Browse
Submit Data
Databases
API
Help

Dataset Information

21 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete mitochondrial genome of pronghorn spiny lobster Panulirus penicillatus (Olivier, 1791).

ABSTRACT: In this paper, we determined and characterized the complete mitochondrial genome of Pronghorn spiny lobster Panulirus penicillatus for the first time from South China Sea. The P. penicillatus mitogenome is 15,671 bp long, and consists of 22 tRNA genes, 2 rRNA genes, 13 protein-coding genes (PCGs), and 1 control region. The nucleotide composition of P. penicillatus mitogenome is significantly biased (A, G, T, and C was 33.62, 13.32, 32.31, and 20.75%, respectively) with A + T contents of 65.93%. Almost PCGs used a standard initiation codon or stop codon, except COX2, ND3, ND4 and ND1 were terminated with an incomplete stop codon T and ND5 ended with TA. One microsatellite (C)₁₂ was identified in the control region of P. penicillatus mitogenome sequences. Phylogenetic tree showed that P. penicillatus was first clustered with P. polyphagus and P. versicolor.

SUBMITTER: Liu H

PROVIDER: S-EPMC7832592 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Genetic isolation between the Western and Eastern Pacific populations of pronghorn spiny lobster Panulirus penicillatus.

Project description:The pronghorn spiny lobster, Panulirus penicillatus, is a circumtropical species which has the widest global distribution among all the species of spiny lobster, ranging throughout the entire Indo-Pacific region. Partial nucleotide sequences of mitochondrial DNA COI (1,142-1,207 bp) and 16S rDNA (535-546 bp) regions were determined for adult and phyllosoma larval samples collected from the Eastern Pacific (EP)(Galápagos Islands and its adjacent water), Central Pacific (CP)(Hawaii and Tuamotu) and the Western Pacific (WP)(Japan, Indonesia, Fiji, New Caledonia and Australia). Phylogenetic analyses revealed two distinct large clades corresponding to the geographic origin of samples (EP and CP+WP). No haplotype was shared between the two regional samples, and average nucleotide sequence divergence (Kimura's two parameter distance) between EP and CP+WP samples was 3.8±0.5% for COI and 1.0±0.4% for 16S rDNA, both of which were much larger than those within samples. The present results indicate that the Pacific population of the pronghorn spiny lobster is subdivided into two distinct populations (Eastern Pacific and Central to Western Pacific), with no gene flow between them. Although the pronghorn spiny lobster have long-lived teleplanic larvae, the vast expanse of Pacific Ocean with no islands and no shallow substrate which is known as the East Pacific Barrier appears to have isolated these two populations for a long time (c.a. 1MY).

| S-EPMC3240654 | biostudies-literature

Genetic isolation among the northwestern, southwestern and central-eastern Indian Ocean populations of the pronghorn spiny lobster Panulirus penicillatus.

Project description:The pronghorn spiny lobster Panulirus penicillatus is a highly valuable species which is widely distributed in Indo-West Pacific and Eastern Pacific regions. Mitochondrial DNA control region sequences (566-571 bp) were determined to investigate the population genetic structure of this species in the Indian Ocean. In total, 236 adult individuals of Panulirus penicillatus were collected from five locations in the Indian Ocean region. Almost all individuals had a unique haplotype. Intrapopulation haplotype (h) and nucleotide (π) diversities were high for each locality, ranging from h = 0.9986-1.0000 and π = 0.031593-0.043441. We observed distinct genetic isolation of population located at the northwestern and southwestern edge of the species range. Gene flow was found within localities in the central and eastern region of the Indian Ocean, probably resulting from an extended planktonic larval stage and prevailing ocean currents.

| S-EPMC4100092 | biostudies-literature

The complete mitochondrial genome of the Caribbean spiny lobster Panulirus argus.

Project description:Panulirus argus is a keystone species and target of the most lucrative fishery in the Caribbean region. This study reports, for the first time, the complete mitochondrial genome of Panulirus argus (average coverage depth nucleotide-1?=?70×) assembled from short Illumina 150?bp PE reads. The AT-rich mitochondrial genome of Panulirus argus was 15 739?bp in length and comprised 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, and 22 transfer RNA genes. A single 801?bp long intergenic space was assumed to be the D-loop. Most of the PCGs were encoded on the H-strand. The gene order observed in the mitochondrial genome of Panulirus argus corresponds to the presumed Pancrustacean ground pattern. KA/KS ratios calculated for all mitochondrial PCGs showed values?<?1, indicating that all these PCGs are evolving under purifying selection. A maximum likelihood phylogenetic analysis (concatenated PCGs [n?=?13], 154 arthropods) supported the monophyly of the Achelata and other infraorders within the Decapoda. Mitochondrial PCGs have enough phylogenetic informativeness to explore high-level genealogical relationships in the Pancrustacea. The complete mitochondrial genome of the Caribbean spiny lobster Panulirus argus will contribute to the better understanding of meta-population connectivity in this keystone overexploited species.

| S-EPMC6283867 | biostudies-literature

The complete mitochondrial genome of longlegged spiny lobster <i>Panulirus longipes</i> (A. Milne Edwards, 1868).

