Amblyopinae Mitogenomes Provide Novel Insights into the Paraphyletic Origin of Their Adaptation to Mudflat Habitats.

The water-to-land transition is one of the most important events in evolutionary history of vertebrates. However, the genetic basis underlying many of the adaptations during this transition remains unclear. Mud-dwelling gobies in the subfamily Amblyopinae are one of the teleosts lineages that show terrestriality and provide a useful system for clarifying the genetic changes underlying adaptations to terrestrial life. Here, we sequenced the mitogenome of six species in the subfamily Amblyopinae. Our results revealed a paraphyletic origin of Amblyopinae with respect to Oxudercinae, which are the most terrestrial fishes and lead an amphibious life in mudflats. This partly explains the terrestriality of Amblyopinae. We also detected unique tandemly repeated sequences in the mitochondrial control region in Amblyopinae, as well as in Oxudercinae, which mitigate oxidative DNA damage stemming from terrestrial environmental stress. Several genes, such as ND2, ND4, ND6 and COIII, have experienced positive selection, suggesting their important roles in enhancing the efficiency of ATP production to cope with the increased energy requirements for life in terrestrial environments. These results strongly suggest that the adaptive evolution of mitochondrial genes has played a key role in terrestrial adaptions in Amblyopinae, as well as in Oxudercinae, and provide new insights into the molecular mechanisms underlying the water-to-land transition in vertebrates.

Effects of plastic contamination on carbon fluxes in a subtropical coastal wetland of East China.

Coastal wetlands are recognized as carbon sinks that play an important role in mitigating global climate change because of the strong carbon uptake by vegetation and high carbon sequestration in the soil. Over the last few decades, plastic waste pollution in coastal zones has become increasingly serious owing to high-intensity anthropogenic activities. However, the influence of plastic waste (including foam waste) accumulation in coastal wetlands on carbon flux remains unclear. In the Yangtze Estuary, we investigated the variabilities of vegetation growth, carbon dioxide (CO2) and methane (CH4) fluxes, and soil properties in a clean Phragmites australis marsh and mudflat and a plastic-polluted marsh during summer and autumn. The clean marsh showed a strong CO2 uptake capacity (a carbon sink), and the clean mudflat showed a weak CO2 sink during the measurement period. However, polluted marshes are a significant source of CO2 emissions. Regardless of the season, the gross primary production and vegetation biomass of the polluted marshes were on average 9.5 and 1.1 times lower than those in the clean marshes, respectively. Ecosystem respiration and CH4 emissions in polluted marshes were significantly higher than those in clean marshes and mudflats. Generally, the soil bulk density and salinity in polluted marshes were lower, whereas the median particle size was higher at the polluted sites than at the clean sites. Increased soil porosity and decreased salinity may favor CO2 and CH4 emissions through gas diffusion pathways and microbiological behavior. Moreover, the concentrations of heavy metals in the soil of plastic-polluted marshes were 1.24-1.49 times higher than those in the clean marshes, which probably limited vegetation growth and CO2 uptake. Our study highlights the adverse effects of plastic pollution on the carbon sink functions of coastal ecosystems, which should receive global attention in coastal environmental management.

Novel gene rearrangement in the mitochondrial genome of Coenobita brevimanus (Anomura: Coenobitidae) and phylogenetic implications for Anomura.

The complete mitochondrial genomes (mitogenomes) can indicate phylogenetic relationships among organisms, as well as useful information about the process of molecular evolution and gene rearrangement mechanisms. However, knowledge on the complete mitogenome of Coenobitidae (Decapoda: Anomura) is quite scarce. Here, we describe in detail the complete mitogenome of Coenobita brevimanus, which is 16,393 bp in length, and contains 13 protein-coding genes, two ribosomal RNA, 22 transfer RNA genes, as well as a putative control region. The genome composition shows a moderate A + T bias (65.0%), and exhibited a negative AT-skew (-0.148) and a positive GC-skew (0.183). Five gene clusters (or genes) involving eleven tRNAs and two PCGs were found to have rearranged with respect to the pancrustacean ground pattern gene order. Duplication-random loss and recombination models were determined as most likely to explain the observed large-scale gene rearrangements. Phylogenetic analysis placed all Coenobitidae species into one clade. The polyphyly of Paguroidea was well supported, whereas the non-monophyly of Galatheoidea was inconsistence with previous findings on Anomura. Taken together, our results help to better understand gene rearrangement process and the evolutionary status of C. brevimanus and lay a foundation for further phylogenetic studies of Anomura.

