Whole mitogenomes or short fragments (i.e., 300-700 bp of the cox1 gene) are the markers of choice for revealing within- and among-species genealogies. Protocols for sequencing and assembling ...mitogenomes include 'primer walking' or 'long PCR' followed by Sanger sequencing or Illumina short-read low-coverage whole genome (LC-WGS) sequencing with or without prior enrichment of mitochondrial DNA. The aforementioned strategies assemble complete and accurate mitochondrial genomes but are time consuming and/or expensive. In this study, I first tested whether mitogenomes can be sequenced from long-read nanopore sequencing data exclusively. Second, I explored the accuracy of the long-read assembled genomes by comparing them to a 'gold' standard reference mitogenome retrieved from the same individual using Illumina sequencing. Third and lastly, I tested if the long-read assemblies are useful for mitophylogenomics and barcoding research. To accomplish these goals, I used the Caribbean spiny lobster Panulirus argus, an ecologically relevant species in shallow water coral reefs and target of the most lucrative fishery in the greater Caribbean region.
LC-WGS using a MinION ONT device and various de-novo and reference-based assembly pipelines retrieved a complete and highly accurate mitogenome for the Caribbean spiny lobster Panulirus argus. Discordance between each of the long-read assemblies and the reference mitogenome was mostly due to indels at the flanks of homopolymer regions. Although not 'perfect', phylogenetic analyses using entire mitogenomes or a fragment of the cox1 gene demonstrated that mitogenomes assembled using long reads reliably identify the sequenced specimen as belonging to P. argus and distinguish it from other related species in the same genus, family, and superorder.
This study serves as a proof-of-concept for the future implementation of in-situ surveillance protocols using the MinION to detect mislabeling in P. argus across its supply chain. Mislabeling detection will improve fishery management in this overexploited lobster. This study will additionally aid in decreasing costs for exploring meta-population connectivity in the Caribbean spiny lobster and will aid with the transfer of genomics technology to low-income countries.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
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
= 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. K
/K
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.
Host monopolization theory predicts symbiotic organisms inhabiting morphologically simple, relatively small and scarce hosts to live solitarily as a result of territorial behaviors. We tested this ...prediction with Tunicotheres moseri, an endosymbiotic crab dwelling in the atrial chamber of the morphologically simple, small, and relatively scarce ascidian Styela plicata. As predicted, natural populations of T. moseri inhabit ascidian hosts solitarily with greater frequency than expected by chance alone. Furthermore, laboratory experiments demonstrated that intruder crabs take significantly longer to colonize previously infected compared to uninfected hosts, indicating as expected, that resident crabs exhibit monopolization behaviors. While territoriality does occur, agonistic behaviors employed by T. moseri do not mirror the overt behaviors commonly reported for other territorial crustaceans. Documented double and triple cohabitations in the field coupled with laboratory observations demonstrating the almost invariable success of intruder crabs colonizing occupied hosts, suggest that territoriality is ineffective in completely explaining the solitary social habit of this species. Additional experiments showed that T. moseri juveniles and adults, when searching for ascidians use chemical cues to avoid hosts occupied by conspecifics. This conspecific avoidance behavior reported herein is a novel strategy most likely employed to preemptively resolve costly territorial conflicts. In general, this study supports predictions central to host monopolization theory, but also implies that alternative behavioral strategies (i.e., conflict avoidance) may be more important than originally thought in explaining the host use pattern of symbiotic organisms.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
•The first complete mitochondrial genome for E. alba is analyzed in detail.•We compare the tRNAs secondary structure of E. alba and M. ussuriensis.•The control region has all three functional domains ...present in most mammals.•Maximum likelihood phylogenetic tree supports the monophyly of Phyllostomidae.
The Honduran white bat, Ectophylla alba (Allen 1982), is one of eight species belonging to the family Phyllostomidae that exclusively roosts in tents. Due to its restricted distribution, habitat specificity, and diet requirements, E. alba has been strongly affected by habitat loss and fragmentation during the last decade. In this study, we developed the first genomic resource for this species; we assembled and analyzed in detail the complete mitochondrial genome of E. alba. The mitogenome of E. alba is 16,664 bp in length and is comprised of 13 protein coding genes (PCGs), 2 ribosomal RNA genes, 22 transfer RNA genes (tRNAs), and a putative Control Region (CR) 1,232 bp in length. Gene arrangement in the mitochondrial chromosome of E. alba is identical to that reported before in other species of co-familiar bats. All PCGs are under purifying selection, with atp8 experiencing the least selective pressure. In all PCGs, codons ending with adenine are preferred over others ending in thymine and cytosine. Except tRNA-Serine 1, all tRNAs exhibit a cloverleaf secondary structure. The CR of E. alba exhibits three domains commonly described in other mammals, including bats; extended terminal associated sequences (ETAS), central, and conserved sequence block (CSB). A ML phylogenetic reconstruction of the family Phyllostomidae based on all 13 mitochondrial PCGs confirms the monophyletic status of the subfamily Sternodermatinae and indicates the close relationship between E. alba and the genus Artibeus. This is the first genomic resource developed for E. alba and represents the first step to improving our understanding of the genomic underpinnings involved in the evolution of specialization as well as acclimatization and adaptation to local and global change of specialist bats.
