The complete mitochondrial genome of the Caribbean spiny lobster Panulirus argus

Characterization of the Complete Mitochondrial Genome of Angulyagra polyzonata and Its Phylogenetic Status in Viviparidae

Angulyagra polyzonata is an economically important mollusk in China, but detailed insights into its mitochondrial genome remain scarce. In this study, we sequenced and comprehensively analyzed the structural features and selection pressures of the A. polyzonata mitochondrial genome. The maximum likelihood method and Bayesian phylogenetic inference method were used to construct a phylogenetic tree of A. polyzonata with 21 other species, including gastropods and bivalves. The full-length mitochondrial genome of 17,379 bp was found to include 22 transfer RNA genes, 2 ribosomal RNA genes, and 13 protein-coding genes, exhibiting similarity to the composition and arrangement of mitochondrial genes in other gastropod species. Notably, the Ka/Ks ratios of mitochondrial protein-coding genes (nad5, cox3, nad3, nad2, cox1, cox2, atp8, atp6, nadl, nad6, cob, nad4l, and nad4) were <1, which indicates that the snail genes of the three genera of the family may have been subjected to strong natural selection pressure during the evolutionary process, so that the number of synonymous mutations (ks) in genes was much more than that of nonsynonymous mutations (ka). Comparative genomic analysis indicated that, apart from the absence of trnW and trnQ, the gene composition of A. polyzonata shares a high degree of homology with other members of the conical snail family. Phylogenetic analysis demonstrated that the selected species could be classified into two primary clades in which A. polyzonata clustered with the Viviparidae family. This study bridges the knowledge gap regarding the mitochondrial genome of A. polyzonata and offers valuable insights into the systematic relationships within the Viviparidae family.

Unraveling the Complete Mitochondrial Genome of Potamalpheops Sp. (Purple Zebra Shrimp) (Crustacea: Decapoda) Provides Insights Into Its Phylogenetic Relationships and Gene Order Rearrangements

Understanding the functions of mitochondrial genomes is crucial for studies related to the evolution of genomes, phylogenomics, and species identification. For the first time, complete mitogenome of Potamalpheops sp. a non-snapping shrimp has been successfully sequenced and characterized from Taiwan that belongs to the Decapoda order, Crustacea class, and Caridea infraorder. This study involved analysis of nucleotide composition, codon usage, gene ordering, evolutionary selection pressure, and comparative mitogenomics. The mitogenome of Potamalpheops sp. is 16,605 base pairs in length and consists of standard set of 37 genes found in metazoans. The gene rearrangements in the mitochondrial genome of this species shows extensive rearrangements comparing to the typical pattern found in pancrustaceans mitogenomes. Therefore, it could be concluded that gene rearrangements most likely happen only in the caridea infraorder. The current investigation discovered transposition of the tRNA and rRNA genes along with reversal in strands in the tRNAs. No other Alpheidae mitochondrial genome that has been investigated thus far has revealed this pattern. All 13 protein coding genes in the mitochondrial genomes of superfamily Alphoidea exhibited Ka/Ks values lower than 1, according to the ratios of nonsynonymous and synonymous substitutions rates. This suggests that a strong purifying selection had taken place. The maximum likelihood tree consisting of 46 mitogenomes of infraorder Caridea along with outgroups, revealed the existence of Potamalpheops sp. in the family Alpheidae and it formed a monophyletic group along with Palaemonoidea and Alpheoidea superfamily.

