Two novel mitogenomes of Dipodidae species and phylogeny of Rodentia inferred from the complete mitogenomes

Two novel mitogenomes of Eozapus setchuanus (KJ648495) and Sicista concolor (KJ648496) were reported and their total lengths were 16,630 bp and 16,493 bp, respectively. Both mitogenomes which were analogous to other rodent mitogenomes, contained 13 protein-coding genes, 22 tRNAs, 2 rRNAs, and a control region. Specifically, the ND2 gene of S. concolor has three amino acids lesser than that of two other Dipodidae species (E. setchuanus and Jaculus jaculus) due to a premature termination codon in the 3′ end. We detected a tandem repeat cluster of 221 bp and 274 bp in the control region of S. concolor and E. setchuanus, respectively. Along with phylogenetic relationship analysis, we speculated that the tandem repeats in control regions might be common in Dipodinae species. Our phylogenetic analysis using concatenated mitochondrial gene datasets suggested five suborder and 16 family monophyletic groups in 54 rodent taxa sampled and strongly supported a basal position of the squirrel-related clade (PP = 1; BP = 100). Dipodidae had a sister-group relationship with Muroidea, and Sicistinae was in the base of Dipodidae clade. The complete mitochondrial genomes showed high resolution in deep-level phylogenetic relationship reconstructions of Rodentia.     

The complete mitochondrial genome of Calappa bilineata: The first representative from the family Calappidae and its phylogenetic position within Brachyura

In this study, we determined the complete mitogenome sequence of Calappa bilineata, which is the first mitogenome of Calappidae up to now. The total length is 15,606 bp and includes 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs and one control region. The genome composition is highly A + T biased (68.7%), and exhibits a negative AT-skew (−0.010) and GC-skew (−0.267). As with other invertebrate mitogenomes, the PCGs start with the standard ATN and stop with the standard TAN codons or incomplete T. Phylogenetic analysis showed that C. bilineata was most closely related to Matuta planipes (Matutidae), and these two species formed a sister clade, constituting a Calappoidea group and forming a sister clade with part of Eriphioidea. The existence of the polyphyletic families raised doubts over the traditional classification system. These results will help to better understand the features of the C. bilineata mitogenome and lay foundation for further evolutionary relationships within Brachyura.     

Effect of salinity on the thermoregulatory behavior of juvenile blue shrimp Litopenaeus stylirostris Stimpson

Preferred temperature (PT) of juveniles of Litopenaeus stylirostris was not modified (P>0.05) by salinity. The final preferendum of juveniles was 27.8 °C.The critical thermal maxima (CTMax) determined at 42 combinations (6 temperatures×7 salinities) in blue shrimp was not affected significantly by salinity (P>0.05). We obtained a direct relationship between the CTMax and the acclimation temperature.The end point of CTMax in L. stylirostris was defined as the loss of righting response (LRR).The acclimation response ratio (ARR) for the juveniles of blue shrimp had an interval of 0.45–0.50, values that agreed with others obtained for crustaceans from tropical and sub tropical climates.     

Characterization of the complete mitochondrial genome of Phodopus roborovskii (Rodentia: Cricetidae) and systematic implications for Cricetinae phylogenetics

Phodopus roborovskii (subfamily Cricetinae) is widely distributed in the northern arid regions of China. This study reports its complete mitochondrial genome (mitogenome) for the first time. The complete sequence was 16,273 bp long, including 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and 1 major noncoding region. The base composition and codon usage were described. The putative origin of replication for the light strand (O_L) of P. roborovskii was approximately 45 bp long and was highly conserved in the stem-loop and adjacent sequences, but the starting sequence of replication varied between genera among Rodentia. We analyzed the three domains of the D-loop region, and the results indicated that the central domain had higher G + C content and lower A + T content than two peripheral domains. Phylogenetic analyses indicated high resolution in four main divergent clades using mitogenomes data within Cricetidae. Within Cricetinae clade, P. roborovskii was at basal position which was in line with previous researches, and it shared a common ancestor with other extant hamsters. This work validated previous molecular and karyotype researches using mitogenomes data, and provided a set of useful data on phylogeny and molecular evolution in Cricetidae species.     