Shading treatment during late stage of seed development promotes subsequent seed germination and seedlings establishment in sunflower.

During the sunflower seed production process, the role of artificial shading treatment (ST) in seed development and subsequent seed germination remains largely unknown. In the present study, sunflower mother plants were artificially shaded during 1-34 (full period-ST, FST), 1-22 (early period-ST, EST), and 22-34 (late period-ST, LST) days after pollination (DAP), to examine the effects of parental shading on subsequent seed germination. Both FST and EST significantly reduced the photosynthetic efficiency of sunflower, manifested as decreased seed dry weight and unfavorable seed germination. On the contrary, LST remarkably increased seed dry weight and promoted subsequent seed germination and seedling establishment. LST enhanced the activities of several key enzymes involved in triglyceride anabolism and corresponding-genes expression, which in turn increased the total fatty acid contents and altered the fatty acid composition. During early germination, the key enzyme activities involved in triglyceride disintegration and corresponding-gene expressions in LST seeds were apparently higher than those in seeds without the shading treatment (WST). Consistently, LST seeds had significant higher contents of ATP and soluble sugar. Moreover, enzyme activities related to abscisic acid (ABA) biosynthesis and corresponding gene expressions decreased within LST seeds, whereas the enzyme activities and corresponding gene expressions associated with gibberellin (GA) biosynthesis were increased. These results were also evidenced by the reduced ABA content but elevated GA level within LST seeds, giving rise to higher GA/ABA ratio. Our findings suggested that LST could promote sunflower seed development and subsequent seed germination as well as seedling establishment through modulating the dynamic metabolism of triglycerides, fatty acid and GA/ABA balance.

Comparative Analysis of Complete Mitochondrial Genome of Ariosoma meeki (Jordan and Snider, 1900), Revealing Gene Rearrangement and the Phylogenetic Relationships of Anguilliformes.

The mitochondrial genome structure of a teleostean group is generally considered to be conservative. However, two types of gene arrangements have been identified in the mitogenomes of Anguilliformes. In this study, we report the complete mitochondrial genome of Ariosoma meeki (Anguilliformes (Congridae)). For this research, first, the mitochondrial genome structure and composition were analyzed. As opposed to the typical gene arrangement pattern in other Anguilliformes species, the mitogenome of A. meeki has undergone gene rearrangement. The ND6 and the conjoint tRNA-Glu genes were translocated to the location between the tRNA-Thr and tRNA-Pro genes, and a duplicated D-loop region was translocated to move upstream of the ND6 gene. Second, comparative genomic analysis was carried out between the mitogenomes of A. meeki and Ariosoma shiroanago. The gene arrangement between them was found to be highly consistent, against the published A. meeki mitogenomes. Third, we reproduced the possible evolutionary process of gene rearrangement in Ariosoma mitogenomes and attributed such an occurrence to tandem repeat and random loss events. Fourth, a phylogenetic analysis of Anguilliformes was conducted, and the clustering results supported the non-monophyly hypothesis regarding the Congridae. This study is expected to provide a new perspective on the A. meeki mitogenome and lay the foundation for the further exploration of gene rearrangement mechanisms.

Projections from anteromedial thalamus nucleus to the midcingulate cortex mediate pain and anxiety-like behaviors in mice.