Mitogenomic recognition of incognito lineages in the mud spiny lobster Panulirus polyphagus (Herbst, 1793): A tale of unique genetic structuring and diversification

This study provides the first documentation of three deep conspecific lineages within Panulirus polyphagus in the Indian Ocean, bridging the gap in genetic research. Comparative mitogenomics between lineages (L) at both species and family levels, evolutionary relationships and heterogeneity of sequence divergence within Decapoda, and divergence time estimation were performed. The characterized mitogenomes ranged from 15,685-15,705 bp in size and exhibited a typical pancrustacean pattern. Among the three lineages, L1 predominated the Bay of Bengal, L2 the Arabian Sea, and L2.a, a less common lineage genetically closer to L2, was restricted to the latter region. A minor lineage L1.a, was observed in the Coral Triangle area. All PCGs displayed evidence of purifying selection across species and family levels. The largest genetic distance (K2P) between lineages was 9 %, notably between L1.a and L2.a. The phylogenetic tree subdivided the Achelates into Palinuridae and Scyllaridae, and the topology demonstrated a distinct pattern of lineage diversification within P. polyphagus. AliGROOVE analysis revealed no discernible divergence in Decapoda. The diversification of P. polyphagus appears to have occurred during Miocene, with further diversification in Pliocene. Furthermore, genetic stocks and population connectivity recognized here will provide valuable insight for spatial management planning of this dwindling resource.

Genomics resources for the Rapa Nui (Eastern Island) spiny lobster Panulirus pascuensis (Crustacea: Decapoda: Achelata)

Background

The Easter Island spiny lobster Panulirus pascuensis (Reed, 1954) or ‘Ura’ in the Rapa Nui language, is a little known species native to the south eastern Pacific Ocean, distributed along the coasts of Easter Island, Pitcairn Island, and the Salas y Gómez Ridge. In Easter Island, P. pascuensis is the target of a small and profitable and probably overexploited fishery. In this study, we profited from a series of bioinformatic analyses to mine biological insight from low-pass short-read next generation sequencing datasets; we have estimated genome size and ploidy in P. pascuensis using a k-mer strategy, discovered, annotated, and quantified mobile elements in the nuclear genome, assembled the 45S rRNA nuclear DNA cassette and mitochondrial chromosome, and explored the phylogenetic position of P. pascuensis within the genus Panulirus using the signal retrieved from translated mitochondrial protein coding genes.

Results

K-mer analyses predicted P. pascuensis to be diploid with a haploid genome size ranging between 2.75 Gbp (with k-mer = 51) and 3.39 Gbp (with k-mer = 18). In P. pascuensis, repetitive elements comprise at least a half and a maximum of three fourths of the nuclear genome. Almost a third (64.94%) of the repetitive elements present in the studied nuclear genome were not assigned to any known family of transposable elements. Taking into consideration only annotated repetitive elements, the most abundant were classified as Long Interspersed Nuclear Elements (22.81%). Less common repetitive elements included Long Terminal Repeats (2.88%), Satellite DNA (2.66%), and DNA transposons (2.45%), among a few others. The 45S rRNA DNA cassette of P. pascuensis was partially assembled into two contigs. One contig, 2,226 bp long, encoded a partially assembled 5′ ETS the entire ssrDNA (1,861 bp), and a partial ITS1. A second contig, 6,714 bp long, encoded a partially assembled ITS1, the entire 5.8S rDNA (158 bp), the entire ITS2, the entire lsrDNA (4,938 bp), and a partial 3′ ETS (549 bp). The mitochondrial genome of P. pascuensis was 15,613 bp long and contained 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, and two ribosomal RNA genes (12S ribosomal RNA [rrnS] and 16S ribosomal RNA [rrnL]). A phylomitogenomic analysis based on PCGs retrieved Panulirus pascuensis as sister to a fully supported clade comprising P. cygnus and P. longipes.

Conclusion

We expect that the information generated in this study will guide the assembly of a chromosome-level nuclear genome for P. pascuensis in the near future. The newly assembled 45S rRNA nuclear DNA cassette and mitochondrial chromosome can support bioprospecting and biomonitoring of P. pascuensis using environmental DNA. The same elements can help to survey the public market place and detect mislabelling of this and other spiny lobsters. Overall, the genomic resources generated in this study will aid in supporting fisheries management and conservation strategies in this iconic spiny lobster that is likely experiencing overexploitation.

