Mitochondrial Genome of Episesarma lafondii(Brachyura:Sesarmidae)and Comparison with Other Sesarmid Crabs

Complete mitochondrial genomes(mitogenomes)can provide useful information for phylogenetic relationships,gene rearrangement,and molecular evolution.Here,the complete mitogenome of Episesarma lafondii(Brachyura:Grapsoidea:Sesarmidae)was sequenced through next-generation sequencing technique for the first time.The 15640 bp mitogenome contains the entire set of 37 genes and an AT-rich region.The rearrangements of two tRNA genes(tRNA-His and tRNA-Gln)are compared with that in the pancrustacean ground pattern,and the tandem duplication/random loss model was selected to explain the observed gene rearrangements.The phylogenetic results showed that all sesarmid crabs belong to the same group,wherein the genus Episesarma showed the closest relationship with Clistocoeloma.Furthermore,the monophyly of each family was well supported except for Xanthidae,Gecarcinidae,and Homolidae.The correlation between the phylogeny of Sesarmidae species and the gaps in the QIM region was analyzed.Evidently,the gaps between Q and I(Gap3 and between I and M(Gap4)degenerated with the evolution process.In general,the results will contribute to the in-depth understanding of gene rearrangements in Sesarmidae mitogenomes and provide new insights into the phylogeny of Brachyura.

Comparative mitochondrial genome analysis of Varunidae and its phylogenetic implications

Complete mitochondrial genomes(mitogenomes)can indicate phylogenetic relationships,as well as useful information for gene rearrangement mechanisms and molecular evolution.Currently,the phylogenetic location of the genus Varuna(Brachyura:Varunidae)has not been well resolved mainly because of limited representatives(only two extant species).Here,we determined a new mitogenome of this genus(Varuna litterata)and added the published mitogenomes to reconstruct the phylogeny of Varunidae.The 16368-bp mitogenome contains the entire set of 37 genes and a putative control region.The characteristics of this newly sequenced mitogenome were described and compared with the other 15 Varunidae mitogenomes.All 16 analyzed mitogenomes have identical gene order and similar molecular features.The sliding window and genetic distance analyses demonstrate highly variable nucleotide diversity,with comparatively low variability of COI and COII,and high variability of ND6.The nonsynonymous/synonymous substitution rates(dN/dS ratio)analysis shows that all 13 PCGs are under purifying selection and ATP8 gene evolves under the least selective pressure.Twelve tRNA genes,two rRNAs,one PCG,and the putative control region are found to be rearranged with respect to the pancrustacean ground pattern gene order.Tandem duplication/random loss model is adopted to explain the large-scale gene rearrangement events occurring in Varunidae mitogenomes.Phylogenetic analyses show that all Varunidae species are placed into one group,and form a sister clade with Macrophthalmidae.Nevertheless,the phylogenetic relationships within Varunidae are not completely consistent based on the two different datasets used in this study.These findings will contribute to a better understanding of gene rearrangement and molecular evolution in Varunidae mitogenomes,as well as provide insights into the phylogenetic studies of Brachyura.

Complete Mitochondrial Genome of Myra affinis(Decapoda:Brachyura:Leucosiidae)and Its Phylogenetic Implications for Brachyura

Knowledge of complete mitochondrial genomes(mitogenomes)can help understand the molecular evolution and phylogenetic relationships of various species.To date,the phylogenetic status of Leucosiidae within Brachyura remains unresolved because of the limited number of mitogenomes available.In the present study,the complete mitogenome of Myra affinis was sequenced using next-generation sequencing to supplement the limited mitogenome information of Leucosiidae.The 15349 bp-long mitogenome includes 13 protein-coding genes(PCGs),22 transfer RNAs(tRNAs),2 ribosomal RNAs(rRNAs),and a putative control region.The overall base composition is 34.5%A,36.1%T,11.5%G,and 17.9%C,with a high AT bias(70.6%).All 13 PCGs start with the standard ATN codon and stop with the TAN codon or incomplete T.Except for tRNA-Ser,all other tRNAs have a typical cloverleaf-like secondary structure.Phylogenetic analyses based on the maximum likelihood and Bayesian inference methods are employed to generate identical phylogenetic topologies,thereby supporting the sister relationship between Leucosiidae and Matutidae for the first time.The monophyly of Eubrachyura is well established,and its sister relationship with Raninoida is strongly supported.The results of this work will not only help achieve a better understanding of the characteristics of the M.affinis mitogenome and the phylogenetic position of Leucosiidae,but also provide relevant information for further studies on the phylogeny of Brachyura.