Prior research has demonstrated the involvement of the midcingulate cortex (MCC) and its downstream pathway in pain regulation. However, the mechanism via which pain information is conveyed to the MCC remains unclear. The present study utilized immunohistochemistry, chemogenetics, optogenetics, and behavior detection methods to explore the involvement of MCC, anteromedial thalamus nucleus (AM), and AM-MCC pathway in pain and emotional regulation. Chemogenetics or optogenetics methods were employed to activate/inhibit MCCCaMKIIα, AMCaMKIIα, AMCaMKIIα-MCC pathway. This manipulation evokes/relieves mechanical and partial heat hyperalgesia, as well as anxiety-like behaviors. In the complete Freund,s adjuvant (CFA) inflammatory pain model, chemogenetic inhibition of the AMCaMKIIα-MCCCaMKIIα pathway contributed to pain relief. Notably, this study presented the first evidence implicating the AM in the regulation of nociception and negative emotions. Additionally, it was observed that the MCC primarily receives projections from the AM, highlighting the crucial role of this pathway in the transmission of pain and emotional information.

Projections from the Rostral Zona Incerta to the Thalamic Paraventricular Nucleus Mediate Nociceptive Neurotransmission in Mice.

Zona incerta (ZI) is an integrative subthalamic region in nociceptive neurotransmission. Previous studies demonstrated that the rostral ZI (ZIR) is an important gamma-aminobutyric acid-ergic (GABAergic) source to the thalamic paraventricular nucleus (PVT), but whether the ZIR-PVT pathway participates in nociceptive modulation is still unclear. Therefore, our investigation utilized anatomical tracing, fiber photometry, chemogenetic, optogenetic and local pharmacological approaches to investigate the roles of the ZIRGABA+-PVT pathway in nociceptive neurotransmission in mice. We found that projections from the GABAergic neurons in ZIR to PVT were involved in nociceptive neurotransmission. Furthermore, chemogenetic and optogenetic activation of the ZIRGABA+-PVT pathway alleviates pain, whereas inhibiting the activities of the ZIRGABA+-PVT circuit induces mechanical hypersensitivity and partial heat hyperalgesia. Importantly, in vivo pharmacology combined with optogenetics revealed that the GABA-A receptor (GABAAR) is crucial for GABAergic inhibition from ZIR to PVT. Our data suggest that the ZIRGABA+-PVT pathway acts through GABAAR-expressing glutamatergic neurons in PVT mediates nociceptive neurotransmission.

Characterization of the complete mitochondrial genome of Ilisha striatula (Clupeiformes, Pristigasteridae) and phylogenetic studies of Clupeiformes.

In this study, the complete mitochondrial genome of Ilisha striatula is presented, and we also discussed its mitochondrial characteristics. The full length of the mitochondrial genome was 16,847 bp, including 13 protein-coding genes (PCGs), 2 ribosomal RNAs, 22 transfer RNA genes, one non-coding control region (CR), and one origin of replication on the light-strand. The total nucleotide composition of the mitochondrial genome was 31.11% A, 24.62% T, 29.10% C, 15.16% G, and AT was 55.73%. The phylogenetic tree based on the ML method supported the placement of I. striatula in a close relationship with I. elongata. These data contribute to a better understanding of the systematics of the Pristigasteridae.

Characterization of the complete mitochondrial genome of Cottiusculus nihonkaiensis (Scorpaeniformes, Cottidae) and phylogenetic studies of Scorpaeniformes.

In this study, the complete mitochondrial genome of Cottiusculus nihonkaiensis was presented, and we also discussed its mitochondrial characteristics. The full length of the mitochondrial genome was 16,612 bp, containing 13 protein-coding genes (PCGs), two ribosomal RNAs (12S and 16S), 22 transfer RNA genes (tRNA), one non-coding control region (CR) and one origin of replication on the light-strand. Overall base composition of the complete mitochondrial DNA was 26.4% A, 17.4% G, 31.5% C, 24.7% T. The phylogenetic tree suggested that C. nihonkaiensis shared the most recent common ancestor with Gymnocanthus herzensteini, Gymnocanthus intermedius and Gymnocanthus tricuspis.

Novel gene rearrangement in the mitochondrial genome of Muraenesox cinereus and the phylogenetic relationship of Anguilliformes.