Nuclear and mitochondrial genome datasets for spiny lobsters genus Panulirus (Decapoda: Achelata: Palinuridae)

Spiny lobsters (Decapoda: Palinuridae) in the genus Panulirus are targets of lucrative fisheries globally and have relevant ecological functions in tropical and subtropical environments. Only a few, but increasing, number of genetic and genomic resources exist for them. Nuclear and mitochondrial genome assemblies can provide insights into their phylogenetic relationships and support fishery management strategies in species that are heavily exploited. Herein, using Illumina short reads whole genome sequencing, we assembled the nuclear and mitochondrial genomes of a total of 14 species. Genomic DNA was extracted from specimens deposited at Clemson University Crustacean Collection and sequenced in a HiSeq X Ten system. The number of paired-end (PE) reads generated for the different studied species varied between 219,917,346 in P. argus and 70,215,423 in P. cygnus. Nuclear and mitochondrial genomes were 'de novo' assembled. Nuclear genomes ranged between 1,624,400,357 bp in P. guttatus and 935,571,898 bp in P. cygnus with scaffold numbers varying between 466,583 in P. versicolor and 852,228 in P. longipes. Mitochondrial genomes varied between 15,613 bp and 15,768 bp in P. pascuensis and P. versicolor, respectively. The totality of the short reads, nuclear, and mitochondrial genome assemblies are available at NCBI's GenBank.

Characterization of the Complete Mitochondrial Genome of the Elongate Loach and Its Phylogenetic Implications in Cobitidae

The elongate loach is an endemic fish in China. Previous studies have provided some insights into the mitochondrial genome composition and the phylogenetic relationships of the elongate loach inferred using protein-coding genes (PCGs), yet detailed information about it remains limited. Therefore, in this study we sequenced the complete mitochondrial genome of the elongate loach and analyzed its structural characteristics. The PCGs and mitochondrial genome were used for selective stress analysis and genomic comparative analysis. The complete mitochondrial genome of the elongate loach, together with those of 35 Cyprinidae species, was used to infer the phylogenetic relationships of the Cobitidae family through maximum likelihood (ML) reconstruction. The results showed that the genome sequence has a full length of 16,591 bp, which includes 13 PCGs, 22 transfer RNA genes (tRNA), 2 ribosomal RNA genes (rRNA), and 2 non-coding regions (CR D-loop and light chain sub-chain replication origin OL). Overall, the elongate loach shared the same gene arrangement and composition of the mitochondrial genes with other teleost fishes. The Ka/Ks ratios of all mitochondrial PCGs were less than 1, indicating that all of the PCGs were evolving under purifying selection. Genome comparison analyses showed a significant sequence homology of species of Leptobotia. A significant identity between L. elongata and the other five Leptobotia species was observed in the visualization result, except for L. mantschurica, which lacked the tRNA-Arg gene and had a shorter tRNA-Asp gene. The phylogenetic tree revealed that the Cobitidae species examined here can be grouped into two clades, with the elongate loach forming a sister relationship with L. microphthalma. This study could provide additional inferences for a better understanding of the phylogenetic relationships among Cobitidae species.

The Complete Mitochondrial Genome of the Hermit Crab Diogenes edwardsii (Anomura: Diogenidae) and Phylogenetic Relationships within Infraorder Anomura

A complete mitochondrial genome (mitogenome) can provide important information for gene rearrangement, molecular evolution and phylogenetic analysis. Currently, only a few mitogenomes of hermit crabs (superfamily Paguridae) in the infraorder Anomura have been reported. This study reports the first complete mitogenome of the hermit crab Diogenes edwardsii assembled using high-throughput sequencing. The mitogenome of Diogenes edwardsii is 19,858 bp in length and comprises 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes. There are 28 and six genes observed on the heavy and light strands, respectively. The genome composition was highly A + T biased (72.16%), and exhibited a negative AT-skew (-0.110) and positive GC-skew (0.233). Phylogenetic analyses based on the nucleotide dataset of 16 Anomura species indicated that D. edwardsii was closest related to Clibanarius infraspinatus in the same family, Diogenidae. Positive selection analysis showed that two residues located in cox1 and cox2 were identified as positively selected sites with high BEB value (>95%), indicating that these two genes are under positive selection pressure. This is the first complete mitogenome of the genus Diogenes, and this finding helps us to represent a new genomic resource for hermit crab species and provide data for further evolutionary status of Diogenidae in Anomura.