Project description:In this study, we first determined and characterized the complete mitochondrial genome of longlegged spiny lobster Panulirus longipes from South China Sea. The P. longipes mitogenome is 15,739 bp long, and consists of 22 tRNA genes, two rRNA genes, 13 protein-coding genes (PCGs), and one control region. The nucleotide composition of P. longipes mitogenome is significantly biased (A, G, T, and C was 32.06%, 14.36%, 32.42%, and 21.16%, respectively) with A + T contents of 64.48%. Among 13 PCGs, COX1 gene used an unusual initiation codon CAA, COX1, COX2, ND4 and CYTB genes were ended with an incomplete stop codon T, and ND5 gene with an abnormal stop codon ATT. One microsatellite (C)10 was identified in P. longipes mitogenome located in the control region. Phylogenetic tree showed that P. longipes was first clustered with Panulirus cygnus, then together with P. japonicus and P. argus.

| S-EPMC7928049 | biostudies-literature

Detection of heteroplasmy and nuclear mitochondrial pseudogenes in the Japanese spiny lobster Panulirus japonicus

Project description:Partial mtDNA cytochrome oxidase subunit I (COI) fragments and near entire stretch of 12S rDNA (12S) and control region (Dloop) of the Japanese spiny lobster (Panulirus japonicus) (n = 3) were amplified by PCR and used for direct nucleotide sequencing and for clone library-based nucleotide sequence analysis. Nucleotide sequences of a total of 75 clones in COI, 77 in 12S and 92 in Dloop were determined. Haplotypes of the clones matched with those obtained by direct sequencing were determined to be genuine mtDNA sequence of the individual. Phylogenetic analysis revealed several distinct groups of haplotypes in all three regions. Genuine mtDNA sequences were observed to form a group with their closely related variables, and most of these variables may be due to amplification error but a few to be heteroplasmy. Haplotypes determined as nuclear mitochondrial pseudogenes (NUMTs) formed distinct groups. Nucleotide sequence divergence (K2P distance) between genuine haplotypes and NUMTs were substantial (7.169–23.880% for COI, 1.336–23.434% for 12S, and 7.897–71.862% for Dloop). These values were comparable to or smaller than those between species of the genus Panulirus, indicating that integration of mtDNA into the nuclear genome is a continuous and dynamic process throughout pre- and post-speciation events. Double peaks in electropherograms obtained by direct nucleotide sequencing were attributed to common nucleotides shared by multiple NUMTs. Information on the heteroplasmy and NUMTs would be very important for addressing their impact on direct nucleotide sequencing and for quality control of nucleotide sequences obtained.

| S-EPMC8571370 | biostudies-literature

Haemolymph microbiome of the cultured spiny lobster Panulirus ornatus at different temperatures.

Project description:Lobsters have an open circulatory system with haemolymph that contains microorganisms even in the healthy individuals. Understanding the role of these microorganisms becomes increasingly important particularly for the diagnosis of disease as the closed life-cycle aquaculture of the spiny lobster Panulirus ornatus nears commercial reality. This study aimed to characterise haemolymph responses of healthy cultured P. ornatus juveniles at control (28?°C) and elevated (34?°C) temperatures. This was assessed by measuring immune parameters (total granulocyte counts, total haemocyte counts, clotting times), and culture-independent (pyrosequencing of haemolymph DNA) and culture-dependent (isolation using nonselective growth medium) techniques to analyse bacterial communities from lobster haemolymph sampled on days 0, 4 and 6 post-exposure to the temperature regimes. Elevated temperature (34?°C) affected lobster survival, total granulocyte counts, and diversity, load and functional potential of the haemolymph bacterial community. Pyrosequencing analyses showed that the core haemolymph microbiome consisted of phyla Proteobacteria and Bacteriodetes. Overall, culture-independent methods captured a higher bacterial diversity and load when compared to culture-dependent methods, however members of the Rhodobacteraceae were strongly represented in both analyses. This is the first comprehensive study providing comparisons of haemolymph bacterial communities from healthy and thermally stressed cultured juvenile P. ornatus and has the potential to be used in health monitoring programs.

| S-EPMC6368590 | biostudies-literature

Isolation and characterization of eight polymorphic microsatellites for the spotted spiny lobster, Panulirus guttatus.