The Amur or Siberian tiger
(Temminck, 1844) is currently restricted to a small region of its original geographical range in northwestern Asia and is considered 'endangered' by the IUCN Red List of ...Threatened Species. This solitary, territorial, and large top predator is in major need of genomic resources to inform conservation management strategies. This study formally tested if complete mitochondrial genomes of
can be assembled from non-enriched metagenomic libraries generated from scat eDNA samples using the Illumina sequencing platform and open-access bioinformatics pipelines. The mitogenome of
was assembled and circularized using the pipeline GetOrganelle with a coverage ranging from 322.7x to 17.6x in four different scat eDNA samples. A nearly complete mitochondrial genome (101x) was retrieved from a fifth scat eDNA sample. The complete or nearly complete mitochondrial genomes of
were AT-rich and composed of 13 protein coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes, and a putative control region. Synteny observed in all assembled mitogenomes was identical to that reported before for
and other felids. A phylogenomic analysis based on all PCGs demonstrated that the mitochondrial genomes assembled from scat eDNA reliably identify the sequenced samples as belonging to
and distinguished the same samples from closely and distantly related congeneric species. This study demonstrates that it is viable to retrieve accurate whole and nearly complete mitochondrial genomes of
(and probably other felids) from scat eDNA samples without library enrichment protocols and using open-access bioinformatics workflows. This new genomic resource represents a new tool to support conservation strategies (bio-prospecting and bio-monitoring) in this iconic cat.
Abstract
The special section on crustacean mitochondrial genomics houses five articles focused on the characterization of mitochondrial genomes in different decapod crustaceans. In this introductory ...article, I highlight details and peculiarities of the workflow used in these articles with which mitochondrial genomes were de novo assembled, annotated, manually curated, and characterized. The workflows used in these studies improves the characterization of mitochondrial genomes and are expected to democratize and advance our knowledge on mitochondrial genomics in non-model crustaceans, while profiting from user-friendly and open access bioinformatics tools.
Whole mitochondrial genomes are quickly becoming markers of choice for the exploration of within-species genealogical and among-species phylogenetic relationships. Most often, 'primer walking' or ...'long PCR' strategies plus Sanger sequencing or low-pass whole genome sequencing using Illumina short reads are used for the assembling of mitochondrial chromosomes. In this study, we first confirmed that mitochondrial genomes can be sequenced from long reads using nanopore sequencing data exclusively. Next, we examined the accuracy of the long-reads assembled mitochondrial chromosomes when comparing them to a 'gold' standard reference mitochondrial chromosome assembled using Illumina short-reads sequencing.
Using a specialized bioinformatics tool, we first produced a short-reads mitochondrial genome assembly for the silky shark C. falciformis with an average base coverage of 9.8x. The complete mitochondrial genome of C. falciformis was 16,705 bp in length and 934 bp shorter than a previously assembled genome (17,639 bp in length) that used bioinformatics tools not specialized for the assembly of mitochondrial chromosomes. Next, low-pass whole genome sequencing using a MinION ONT pocket-sized platform plus customized de-novo and reference-based workflows assembled and circularized a highly accurate mitochondrial genome in the silky shark Carcharhinus falciformis. Indels at the flanks of homopolymer regions explained most of the dissimilarities observed between the 'gold' standard reference mitochondrial genome (assembled using Illumina short reads) and each of the long-reads mitochondrial genome assemblies. Although not completely accurate, mitophylogenomics and barcoding analyses (using entire mitogenomes and the D-Loop/Control Region, respectively) suggest that long-reads assembled mitochondrial genomes are reliable for identifying a sequenced individual, such as C. falciformis, and separating the same individual from others belonging to closely related congeneric species.