Evolutionary relatedness of mackerels of the genus Scomber based on complete mitochondrial genomes: Strong support to the recognition of Atlantic Scomber colias and Pacific Scomber japonicus as distinct species

Mackerels of the genus Scomber are commercially important species, but their taxonomic status is still controversial. Although previous phylogenetic data support the recognition of Atlantic Scomber colias and Pacific Scomber japonicus as separate species, it is only based on the analysis of partial mitochondrial and nuclear DNA sequences. In an attempt to shed light on this relevant issue, we have determined the complete mitochondrial DNA sequence of S. colias, S. japonicus, and Scomber australasicus. The total length of the mitogenomes was 16,568 bp for S. colias and 16,570 bp for both S. japonicus and S. australasicus. All mitogenomes had a gene content (13 protein-coding, 2 rRNAs, and 22 tRNAs) and organization similar to that observed in Scomber scombrus and most other vertebrates. The major noncoding region (control region) ranged between 865 and 866 bp in length and showed the typical conserved blocks. Phylogenetic analyses revealed a monophyletic origin of Scomber species with regard to other scombrid fish. The major finding of this study is that S. colias and S. japonicus were significantly grouped in distinct lineages within Scomber cluster, which phylogenetically constitutes evidence that they may be considered as separate species. Additionally, molecular data here presented provide a useful tool for evolutionary as well as population genetic studies.     

Salinity and water-type preferences of four species of postlarval shrimp (Penaeus) from west Mexico

Preference for low salinity inland water may be an important factor in the immigration of postlarval penaeid shrimp from the sea to their nursery grounds, such as estuaries, bays, and coastal lagoons. In the present work, it was shown that four species from west Mexico - Penaeus vannamei Boone, P stylirostris Stimpson, P. californiesis (Holmes), and P. brevirostris Kingsley - all prefer salinities less than that of normal sea water. Older or larger postlarvae preferred lower salinities than early postlarvae. Of the four species, P. vannamei has the lowest preference and this species predominates in the coastal lagoon fisheries of the area. Postlarvae of P. californiensis and P. brevirostris were also shown to prefer lagoon water to sea water. The importance of these preferences is discussed in relation to the normal postlarval migrations.     

Two mitogenomes in Gruiformes (<Emphasis Type="Italic">Amaurornis akool</Emphasis>/<Emphasis Type="Italic">A. phoenicurus</Emphasis>) and the phylogenetic placement of Rallidae

Rallidae, with 34 genera including 142 species, is the largest family in the Gruiformes, the phylogenetic placement of this family was still in debate. The complete mitochondrial genomes (mitogenomes), with many advantageous characters, have become popular markers in phylogenetic analyses. We sequenced the mitogenomes of brown crake (Amaurornis akool) and white-breasted waterhen (Amaurornis phoenicurus), analyzed the genomic characters of mitogenomes in Rallidae, and explored the phylogenetic relationships between Rallidae and other four families in Gruiformes based on mitogenome sequences of 32 species with Bayesian method. The mitogenome of A. akool/A. phoenicurus was 16,950/17,213 bp in length, and contained 37 genes typical to avian mitogenomes and one control region, respectively. The genomic characters of mitogenomes in Rallidae were similar. The phylogenetic results indicated that, among five families, Rallidae had closest relationship with Heliornithidae, which formed a sister taxa to Gruidae, while Rhynochetidae located in the basal lineage. Within Rallidae, Rallina was ancestral clade. Gallirallus & Rallus and Aramides were closely related, Gallicrex & Amaurornis and Fulica & Gallinula had close relationships, and these two taxa formed a sister clade to Porphyrio & Coturnicops. Our phylogenetic analyses provided solid evidence for the phylogenetic placement of Rallidae and the evolutionary relationships among different genus within this family. In addition, the mitogenome data presented here provide useful information for further molecular systematic investigations on Gruiformes as well as conservation biology research of these species.     