Project description:Microsatellite sequences were isolated from enriched genomic libraries of the spotted spiny lobster, Panulirus guttatus using 454 pyrosequencing. Twenty-nine previously developed polymerase chain reaction primer pairs of Panulirus argus microsatellite loci were also tested for cross-species amplification in Panulirus guttatus. In total, eight consistently amplifying, and polymorphic loci were characterized for 57 individuals collected in the Florida Keys and Bermuda. The number of alleles per locus ranged from 8 to 20 and observed heterozygosities ranged from 0.409 to 0.958. Significant deviations from Hardy-Weinberg equilibrium were found in one locus from Florida and three loci from Bermuda. Quality control testing indicated that all loci were easy to score, highly polymorphic and showed no evidence of linkage disequilibrium. Null alleles were detected in three loci with moderate frequencies ranging from (20% to 22%). These eight microsatellites provide novel molecular markers for future conservation genetics research of P. guttatus.

| S-EPMC4741071 | biostudies-literature

Evolutionary divergence of geographic subspecies within the scalloped spiny lobster Panulirus homarus (Linnaeus 1758).

Project description:Panulirus homarus is an economically important spiny lobster that is widespread through the Indo-West Pacific Region, but has an uncertain taxonomic status, with three or four geographic subspecies having been described. This study used mitochondrial (16S, COI and control region) and nuclear (18S, ITS-1) DNA sequences to examine specimens of all putative subspecies and forms from throughout their range, in order to determine their genetic validity, and understand the evolutionary history of this species. Despite the range of diversity present in the loci examined, the results were consistent across genes. P. h. rubellus from the SW Indian Ocean comprised the most divergent lineage that was reciprocally monophyletic with respect to all other P. homarus (approx. 9% divergence in COI), and has likely evolved reproductive barriers. The putative P. h. "Brown" subspecies from the Marquesas Is in the central Pacific also comprised a somewhat divergent monophyletic lineage (approx. 3% in COI), but may simply be an allopatric population. The widespread P. h. homarus was not diverged at all from the described P. h. megasculpta from the NW Indian Ocean. The degree of evolutionary divergence of populations at the extremes distribution of the species is somewhat surprising, given the long pelagic larval stage, but suggests that allopatric speciation has been an important driver in the evolution of the genus.

| S-EPMC4043530 | biostudies-literature

Predatory bacteria in the haemolymph of the cultured spiny lobster <i>Panulirus ornatus</i>.

Project description:Bdellovibrio and like organisms (BALOs) are Gram-negative obligate predators of other bacteria in a range of environments. The recent discovery of BALOs in the circulatory system of cultured spiny lobster P. ornatus warrants more investigation. We used a combination of co-culture agar and broth assays and transmission electron microscopy to show a Halobacteriovorax sp. strain Hbv preyed upon the model prey bacterium Vibrio sp. strain Vib. The haemolymph microbiome of juvenile P. ornatus was characterised following injection of phosphate buffered saline (control) or prey and/or predator bacteria for 3 d. The predator Hbv had no effect on survival compared to the control after 3 d. However, when compared to the prey only treatment group, lobsters injected with both prey and predator showed significantly lower abundance of genus Vibrio in the haemolymph bacterial community composition. This study indicates that predatory bacteria are not pathogenic and may assist in controlling microbial population growth in the haemolymph of lobsters.

| S-EPMC8743626 | biostudies-literature

Cloning of sarco-endoplasmic reticulum Ca2+ -ATPase (SERCA) from Caribbean spiny lobster Panulirus argus.

Project description:We have previously reported on calcium transport mechanisms in American lobster, Homarus americanus, using (45)Ca(2+) coupled with vesicle preparations of hepatopancreatic endoplasmic reticulum. The active transport of calcium across membranes bordering calcium-sequestering stores such as sarcoplasmic or endoplasmic reticulum is catalyzed by membrane-spanning proteins, the sarco-endoplasmic Ca(2+)-ATPases (SERCAs). In the study described here we used advanced bioinformatics and molecular techniques to clone SERCA from the economically important Caribbean spiny lobster, Panulirus argus. We report the complete cloning of a full-length SERCA from P. argus antenna cDNA (GenBank accession number AY702617). This cDNA has a 1020-amino acid residue open reading frame which is 90% identical to published sequences of other crustacean SERCA proteins. Our data support the hypothesis that one crustacean and three vertebrate genes controlling calcium transport were derived from a common ancestral gene.

| S-EPMC3397473 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data