The structure and gene sequence of the fish mitochondrial genome are generally considered to be conservative. However, two types of gene arrangements are found in the mitochondrial genome of Anguilliformes. In this paper, we report a complete mitogenome of Muraenesox cinereus (Anguilliformes: Muraenesocidae) with rearrangement phenomenon. The total length of the M. cinereus mitogenome was 17,673 bp, and it contained 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNA genes, and two identical control regions (CRs). The mitochondrial genome of M. cinereus was obviously rearranged compared with the mitochondria of typical vertebrates. The genes ND6 and the conjoint trnE were translocated to the location between trnT and trnP, and one of the duplicated CR was translocated to the upstream of the ND6. The tandem duplication and random loss is most suitable for explaining this mitochondrial gene rearrangement. The Anguilliformes phylogenetic tree constructed based on the whole mitochondrial genome well supports Congridae non-monophyly. These results provide a basis for the future Anguilliformes mitochondrial gene arrangement characteristics and further phylogenetic research.

The complete mitochondrial genome of ostorhinchus fleurieu (kurtiformes: Apogonidae) and phylogenetic studies of apogoninae.

The complete mitochondrial genome of Ostorhinchus fleurieu was first determined, which was 16,521 bp in length, containing 13 protein-coding genes, two rRNA genes, 22 tRNA genes, a putative control region and one origin of replication on the light-strand. The overall base composition included C(29.2%), A(26.7%), T(26.7%) and G(17.4%). Moreover, the 13 PCGs encoded 3800 amino acids in total, twelve of which used the initiation codon ATG except for COI started with GTG. Most of them ended with complete stop codon, whereas three protein-coding genes (COII, ND4 and Cytb) used incomplete stop codon and represented as T. The phylogenetic tree based on the Neighbour Joining method was constructed to provide relationship within Apogoninae, which could be a useful basis for management of this species.

Complete mitochondrial genome of Ophichthus brevicaudatus reveals novel gene order and phylogenetic relationships of Anguilliformes.

Generally, a teleostean group possesses only one type or a set of similar mitochondrial gene arrangement. However, two types of gene arrangement have been identified in the mitochondrial genomes (mitogenomes) of Anguilliformes. Here, a newly sequenced mitogenome of Ophichthus brevicaudatus (Anguilliformes; Ophichthidae) was presented. The total length of the O. brevicaudatus mitogenome was 17,773 bp, and it contained 13 protein-coding genes (PCGs), two ribosomal RNAs (rRNAs), 22 transfer RNA (tRNA) genes, and two identical control regions (CRs). The gene order differed from that of the typical vertebrate mitogenomes. The genes ND6 and the conjoint trnE were translocated to the location between trnT and trnP, and one of the duplicated CR was translocated to the upstream of the ND6. The duplication-random loss model was adopted to explain the gene rearrangement events in this mitogenome. The most comprehensive phylogenetic trees of Anguilliformes based on complete mitogenome was constructed. The non-monophyly of Congridae was well supported, whereas the non-monophyly of Derichthyidae and Chlopsidae was not supported. These results provide insight into gene arrangement features of anguilliform mitogenomes and lay the foundation for further phylogenetic studies on Anguilliformes.

Identification, characterization and mRNA transcript abundance profiles of estrogen related receptor (ERR) in Sepiella japonica imply its possible involvement in female reproduction.

Estrogen related receptors (ERRs) are widely detected in vertebrates and apparently have functions in reproduction. The functions of ERRs in reproduction of invertebrates, especially in mollusk cephalopods, are largely unknown. In the present study, An homologue of vertebrate ERR gene was first cloned from female Sepiella japonica, an important Cephalopod species in coastal water of China. Results indicate the S. japonica ERR (sjERR) gene is comprised of 1513 nucleotides, containing a 1389 bp open reading frame, which encode for 463 amino acid (aa) residues. The deduced sjERR protein possessed six typical nuclear receptors (NR) domains (A-F), with a DNA-binding domain (DBD) and a highly conserved ligand-binding domain (LBD), compared to the other molluscan ERRs. Results from tissue analyses indicated that sjERR mRNA transcript abundance was in largest amounts in tissues of the brain, liver, ovary that are possibly involved in reproduction. The sjERR mRNA transcript abundance was temporally regulated during the different sexual maturation phases of female S. japonica and was affected by in vivo administrations of vertebrate steroid estradiol-17ß (E2). An in vivo knockdown of sjERR gene expression resulted in a marked down-regulation in expression of genes involved in ovarian development, such as Vitellogenin, CDK1, and Cyclin B, indicating there is a possible involvement of sjERR in reproduction. Both fusion protein transient transfections and immunohistochemical analyses indicated a presence of sjERR in the nucleus, implying a possible mechanism of action of the sjERR in the nucleus through activation of specific gene transcriptions.