Comparative mitochondrial genome analysis of Sesarmidae and its phylogenetic implications

Here,we sequenced the complete mitogenome of Parasesarma eumolpe(Brachyura:Grapsoidea:Sesarmidae)for the first time.The characteristics of this newly sequenced mitogenome were described and compared with other Sesarmidae species.The 15646-bp mitogenome contains 13 protein-coding genes(PCGs),two ribosomal RNA genes(r RNAs),22 transfer RNA genes(t RNAs),and an A-T rich region.All of the PCGs are initiated by the start codon ATN and terminated by the standard TAN codon or an incomplete T.The pairwise Ka/Ks ratio analysis shows that all 13 PCGs are under purifying selection,whereas the ATP8 gene is an outlier,with pairwise comparison values ranging from neutral selection(0.000)to positive selection(1.039).The gene arrangement of P.eumolpe compared with ancestral Decapoda shows the translocation of two t RNAs(t RNA-His and t RNA-Gln),which is identical to other Sesarmidae species.Phylogenetic analyses show that all Sesarmidae species are placed into one group,and the polyphyly of Eriphioidea,Ocypodoidea,and Grapsoidea is well supported.The relationship between gaps in the QIM region and the phylogeny of Sesarmidae is analyzed.It is obvious that both the G5(the gap between Q and I)and G6(the gap between I and M)decrease progressively with the evolution process.These results will help to better understand the genomic evolution within Sesarmidae and provide insights into the phylogeny of Brachyura.

Comparative mitochondrial genome analysis of Cynoglossidae(Teleost:Pleuronectiformes)and phylogenetic implications

Generally,a teleostean group(e.g.,family or genus)owns one type or a set of similar mitochondrial gene arrangement.It is interesting,however,that four different types of gene arrangement have been found in the mitochondrial genome(mitogenome)of Cynoglossidae species.So far,the possible mechanisms of mitogenomic gene rearrangement and its potential implications have aroused widespread attention and caused lots of controversy.Here,a total of 21 Cynoglossidae mitogenomes and a newly sequenced mitogenome of Cynoglossus puncticpes(Pleuronectiformes:Cynoglossidae)were compared.The length ranges from 16417 bp to 18369 bp,which is mainly caused by the length heteroplasmy of control region(CR).Further analysis reveals that the difference of tandem repeats acts as a determining factor resulting in the length heterogeneity.Like most gene rearrangements of Cynoglossinae mitogenomes,tRNA-Gln gene encoded by the L-strand has translocated to the H-strand(Q inversion),accompanied by the translocation of CR in C.puncticpes mitogenome.The typical IQM order(tRNA-Ile-Gln-Met)changed to QIM order.Tandem duplication/random loss and mitochondrial recombination were accepted as the most possible models to account for the rearrangements in C.puncticpes mitogenome.Phylogenetic trees showed a strong correlation between the gap spacer in the rearranged QIM area and phylogeny,which provides a fresh idea for phylogenetic studies in future.