Protection of blue shrimp (Litopenaeus stylirostris) against the White Spot Syndrome Virus (WSSV) when injected with shrimp lysozyme

In this study we found that a blue shrimp (Litopenaeus stylirostris) lysozyme gene (Lslzm) was up-regulated in WSSV-infected shrimp, suggesting that lysozyme is involved in the innate response of shrimp to this virus. Shrimp were intramuscularly injected with Lslzm protein to identify how this recombinant protein protects L. stylirostris from WSSV infection and to determine how this protein influences nonspecific cellular and humoral defense mechanisms. Higher survival rates and a lower viral load (compared with controls) were reported for shrimps that were first injected with the Lslzm protein and then infected with WSSV. In addition, the Lslzm expression level and the immunological parameters (including THC, phagocytic activity, respiratory burst activity, phenoloxidase activity and lysozyme activity) were all significantly higher in the WSSV-infected shrimp treated with the Lslzm protein, compared with the controls. These results indicate that lysozyme is effective at blocking WSSV infection in L. stylirostris and that lysozyme modulates the cellular and humoral defense mechanisms after they are suppressed by the WSSV virus.     

Fourteen complete mitochondrial genomes of butterflies from the genus Lethe (Lepidoptera,Nymphalidae, Satyrinae) with mitogenome-based phylogenetic analysis

The mitochondrial genome (mitogenome) can help us understand the phylogenetic relationships within the genus Lethe and the subfamily Satyrinae. In this study, we sequenced the complete mitogenomes of 14 Lethe species, which range in size from 15,225 to 15,271 bp, with both 37 genes (13 PCGs, 22 tRNAs, 2 rRNAs) and a noncoding A + T-rich region. The gene arrangement and orientation is similar to typical mitogenomes of Lepidoptera. The Ka/Ks ratio shows that cox1 has the slowest evolutionary rate. The secondary structure of trnN lacks the Pseudouracil loop (TψC loop) in most Lethe species. The inferred phylogenetic analyses show that Lethe is a well-supported monophyletic group, and reveal 2 major clades within the genus Lethe, which is consistent with previous morphological classifications.     

Characterization of the complete mitogenome of Trachylophus sinensis (Coleoptera: Cerambycidae: Cerambycinae), the type species of Trachylophus and its phylogenetic implications

Complete mitochondrial genomes (mitogenomes) have long been proved as reliable markers for phylogenetic reconstruction among diverse animal groups, especially benefited from recent rapid development of sequencing techniques. However, the mitogenomes of many important clades remain poorly represented, which restricted the understanding of macroscale evolutionary history of these groups. Here, we sequenced and characterized the complete mitogenome of Trachylophus sinensis, a type species of the Trachylophus genus, which also represents the first sequenced mitogenome in this genus. The complete circular mitogenome was 15,746 bp in length, containing 37 typical genes and one noncoding AT-rich control region. The nucleotide composition of the mitogenome was highly A + T biased, accounting for 70.07 % of the whole mitogenome with a slightly positive AT skewness (0.106). The 13 Protein coding genes (PCGs) used ATN as their start codons, except nad1 which used TTG. All tRNA genes were predicted with a characteristic cloverleaf secondary structure except trnS1^(AGN), whose dihydrouridine (DHU) arm was replaced by a simple loop. Phylogenetic analyses recovered Cerambycinae as a monophyletic group with high node supports and the sister relationship between T. sinensis and Nadezhdiella cantori. However, we found that deeper nodes showed not strong support, which may be caused by limited taxa sampling in our study. More mitogenomes should be sequenced representing various taxonomic levels, especially closely related species, which will enhance our understanding of phylogenetic relationships among Cerambycinae.     