The complete mitochondrial genome of the roosterfish Nematistius pectoralis Gill 1862: purifying selection in protein coding genes, organization of the control region, and insights into family-level phylogenomic relationships in the recently erected order Carangiformes

The roosterfish Nematistius pectoralis is considered as one of the most magnificent sportfishes worldwide. This study developed the first genomic resource for this trophy-fish that is heavily targeted by the fly-fishing industry. The complete mitochondrial genome of N. pectoralis was assembled using short read sequences and analyzed in detail. The mitochondrial genome of N. pectoralis is 16,537 bp in length and comprises 13 protein-coding genes (PCGs), 2 ribosomal RNA genes (12S and 16S), and 22 transfer RNA genes. A long intergenic space 770 bp in length was assumed to be the D-loop or Control Region (CR). Most of the PCGs and tRNA genes are encoded in the L-strand. All PCGs are under purifying selection and atp8 and nad6 experienced the least selective pressure. All tRNAs exhibit a cloverleaf secondary structure except tRNA-Serine 1 that lacked the D-arm loop. The D-loop of N. pectoralis exhibits three domains commonly described in other fishes; extended terminal associated sequences (ETAS), central, and conserved sequence block (CSB). A ML phylogenetic reconstruction of the newly recognized order Carangiformes based on all 13 mitochondrial PCGs did not support the monophyly of this clade but recognized several families as monophyletic, including Bothidae, Carangidae, Istiophoridae, Latidae, Paralichthyidae, Polynemidae, and Rhombosoleidae. Nematistius pectoralis was sister to a clade composed of Toxotes chatareus (fam. Toxotidae) + Lactarius lactarius (fam. Lactariidae). This genomic resource developed for N. pectoralis will aid in improving our understanding of the population genomics of and strengthen conservation and management strategies in this remarkable trophy-fish.

Unfolding the mitochondrial genome structure of green semilooper (Chrysodeixis acuta Walker): An emerging pest of onion (Allium cepa L.)

Onion is the most important crop challenged by a diverse group of insect pests in the agricultural ecosystem. The green semilooper (Chrysodeixis acuta Walker), a widespread tomato and soybean pest, has lately been described as an emergent onion crop pest in India. C. acuta whole mitochondrial genome was sequenced in this work. The circular genome of C. acuta measured 15,743 base pairs (bp) in length. Thirteen protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and one control region were found in the 37 sequence elements. With an average 395 bp gene length, the maximum and minimum gene length observed was 1749 bp and 63 bp of nad5 and trnR, respectively. Nine of the thirteen PCGs have (ATN) as a stop codon, while the other four have a single (T) as a stop codon. Except for trnS1, all of the tRNAs were capable of producing a conventional clover leaf structure. Conserved ATAGA motif sequences and poly-T stretch were identified at the start of the control region. Six overlapping areas and 18 intergenic spacer regions were found, with sizes ranged from 1 to 20 bp and 1 to 111 bp correspondingly. Phylogenetically, C. acuta belongs to the Plusiinae subfamily of the Noctuidae superfamily, and is closely linked to Trichoplusia ni species from the same subfamily. In the present study, the emerging onion pest C. acuta has its complete mitochondrial genome sequenced for the first time.