The complete mitochondrial genome of Poecilia formosa (Poecilia, Cyprinodontidae) and phylogenetic studies of cyprinodontiformes.

We report the complete mitochondrial genome sequence of Poecilia formosa. The genome is found to be 16636 bp in length and has a base composition of A (29.59%), G (14.61%), C (28.26%), and T (27.54%). Similar to other Poecilia species, it contains a typically conserved structure including 13 protein-coding genes, 2 rRNA genes, 1 control region (D-loop), and 22tRNA genes. The proportion of coding sequences with a total length of 11,533 bp is 69.33%, which encodes 3837 amino acids. All protein-coding genes started with Met, ND1, CO1, ATP8, ATP6, CO3, ND4L, ND5, ND6 and CytB ended by TAA as a stop codon, ND2 and ND3 ended by TAG as a stop codon, CO3 and ND4 ended by a single T. The lengths of 12S ribosomal RNA is 948 bp, ranging from 70 bp to 1018 bp, and the lengths of 16S ribosomal RNA is 1674 bp, ranging from 1090 bp to 2764 bp. The length of control region is 879 bp, ranging from 15757 bp to 16636 bp, respectively. The complete mitochondrial genome sequence provided here would be useful for further understanding the evolution of ratite and conservation genetics of Poecilia formosa.

The complete mitochondrial genome of Hemigrammus bleheri (Characiformes: Hemigrammus) and phylogenetic studies of Characiformes.

Complete mitochondrial genome of the characiform fish Hemigrammus bleheri was characterized in the present study. The whole mitogenome was 17,021 bp in size and consisted of 13 protein-coding genes (PCGs), 22 tRNAs, 2 rRNAs genes, a control region, and origin of light-strand replication. The proportion of coding sequences with a total length of 11,415 bp is 67.06%, which encodes 3805 amino acids. Similar to other Hemigrammus species, the base composition of H. bleheri was 29.30% for A, 25.26% for C, 16.36% for G, and 29.08% for T. All PCGs started with Met. ND1, ND3, ND4L, ND6, and CytB ended with TAA as the stop codon. ND2, ATP8, and ND5 ended with TAG as a stop codon, CO2, ATP6, CO3, and ND4 ended simply by T, and CO1 ended by a single AGG. The lengths of 12S ribosomal RNA and 16S ribosomal RNA were 924 bp and 1681 bp, respectively. The length of control region (D-loop) was 1308 bp, ranging from 15,714 to 17,021 bp. The complete mitochondrial genome sequence provided here would be helpful in further understanding the evolution of characiformes and conservation genetics of H. bleheri.

Phylogenetic analysis of the complete mitochondrial genome of Orestias ascotanensis (Cyprinodontiformes, Cyprinodontidae).

The complete mitochondrial genome of this species was first determined in this study, which is 16,617 bp in length, containing 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, a putative control region, and 1 origin of replication on the light-strand. The overall base composition includes C(27.11%), A(26.68%), T(29.15%), G(17.04%) and three degenerate bases are R, R and S. Moreover, the 13 PCGs encode 3800 amino acids in total, 12 of which use the initiation codon ATG except COI that uses GTG. Most of them have TAA as the stop codon, whereas ND5 ends with AGA, four protein-coding genes (ND1, ND2, ND3 and Cytb) ended with TAG, and two protein-coding genes (COII and ND4) ended with the incomplete stop codon represented as a single T. The phylogenetic tree based on the Neighbor Joining method was constructed to provide relationship within Cyprinodontidae, which could be a useful basis for management of this species.