White shrimp Litopenaeus vannamei catalase: Gene structure,expression and activity under hypoxia and reoxygenation

Catalase (EC 1.11.1.6) is an antioxidant enzyme involved in redox equilibrium, regulating hydrogen peroxide (H₂O₂) concentration, a harmful reactive oxygen species (ROS) that is produced during hypoxia. Hypoxia occurs commonly in aquatic environments and in shrimp farms. We studied the catalase gene of the shrimp Litopenaeus vannamei and tested its expression and enzyme activity during hypoxia (1.5 mg/L O₂; 6 and 24 h) and reoxygenation (1 h after hypoxia). The complete gene is 2974 bp long and has four introns of 821, 223, 114 and 298 bp, respectively. The first intron has tree microsatellites, with GT and (T)AT(GT) repeated sequences. L. vannamei catalase is part of an invertebrate clade including crustaceans and rotifers. Catalase expression and activity is different in gills and hepatopancreas. Expression in gills increased 3.2 and 3-fold in response to hypoxia and reoxygenation (6 and 24 h hypoxia, followed by 1 h reoxygenation) compared to normoxia, while no differences were detected in the expression and activity in hepatopancreas. Catalase activity in gills had a contrary response to expression in hypoxia and reoxygenation.     

Mitochondrial genomes of the Dorcus velutinus complex (Coleoptera: Lucanidae) with the large intergenic spacer showing unique short sequence repeats and their implications for systematics

Mitochondrial genomes of the three lucanid species in the Dorcus velutinus complex – Dorcus velutinus Thomson, D. ursulus Arrow and D. tenuihirsutus Kim and Kim – were assembled and analyzed through next generation sequencing. The mitogenome sequences were used to infer phylogenetic relationships among Dorcus species. Our analyses revealed that the newly sequenced mitogenomes are comparable in their size, content, and gene arrangement to other lucanid mitogenomes reported to date. However, we confirmed the presence of a large intergenic spacer (IGS) between trnS^(UCN) and ND1 genes, whose length varied from 170 bp (in D. tenuihirsutus) to 193 bp (in D. ursulus and D. velutinus). Within this IGS region, a short sequence fragment (TACTAAATT) was found uniquely across the three species of Dorcus velutinus complex. Our phylogenetic analyses show that the D. velutinus complex constitutes a distinct clade with a significant divergence from other species of the genus Dorcus sensu stricto. Furthermore, we reaffirm the validity of D. tenuihirsutus – a species originally described from Korea – as a distinct species, though the taxonomic status of D. ursulus remains to be studied further. Finally, we find the presence and location of large IGSs to be useful for studying evolutionary history and species delimitation in stag beetles.     

A novel gene of tumor necrosis factor ligand superfamily from kuruma shrimp,Marsupenaeus japonicus

A tumor necrosis factor (TNF) gene has been isolated and characterized in kuruma shrimp, Marsupenaeus japonicus, providing the first conclusive evidence for the existence of the TNF ligand in shrimp. The kuruma shrimp TNF (MjTNF) cDNA was composed of 1868 bp with a 262 bp 5′-untranslated region (UTR) and a 220 bp 3′-UTR, which was translated into a protein of 462 amino acid residues that included a predicted transmembrane domain of 23 amino acid residues (Trp20–Val42) and the TNF family signature (Pro321–Leu448). Homology analysis of MjTNF showed 30.7% and 26.7% identities with fruit fly (Drosophila melanogaster) Eiger and human (Homo sapiens) ectodysplasin A, respectively. The MjTNF gene was constitutively expressed in unstimulated organs of shrimp such as the muscle, stomach, brain and gill. In lymphoid organ cells, an enhanced expression of the MjTNF gene was observed following stimulation with peptidoglycan and polycytidylic acid. A high expression level of MjTNF was observed in vivo 2 h and 4 h after stimulation with lipopolysaccharide and Vibrio penaeicida, respectively. These observations suggest that MjTNF plays a role in the innate immune defense in kuruma shrimp. The discovery of shrimp TNF will allow a more complete and concrete understanding of shrimp inflammatory responses.     