The First Complete Mitochondrial Genome of Eucrate crenata (Decapoda: Brachyura: Goneplacidae) and Phylogenetic Relationships within Infraorder Brachyura

Characterizing the complete mitochondrial genome (mitogenome) of an organism is useful for genomic studies in taxonomy and evolution. The mitogenomic characteristics of Eucrate crenata (Decapoda: Brachyura: Goneplacidae) have never been studied. The present study decodes the first mitogenome of E. crenata by high-throughput sequencing (HTS). The length of the mitogenome is 15,597 bp, and it contains 13 protein-coding genes, 2 ribosomal RNA genes (rrnS and rrnL), and 22 transfer RNA genes. There are 14 and 23 genes observed on the heavy and light strands, respectively. E. crenata possesses a trnH-cac translocation, with the trnH-cac shifted between trnE-gaa and trnF-ttc instead of the usual location between nad5 and nad4 in decapods. Phylogenetic analyses based on the current dataset of 33 Brachyuran mitogenomes indicate that E. crenata. is closely related to Ashtoret lunaris of Matutidae. The similar codon usage and rearrangements in the two species provide evidence for their close phylogenetic relationship. Positive selection analysis showed that one residue located in cox1 was identified as a positively selected site with high BEB value (>95%), indicating that this gene was under positive selection pressure. This study is the first complete mitogenome record for the family Goneplacidae, and the results obtained may improve the understanding of the phylogeny of Goneplacidae in Brachyura.

Are we there yet? Benchmarking low-coverage nanopore long-read sequencing for the assembling of mitochondrial genomes using the vulnerable silky shark Carcharhinus falciformis

Background

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.

Results

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.

Conclusions

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.

Characterization of The Complete Mitochondrial Genome of the Bromeliad Crab Metopaulias depressus (Rathbun, 1896) (Crustacea: Decapoda: Brachyura: Sesarmidae)

Metopaulias depressus is a non-marine crab endemic to Jamaica that dwells in rainforest bromeliads and exhibits elaborate active parental care behavior. Current genomic resources on M. depressus are rare, limiting the understanding of its adaptation to terrestrial life in species that evolved from marine ancestors. This study reports the complete mitochondrial genome of M. depressus assembled using Sanger sequencing. The AT-rich mitochondrial genome of M. depressus is 15,765 bp in length and comprises 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, and 22 transfer RNA genes. A single 691 bp-long intergenic space is assumed to be the control region (CR) or D-loop. A set of selective pressure analyses indicate that the entirety of the PCGs experience purifying selection. Cox1, cox2, nad5, cox3, and atp6 experience strong purifying selection, and atp8 experiences weak purifying selection compared to the rest of the PCGs. The secondary structures of most tRNA genes exhibit a standard ‘cloverleaf’ structure, with the exception of trnS1, which lacks the dihydroxyuridine (DHU) arm but not the loop, the trnH gene, which lacks the thymine pseudouracil cytosine (T) loop but not the arm, and trnM, which exhibits an overly developed T loop. A maximum likelihood phylogenetic analysis based on all PCGs indicated that M. depressus is more closely related to the genera Clistocoeloma, Nanosesarma, and Parasesarma than to Chiromantes, Geosesarma, and Orisarma. This study contributes to deciphering the phylogenetic relationships within the family Sesarmidae and represents a new genomic resource for this iconic crab species.

The complete mitochondrial genome of the 'Zacatuche' Volcano rabbit (Romerolagus diazi), an endemic and endangered species from the Volcanic Belt of Central Mexico

BACKGROUND

The 'Zacatuche', 'Teporingo', or Volcano rabbit (Romerolagus diazi) belongs to the family Leporidae, is an endemic species restricted to the Central part of the Trans-Mexican Volcanic Belt, and is considered 'endangered' by the IUCN Red List of Threatened Species.