Two complete mitogenomes of Ocypodoidea(Decapoda: Brachyura), Cleistostoma dilatatum(Camptandriidae) and Euplax sp.(Macrophthalmidae) and its phylogenetic implications

Complete mitochondrial genomes(mitogenomes) can provide useful information for phylogenetic relationships,gene rearrangement, and molecular evolution. In the present study, two newly sequenced mitogenomes of Ocypodoidea(Cleistostoma dilatatum and Euplax sp.) were reported for the first time, which are 15 444 bp and16 129 bp in length, respectively. Cleistostoma dilatatum is the first species in the family Camptandriidae whose complete mitogenome was sequenced. Each mitogenome contains an entire set of 37 genes and a putative control region, but their gene arrangements are largely different. Tandem duplication and random loss model is proposed to account for their gene arrangements. Comparative genomic analyses of 19 mitogenomes clustering in one branch reveal that 18 of them shared the same gene rearrangement, while that of C. dilatatum mitogenome was consistent with the ancestral gene arrangement of Brachyura. The dN/dS ratio analysis shows that all PCGs are evolving under purifying selection. Phylogenetic analyses show that all Macrophalmidae species cluster together as a group, and then form a sister clade with Camptandriidae. Moreover, the polyphyly of three superfamilies(Ocypodoidea, Eriphioidea, and Grapsoidea) is reconfirmed. These findings help to confirm the phylogenetic position of Camptandriidae, as well as provide new insights into the phylogeny of Brachyura.

Complete Mitochondrial Genome Analysis of Daphniopsis tibetana(Branchiopoda:Diplostraca):New Insights into the Taxonomy of the Genus and Its Phylogenetic Implications for Branchiopoda

Daphniopsis tibetana is widely distributed in Xinjiang,Qinghai,Tibet of China,as well as in Russia and India,which is the dominant zooplankton in many high-altitude(4000 m)salt lakes.D.tibetana can adapt to saline waters,whereas the other species of the superorder Cladocera can only inhabit in freshwater.However,the phylogenetic status of D.tibetana in Branchiopoda remains unclear primarily because of limited mitogenome.In this study,complete mitochondrial genome sequences of D.tibetana were sequenced and annotated for the first time to obtain a comprehensive understanding of its phylogenetic status.The complete mitogenome of D.tibetana is 16196 bp in length.It contains 37 genes,including two ribosomal RNAs(12S and 16S rRNAs)genes,22 transfer RNA(tRNA)genes,13 protein-coding genes,and one non-coding region.The overall base composition is 29.6%A,33.2%T,19.0%G,and 18.2%C with a high AT bias(62.8%).Except for trnS1(GCT),most tRNAs have a typical cloverleaf secondary structure.Phylogenetic analysis based on maximum likelihood and Bayesian inference generates identical phylogenetic topology and shows the phylogenetic status of D.tibetana,which reconfirm the distinction between the genera Daphniopsis and Daphnia.Meanwhile,the class Branchiopoda is clustered into three clades(Anostraca,Notostraca,and Diplostraca)with high support values.These results provide not only a comprehensive understanding of the characteristics of D.tibetana mitogenome and its phylogenetic position in Diplostraca,but also information for future research on the phylogeny of Branchiopoda.

The complete mitochondrial genome of Parachiloglanis hodgarti and its phylogenetic position within Sisoridae

The complete mitogenome of Parachiloglanis hodgarti was sequenced and characterized,which is the first mitogenome of the genus Parachiloglanis within Sisoridae.The mitogenome is 16511-bp long and included 13 protein-coding genes,22 transfer RNAs,two ribosomal RNAs,and one control region.The genome composition was A+T biased(58.64%)and exhibited a positive AT-skew(0.095)and a negative GC-skew(-0.283).Compared with other Sisoridae fishes,the characteristics of nucleotide skews,codon usage,and amino acid usage of the P.hodgarti mitogenome are more similar to those of non-Glyptosternoid fishes.Furthermore,the phylogenetic trees show that Sisoridae fishes fall into four major clades and P.hodgarti(CladeⅠ)is basal to the Sisoridae family,forming a sister clade to the Glyptosternoids(CladeⅣ).The topological structures constructed in this study raised doubts over the traditional classification system.These results will help better understand the feature s of the P.hodgarti mitogenome and provide a reference for further phylogenetic research on Sisoridae species.

Chromosome-level genome assembly of the dotted gizzard shad(Konosirus punctatus) provides insights into its adaptive evolution

Konosirus punctatus is an economically important marine fishery resource and is widely distributed from the Indian to Pacific oceans.It is a good non-model species for genetic studies on salinity and temperature adaptation.However,a high-quality reference genome has not yet been reported.