Sperm ultrastructure of shrimps from the family Penaeidae (Crustacea: Dendrobranchiata) in a phylogenetic context

We describe the sperm ultrastructure of six penaeid species, including at least one member of each tribe (Penaeini, Parapenaeini and Trachypenaeini). Fragments of the vas deferens of the Penaeidae Farfantepenaeus brasiliensis, Farfantepenaeus paulensis, Litopenaeus schmitti, Parapenaeus americanus, Rimapenaeus constrictus and Xiphopenaeus kroyeri were fixed and processed according to the routine for transmission electron microscopy. The morphological results were contextualized in an evolutionary perspective using molecular markers for the phylogenetic reconstruction of this group. A phylogram was proposed by Bayesian inference based on 1007 bp of 33 sequences of the combined genes (16S rDNA and COI mtDNA) from 27 dendrobranchiate specimens. Our findings show that morphological differences in the sperm ultrastructures of members among the tribes of Penaeidae can be used as a baseline to understand their evolutionary relationships. Individuals from the Penaeini tribe show plesiomorphic characteristics in the sperm ultrastructure compared to the Trachypenaeini tribe from which they were derived, such as shrimp from family Sicyoniidae. The morphological complexity of the sperm of the different penaeid members corroborated with the genetic phylogeny, which showed different clades for each tribe and the close relationship with Sicyoniidae. The sperm features of the selected species studied here reflected their evolutionary history. These features confirm the previous phylogenetic hypothesis and question the monophyly of Penaeidae, which should be verified in the future with a more complete set of representative members of each tribe.     

Complete mitochondrial genomes of three sea basses Lateolabrax (Perciformes,Lateolabracidae) species: Genome description and phylogenetic considerations

Genus Lateolabrax consists of three species, Japanese sea bass Lateolabrax japonicus, spotted sea bass Lateolabrax maculatus and blackfin sea bass Lateolabrax latus. The complete mitochondrial DNA (mtDNA) of the three sea basses were amplified and sequenced to characterize and discuss their phylogenetic relationships. The length of mitogenomes was 16,593 bp, 16,479 bp and 16,600 bp, respectively, and all of them consisted of 13 protein-coding genes, 2 ribosomal RNA (rRNA), 22 transfer RNA (tRNA) and a control region, which are typical for mtDNA of vertebrate. Most genes were encoded on the H-strand, except for the ND6 and eight tRNA genes encoding on the L-strand. A significant variation among the three species was detected in length of the control region. Phylogenetic relationship among the three species was constructed based on the datasets, including the 12 protein-coding genes (except ND6 gene), 22 tRNA and 2 rRNA sequences. The results supported the sister taxon between L. japonicus and L. maculatus. The genetic resources reported here are useful for further studies in taxonomy and phylogeny of the three sea basses and related species.     

Characterization of the complete mitochondrial genome of Drawida gisti (Metagynophora,Moniligastridae) and comparison with other Metagynophora species

Here, the complete mitochondrial genome (mitogenome) of Drawida gisti was sequenced and compared with the mitogenomes of other Metagynophora species. The circular mitogenome was 14,648 bp in length and contained two ribosomal RNA genes (rRNAs), 13 protein-coding genes (PCGs), and 22 transfer RNA genes (tRNAs). The types of constitutive genes and the direction of the coding strand that appeared in Drawida mitogenome were identical to those observed in other Metagynophora species, except for a missing lengthy non-coding region. The conservative relationships between Drawida species were supported by the overall analyses of 13 PCGs, two rRNAs, and 22 tRNAs. A comparison of the Metagynophora mitogenomes revealed that the ATP8 gene possessed the highest polymorphism among the 13 PCGs and two rRNAs. Phylogenetic analysis suggested that the Moniligastridae contained Drawida, which is a primitive Metagynophora group. Our study provides a step forward toward elucidating the evolutionary linkages within Drawida and even Metagynophora.