METHODS AND RESULTS

This study reports, for the first time, the complete mitochondrial genome of R. diazi and examined the phylogenetic position of R. diazi among other closely related co-familiar species using mitochondrial protein-coding genes (PCGs). The mitogenome of R. diazi was assembled from short Illumina 150 bp pair-end reads with a coverage of 189x. The AT-rich mitochondrial genome of R. diazi is 17,400 bp in length and is comprised of 13 PCGs, two ribosomal RNA genes, and 22 transfer RNA genes. The gene order observed in the mitochondrial genome of R. diazi is identical to that reported for other leporids. Phylogenetic analyses based on PCGs support the basal position of Romerolagus within the Leporidae, at least when compared to the genera Oryctolagus and Lepus. Nonetheless, additional mitochondrial genomes from species belonging to the genera Bunolagus, Sylvilagus, and Pronolagus, among others, are needed before a more robust conclusion about the derived vs basal placement of Romerolagus within the family Leporidae can be reached based on mitochondrial PCGs.

CONCLUSIONS

This is the first genomic resource developed for R. diazi and it represents a tool to improve our understanding about the ecology and evolutionary biology of this iconic and endangered species.

The mitochondrial genome of Faughnia haani (Stomatopoda): novel organization of the control region and phylogenetic position of the superfamily Parasquilloidea

BACKGROUND

Stomatopod crustaceans are aggressive marine predators featuring complex compound eyes and powerful raptorial appendages used for "smashing" or "spearing" prey and/or competitors. Among them, parasquilloids (superfamily Parasquilloidea) possess eyes with 2-3 midband rows of hexagonal ommatidia and spearing appendages. Here, we assembled and analyzed the complete mitochondrial genome of the parasquilloid Faughnia haani and explored family- and superfamily-level phylogenetic relationships within the Stomatopoda based on mitochondrial protein coding genes (PCGs).

RESULTS

The mitochondrial genome of F. haani is 16,089 bp in length and encodes 13 protein coding genes (PCGs), 22 transfer RNA genes, 2 ribosomal RNA genes, and a control region that is relatively well organized, containing 2 GA-blocks, 4 poly-T stretches, various [TA(A)]n-blocks, and 2 hairpin structures. This organized control region is likely a synapomorphic characteristic in the Stomatopoda. Comparison of the control region among superfamilies shows that parasquilloid species are more similar to gonodactyloids than to squilloids and lysiosquilloids given the presence of various  poly-T stretches between the hairpin structures and [TA(A)]n-blocks. Synteny is identical to that reported for other stomatopods and corresponds to the Pancrustacea ground pattern. A maximum-likelihood phylogenetic tree based on PCGs revealed that Parasquilloidea is sister to Lysiosquilloidea and Gonodactyloidea and not to Squilloidea, contradicting previous phylogenetic studies.

CONCLUSIONS

The novel phylogenetic position of Parasquilloidea revealed by our study indicates that 'spearing' raptorial appendages are plesiomorphic and that the 'smashing' type is either derived (as reported in previous studies) or apomorphic. Our results raise the possibility that the spearing raptorial claw may have independently evolved twice. The superfamily Parasquilloidea exhibits a closer relationship with other stomatopod superfamilies with a different raptorial claw type and with dissimilar numbers of midband rows of hexagonal ommatidia. Additional studies focusing on the assembly of mitochondrial genomes from species belonging to different genera, families, and superfamilies within the order Stomatopoda are warranted to reach a robust conclusion regarding the evolutionary history of this iconic clade based on mitochondrial PCGs.

Comparative mitochondrial genomics of sponge-dwelling snapping shrimps in the genus Synalpheus: Exploring differences between eusocial and non-eusocial species and insights into phylogenetic relationships in caridean shrimps

