, the caudal fin generated momentum that opposes the escape during stage one, whereas the body bending during stage one contributed substantial propulsive momentum. Additionally, the dorsal and anal fins each contributed substantial momentum. The results underscore the importance of the dorsal and anal fins as propulsors and suggest that the size and placement of these fins may be a key determinant of fast start performance.
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Project description:Fishes generate force to swim by activating muscles on either side of their flexible bodies. To accelerate, they must produce higher muscle forces, which leads to higher reaction forces back on their bodies from the environment. If their bodies are too flexible, the forces during acceleration could not be transmitted effectively to the environment, but fish can potentially use their muscles to increase the effective stiffness of their body. Here, we quantified red muscle activity during acceleration and steady swimming, looking for patterns that would be consistent with the hypothesis of body stiffening. We used high-speed video, electromyographic recordings, and a new digital inertial measurement unit to quantify body kinematics, red muscle activity, and 3D orientation and centre of mass acceleration during forward accelerations and steady swimming over several speeds. During acceleration, fish co-activated anterior muscle on the left and right side, and activated all muscle sooner and kept it active for a larger fraction of the tail beat cycle. These activity patterns are both known to increase effective stiffness for muscle tissue in vitro, which is consistent with our hypothesis that fish use their red muscle to stiffen their bodies during acceleration. We suggest that during impulsive movements, flexible organisms like fishes can use their muscles not only to generate propulsive power but to tune the effective mechanical properties of their bodies, increasing performance during rapid movements and maintaining flexibility for slow, steady movements.
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