Frequent recombination in Cynoglossus abbreviatus(Pleuronectiformes:Cynoglossidae)ribosomal 18S rDNA

The conventional theory of concerted evolution has been used to explain the lack of sequence variation in ribosomal RNA(rRNA)genes across diverse eukaryotic species.However,recent investigations into rRNA genes in flatfish genome have resulted in controversial findings.This study focuses on 18S rRNA genes of the widely distributed tongue sole,Cynoglossus abbreviatus(Pleuronectiformes:Cynoglossidae),aiming to explore sequence polymorphism.Five distinct 18S rDNA sequence types(Type A,B,R1,R2,and R3)were identified,suggesting a departure from concerted evolution.A combination of general criteria and variations in highly conserved regions were employed to detect pseudogenes.The results pinpointed Type A sequences as potential pseudogenes due to significant sequence variations and deviations in secondary structure within highly conserved regions.Three types(Type R1,R2,and R3)were identified as recombinants between Type A and B sequences,with simple crossing over and gene conversion as the most likely recombination mechanisms.These findings not only contribute to rRNA pseudogene identification but also shed light on the evolutionary dynamics of rRNA genes in teleost genomes.

Distinct and shared endothermic strategies in the heat producing tissues of tuna and other teleosts

Although most fishes are ectothermic,some,including tuna and billfish,achieve endothermy through specialized heat producing tissues that are modified muscles.How these heat producing tissues evolved,and whether they share convergent molecular mechanisms,remain unresolved.Here,we generated a high-quality genome from the mackerel tuna(Euthynnus affinis)and investigated the heat producing tissues of this fish by single-nucleus and bulk RNA sequencing.Compared with other teleosts,tuna-specific genetic variation is strongly associated with muscle differentiation.Single-nucleus RNA-seq revealed a high proportion of specific slow skeletal muscle cell subtypes in the heat producing tissues of tuna.Marker genes of this cell subtype are associated with the relative sliding of actin and myosin,suggesting that tuna endothermy is mainly based on shivering thermogenesis.In contrast,cross-species transcriptome analysis indicated that endothermy in billfish relies mainly on nonshivering thermogenesis.Nevertheless,the heat producing tissues of the different species do share some tissue-specific genes,including vascular-related and mitochondrial genes.Overall,although tunas and billfishes differ in their thermogenic strategies,they share similar expression patterns in some respects,highlighting the complexity of convergent evolution.

New perspectives on the genetic structure of dotted gizzard shad(Konosirus punctatus)based on RAD-seq

To maintain,develop and rationally utilize marine organisms,understanding their genetic structure and habitat adaptation pattern is necessary.Konosirus punctatus,which is a commercial fish species inhabiting the Indo-west Pacific Ocean,has shown an obvious annual global capture and aquaculture production decline due to climate changes and human activities.In the present study,restriction-site associated DNA sequencing(RAD-seq)was used to describe its genome-wide single nucleotide polymorphisms panel(SNPs).Among 146 individuals collected at nine locations scattered in China,Korea and Japan,a set of 632,090 SNPs were identified.Population genetic analysis showed that K.punctatus individuals were divided into two significant genetic clusters.Meanwhile,potential genetic differentiation between northern and southern population of K.punctatus was found.Treemix results indicated that gene flow existed among sampling locations of K.punctatus,especially from southern Japan to others.Moreover,candidate genes associated with habitat adaptations of K.punctatus were identified,which are involved in diverse physiological processes of K.punctatus including growth and development(e.g.,KIDINS220,PAN3),substance metabolism(e.g.,PGM5)and immune response(e.g.,VAV3,CCT7,HSPA12B).Our findings may aid in understanding the possible mechanisms for the population genetic structure and local adaptation of K.punctatus,which is beneficial to establish the management and conservation units of K.punctatus,guiding the rational use of resources,with reference significance for a profound understanding of the adaptative mechanisms of other marine organisms to the environment.