The genus Synalpheus is a cosmopolitan clade of marine shrimps found in most tropical regions. Species in this genus exhibit a range of social organizations, including pair-forming, communal breeding, and eusociality, the latter only known to have evolved within this genus in the marine realm. This study examines the complete mitochondrial genomes of seven species of Synalpheus and explores differences between eusocial and non-eusocial species considering that eusociality has been shown before to affect the strength of purifying selection in mitochondrial protein coding genes. The AT-rich mitochondrial genomes of Synalpheus range from 15,421 bp to 15,782 bp in length and comprise, invariably, 13 protein-coding genes (PCGs), two ribosomal RNA genes, and 22 transfer RNA genes. A 648 bp to 994 bp long intergenic space is assumed to be the D-loop. Mitochondrial gene synteny is identical among the studied shrimps. No major differences occur between eusocial and non-eusocial species in nucleotide composition and codon usage profiles of PCGs and in the secondary structure of tRNA genes. Maximum likelihood phylogenetic analysis of the complete concatenated PCG complement of 90 species supports the monophyly of the genus Synalpheus and its family Alpheidae. Moreover, the monophyletic status of the caridean families Alvinocaridae, Atyidae, Thoridae, Lysmatidae, Palaemonidae, and Pandalidae within caridean shrimps are fully or highly supported by the analysis. We therefore conclude that mitochondrial genomes contain sufficient phylogenetic information to resolve relationships at high taxonomic levels within the Caridea. Our analysis of mitochondrial genomes in the genus Synalpheus contributes to the understanding of the coevolution between genomic architecture and sociality in caridean shrimps and other marine organisms.

Genome survey sequencing of the Caribbean spiny lobster Panulirus argus: Genome size, nuclear rRNA operon, repetitive elements, and microsatellite discovery

BACKGROUND

Panulirus argus is an ecologically relevant species in shallow water hard-bottom environments and coral reefs and target of the most lucrative fishery in the greater Caribbean region.

METHODS

This study reports, for the first time, the genome size and nuclear repetitive elements, including the 45S ribosomal DNA operon, 5S unit, and microsatellites, of P. argus.

RESULTS

Using a k-mer approach, the average haploid genome size estimated for P. argus was 2.17 Gbp. Repetitive elements comprised 69.02% of the nuclear genome. In turn, 30.98% of the genome represented low- or single-copy sequences. A considerable proportion of repetitive sequences could not be assigned to known repeat element families. Taking into account only annotated repetitive elements, the most frequent belonged to Class I-LINE which were noticeably more abundant than Class I-LTR-Ty- 3/Gypsy, Class I-LTR-Penelope, and Class I-LTR-Ty-3/Bel-Pao elements. Satellite DNA was also abundant. The ribosomal operon in P. argus comprises, in the following order, a 5' ETS (length = 707 bp), ssrDNA (1,875 bp), ITS1 (736 bp), 5.8S rDNA (162 bp), ITS2 (1,314 bp), lsrDNA (5,387 bp), and 3' ETS (287 bp). A total of 1,281 SSRs were identified.

Yes, we can use it: a formal test on the accuracy of low-pass nanopore long-read sequencing for mitophylogenomics and barcoding research using the Caribbean spiny lobster Panulirus argus

Background

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.

Results

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.

Conclusions

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.

A first genomic portrait of the Florida stone crab Menippe mercenaria: Genome size, mitochondrial chromosome, and repetitive elements

The Florida stone crab, Menippe mercenaria, is an ecologically relevant species in shallow water hard-bottom environments and a target of a profitable fishery in the western Atlantic. Using low coverage short Illumina 250bp pair-end reads sequencing, this study reports, for the first time, the genome size, mitochondrial chromosome, and nuclear repetitive elements, including microsatellites, in M. mercenaria. The average haploid genome size estimated using a k-mer approach was 33 Mbp which is smaller than the 1.76 Gbp size estimated using static cell fluorometry. The mitochondrial genome of M. mercenaria is 15,644bp in length and comprised of 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes. Repetitive elements constituted ~83.5% of the nuclear genome while ~16.5% of the genome represented single- or low-copy sequences. A large portion of repetitive sequences could not be assigned to known repeat element families. Considering only annotated repetitive elements, the most ubiquitous belonged to Class I-LINE and Class I-LTR-Ty-3/Gypsy elements. A total of 66 SSRs were identified. These newly developed genomic resources will contribute to the better understanding of meta-population connectivity, hybridization with the congeneric M. adina, and putative genomic mechanisms involved in the acclimatization and adaptation to climate change of the Florida stone crab.