This study confirms that mitochondrial genomes can be sequenced from long-reads nanopore sequencing data exclusively. With further development, nanopore technology can be used to quickly test in situ mislabeling in the shark fin fishing industry and thus, improve surveillance protocols, law enforcement, and the regulation of this fishery. This study will also assist with the transferring of high-throughput sequencing technology to middle- and low-income countries so that international scientists can explore population genomics in sharks using inclusive research strategies. Lastly, we recommend assembling mitochondrial genomes using specialized assemblers instead of other assemblers developed for bacterial and/or nuclear genomes.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Minuca minax is a semi-terrestrial crustacean that commonly lives in low salinity, riverine habitats along the shores of the eastern United States. This study reports, for the first time, the ...complete mitochondrial genome of M. minax. The AT-rich mitochondrial genome of M. minax is 15,937 bp in length and comprised of 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, and 22 transfer RNA genes. A single 737 bp long intergenic space is assumed to be the D-loop. Most of the PCGs and tRNA genes are encoded in the L-strand. The gene order observed in the mitochondrial genome of M. minax is new although almost identical to that reported in confamiliar species. In all other confamiliar species to which M. minax is compared, the positions of the trnQ gene and the trnI gene are switched. KA/KS ratios calculated for all mitochondrial PCGs show values of <1, indicating that these PCGs are evolving under purifying selection. A maximum likelihood phylogenetic analysis (concatenated PCGs n = 13, 15 species) supports the monophyly of the subfamilies Ocypodinae and Gelaminidae. Mitochondrial PCGs have enough phylogenetic information to reveal relationships supporting higher taxonomic levels within this family. The knowledge of a complete mitochondrial genome from the red-jointed brackish-water fiddler crab M. minax contributes to the better understanding of meta-population connectivity and the mechanisms involved in the adaptation of marine organisms to near-limnic conditions.
•This study reports, for the first time, the complete mitochondrial genome of M. minax.•The mitochondrial genome is 15,937 bp in length and comprised of 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, and 22 transfer RNA genes.•Gene order in the mitochondrial genome of M. minax is new although almost identical to that reported in confamiliar species.•All PCGs are evolving under purifying selection.•A maximum likelihood phylogenetic analysis supports the monophyly of the subfamilies Ocypodinae and Gelaminidae.
Monogamy in a Hyper-Symbiotic Shrimp Baeza, J Antonio; Simpson, Lunden; Ambrosio, Louis J ...
PloS one,
03/2016, Letnik:
11, Številka:
3
Journal Article
Recenzirano
Odprti dostop
Theory predicts that monogamy is adaptive in resource-specialist symbiotic crustaceans inhabiting relatively small and morphologically simple hosts in tropical environments where predation risk away ...from hosts is high. We tested this prediction in Pontonia manningi, a hyper-symbiotic shrimp that dwells in the mantle cavity of the Atlantic winged oyster Pteria colymbus that, in turn, infects gorgonians from the genus Pseudopterogorgia in the Caribbean Sea. In agreement with theory, P. manningi were found dwelling as heterosexual pairs in oysters more frequently than expected by chance alone. Males and females also inhabited the same host individual independent of the female gravid condition or of the developmental stage of brooded embryos. While the observations above argue in favor of monogamy in P. manningi, there is evidence to suggest that males of the studied species are moderately promiscuous. That females found living solitary in oysters most often brooded embryos, and that males allocated more to weaponry (major claw size) than females at any given size suggest that males might be roaming among host individuals in search of and, fighting for, receptive females. All available information depicts a rather complex mating system in P. manningi: primarily monogamous but with moderately promiscuous males.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Sustainability requirements are gaining importance in the construction industry, which needs to take specific measures in the design and construction of concrete structures. The use of recycled ...aggregates in concrete may be of special interest. Recycling a construction waste will close the life cycle of the original materials (e.g., concrete). Thus, environmental benefits would come from the lower waste generation, and from a lower necessity of raw materials for new structures. The current Spanish code for structural concrete considers the use of recycled aggregates in replacement rates up to 20% by aggregate mass, assimilating their properties with those of concretes without aggregate replacement. Higher substitution percentages would require further testing. In this work, substitution of coarse aggregate for recycled aggregates (with replacement percentages of 25%, 50% and 100%) has been studied, and the concrete's residual properties after exposure to high temperatures (between 350 °C and 850 °C) have been assessed. Compressive strength and capillary water absorption tests were made after heating, and the experiments showed higher residual strength in concretes with the greatest content of recycled aggregates. However, a statistical analysis made with additional data available in the literature seemed to predict otherwise, and the recycled aggregate replacement would have a negative effect on the residual strength.
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