Large-scale mitochondrial gene rearrangements in the hermit crab Pagurus nigrofascia and phylogenetic analysis of the Anomura.

Complete mitochondrial genome (mitogenome) provides important information for better understanding of gene rearrangement, molecular evolution and phylogenetic analysis. Currently, only a few Paguridae mitogenomes have been reported. Herein, we described the complete mitogenome of hermit crab Pagurus nigrofascia. The total length was 15,423 bp, containing 13 protein-coding genes (PCGs), two ribosomal RNA, 22 transfer RNA genes, as well as an AT-rich region. The genome composition was highly A + T biased (71.4%), and exhibited a negative AT-skew (-0.006) and GC-skew (-0.138). Eight tRNA genes, two PCGs and an AT-rich region found to be rearranged with respect to the pancrustacean ground pattern gene order. Duplication-random loss and recombination model were adopted to explain the large-scale gene rearrangement events. Two phylogenetic trees of Anomura involving 12 families were constructed. The results showed that all Paguridae species were clustered into one clade except Pagurus longicarpus, which for the first time imposed raises doubt about the morphological taxonomy of this species. Furthermore, the present study found that higher- level phylogenetic relationships within Anomura were controversial, compared with the previous studies. Our results help to better understand gene rearrangements and the evolutionary status of P. nigrofascia and lay foundation for further phylogenetic study of Anomura.

The complete mitochondrial genome of Trachidermus fasciatus (Scorpaeniformes: Cottidae) and phylogenetic studies of Cottidae.

Trachidermus fasciatus is a small catadromous fish and has been listed as a second class state protected aquatic animal since 1988 in China due to the declines in its abundance. We describe the complete mitogenome of T. fasciatus in this study. The mitogenome is 16,536 nucleotides long and contains 13 protein-coding genes (PCGs), two ribosomal RNA genes, 22 transfer RNA genes, and two main non-coding regions. The overall base composition includes C (30%), A (26.3%), T (25.5%), and G (18.2%). Moreover, the 13 PCGs encode 3800 amino acids in total, all the PCGs use the initiation codon ATG except COI uses GTG. Most of them have TAA or TAG as the stop codon, except COII, ND4 and Cytb use an incomplete stop codon T. The phylogenetic tree based on the neighbour joining method was constructed to provide relationship within Cottidae, which could be a useful basis for management of this species.

The complete mitochondrial genome of Chaetodon octofasciatus (Perciformes: Chaetodontidae) and phylogenetic studies of Percoidea.

The complete mitochondrial genome of this species was first determined in this study, which is 16,485 bp in length, containing 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, a putative control region, and 1 origin of replication on the light-strand. The overall base composition includes C(28.2%), A(28.3%), T(27.4%), and G(16.1%). Moreover, the 13 PCGs encode 3796 amino acids in total, 12 of which use the initiation codon ATG except COI that uses GTG. Most of them have TAA as the stop codon, whereas ND3 ends with TAG, and three protein-coding genes (COII, ND4, and Cytb) ended with the incomplete stop codon represented as a single T. The phylogenetic tree based on the Neighbor Joining method was constructed to provide relationship within Percoidea, which could be a useful basis for management of this species.

Phylogenetic analysis of the complete mitochondrial genome of Anguilla japonica (Anguilliformes, Anguillidae).

The Japanese eel (Anguilla japonica), which was listed as Endangered (EN) under the International Union for the Conservation of Nature due to the declines in its abundance, overfishing, and its narrow range distribution. To better protect this species, we described the complete mitogenome of A. japonica in this study. The mitogenome is 16717bp in length and contains 13PCGs, two rRNA genes (12S rRNA and 16S rRNA), 22 tRNA genes, and a putative control region (CR) and one origin of replication on the light-strand (OL). Moreover, the 13 PCGs encode 3813 amino acids in total, all the protein-coding genes use the initiation codon ATG except COI uses GTG. Most of them have TAA or TAG as the stop codon, except COI uses AGG and two PCGs (COII and ND4) use an incomplete stop codon T. A phylogenetic tree based on the Neighbour Joining method was constructed to provide relationship within Anguilla, which could be a useful basis for conservation of this species.