The complete mitochondrial genome of the red-jointed brackish-water fiddler crab Minuca minax (LeConte 1855) (Brachyura: Ocypodidae): New family gene order, and purifying selection and phylogenetic informativeness of protein coding genes

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. K_A/K_S 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.

The complete mitochondrial genome of the Columbia lance nematode, Hoplolaimus columbus, a major agricultural pathogen in North America

BACKGROUND

The plant-parasitic nematode Hoplolaimus columbus is a pathogen that uses a wide range of hosts and causes substantial yield loss in agricultural fields in North America. This study describes, for the first time, the complete mitochondrial genome of H. columbus from South Carolina, USA.

METHODS

The mitogenome of H. columbus was assembled from Illumina 300 bp pair-end reads. It was annotated and compared to other published mitogenomes of plant-parasitic nematodes in the superfamily Tylenchoidea. The phylogenetic relationships between H. columbus and other 6 genera of plant-parasitic nematodes were examined using protein-coding genes (PCGs).

RESULTS

The mitogenome of H. columbus is a circular AT-rich DNA molecule 25,228 bp in length. The annotation result comprises 12 PCGs, 2 ribosomal RNA genes, and 19 transfer RNA genes. No atp8 gene was found in the mitogenome of H. columbus but long non-coding regions were observed in agreement to that reported for other plant-parasitic nematodes. The mitogenomic phylogeny of plant-parasitic nematodes in the superfamily Tylenchoidea agreed with previous molecular phylogenies. Mitochondrial gene synteny in H. columbus was unique but similar to that reported for other closely related species.

CONCLUSIONS

The mitogenome of H. columbus is unique within the superfamily Tylenchoidea but exhibits similarities in both gene content and synteny to other closely related nematodes. Among others, this new resource will facilitate population genomic studies in lance nematodes from North America and beyond.

De novo assembly and functional annotation of the heart + hemolymph transcriptome in the Caribbean spiny lobster Panulirus argus

The spiny lobster, Panulirus argus, is an ecologically relevant species in shallow water coral reefs and a target of the most lucrative fishery in the greater Caribbean region. This study reports, for the first time, the heart + hemolymph transcriptome of the Caribbean spiny lobster Panulirus argus assembled from short Illumina 150bp PE raw reads. A total of 80,152,094 raw reads were assembled using the Oyster River Protocol pipeline. The assembly resulted in a total of 254,773 transcripts. Functional gene annotation was conducted using the software package 'dammit'. Lastly, gene enrichment analyses were conducted using the Gene Ontology (GO) and KEGG pathway (Kaas) databases. This resource will be of utmost importance in future research aiming at exploring the effect of local and regional anthropogenic disturbances, as well as global climate change on the molecular physiology of this overexploited species.

The complete mitochondrial genome of the eusocial sponge-dwelling snapping shrimp Synalpheus microneptunus

In the marine realm, eusociality is only known to have evolved within a clade of sponge-dwelling snapping shrimps in the genus Synalpheus. Deciphering the genomic underpinnings of eusociality in these marine shrimps has been limited by the sparse genomic resources in this genus. Here, we report, for a eusocial shrimp Synalpheus microneptunus, a complete mitochondrial genome (22X coverage) assembled from short Illumina 150 bp paired-end reads. The 15,603 bp long mitochondrial genome of S. microneptunus is AT-rich and includes 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, 22 transfer RNA genes and an 834 bp intergenic region assumed to be the D-loop. The gene order is identical to that reported for most caridean shrimps and corresponds to the presumed Pancrustacean ground pattern. All PCGs showed signs of purifying selection, with K_A/K_S <<1 across the whole PCGs and most sliding windows within PCGs. Maximum-likelihood and Bayesian inference phylogenetic analyses of 13 PCGs and 68 terminals supports the monophyly of the Caridea and the family Alpheidae. The complete mitochondrial genome of the eusocial shrimp Synalpheus microneptunus will contribute to a better understanding of the selective pressures and rates of molecular evolution in marine eusocial animals.