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Tigriopus californicus

Overview

Distributed along the Pacific Coast of North America from Baja California, Mexico to Alaska, USA, the harpacticoid copepod Tigriopus californicus inhabits splash pools located in rocky high intertidal habitats. This species has become the focus of numerous studies from ecology and evolution to physiology and neurobiology. Despite a its wide distribution, dispersal is very restricted; T. californicus populations show sharp and temporally stable genetic differentiation over short geographic distances (as little as 500 m). Mitochondrial DNA shows particularly rapid differentiation among populations, often exceeding 20% sequence divergence.

Laboratory crosses of copepods from different populations generate offspring exhibiting a pattern known as hybrid breakdown. This means that second or later generation hybrids have lower and more variable fitness than their parental stocks. Such breakdown in fitness occurs across several life history traits (fecundity, developmental time, and metamorphosis rate) as well as in specific cellular pathways (ATP synthesis and oxidative stress). Because of these features, T. californicus is particularly useful model for investigating the genetic mechanisms underlying reproductive isolation and speciation.

The splash pools inhabited by T. californicus undergo dramatic fluctuations in abiotic factors, such as salinity and temperature, over the course of hours or days. This species has evolved the ability to thrive in these environments, which has motivated several studies of physiology and adaptation. For instance, different populations have been shown to be adapted to their local thermal environments, with southern populations exhibiting higher tolerance to heat stress than northern populations.

Genomic studies in T. californicus have focused on transcriptome characterization, both at the structural and regulatory levels. The current effort to sequence and annotate the T. californicus genome will greatly increase the power of studies addressing fundamental questions of speciation and adaptation in this emerging model system.

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Image Credit: Copyright Greg Rouse

Assembly Information

Analysis Name
Whole Genome Assembly of Tigriopus californicus provided by the Weizhong Li lab, UCSD Calit2
Software
Allpaths
Source
Tigriopus californicus TCALIF_genome_v1.0 Assembly (1.0)
Date performed
2013-08-08
Materials & Methods
Illumina Hi-Seq (200bp): 200bp, 500bp, 800bp, 2kb, 5kb.
BioProject - SRP037576; BioSample - SRS556701; Libraries - SRX469409 through SRX469413.
See the NCBI BioProject page for more information

Assembly Metrics

Contig N50
14791
Scaffold N50
298012
GC Content
41.98

Data Files

NameLast modifiedSize
folder-parentParent Directory
folderCurrent Genome Assembly2015-03-19 13:42
folderTCALIF_genome_v1.02015-03-19 13:42