Three New Ranidae Mitogenomes and the Evolution of Mitochondrial Gene Rearrangements among Ranidae Species

Various types of gene rearrangements have been discovered in the mitogenoes of the frog family Ranidae.In this study,we determined the complete mitogenome sequence of three Rana frogs.By combining the available mitogenomic data sets from Gen Bank,we evaluated the phylogenetic relationships of Ranidae at the mitogenome level and analyzed mitogenome rearrangement cases within Ranidae.The three frogs shared an identical mitogenome organization that was extremely similar to the typical Neobatrachian-type arrangement.Except for the genus Babina,the monophyly of each genus was well supported.The genus Amnirana occupied the most basal position among the Ranidae.The[Lithobates+Rana]was the closest sister group of Odorrana.The diversity of mitochondrial gene arrangements in ranid species was unexpectedly high,with 47 mitogenomes from 40 ranids being classified into 10 different gene rearrangement types.Some taxa owned their unique gene rearrangement characteristics,which had significant implication for their phylogeny analysis.All rearrangement events discovered in the Ranidae mitogenomes can be explained by the duplication and random loss model.     

The complete mitochondrial genomes of two ghost moths, Thitarodes renzhiensis and Thitarodes yunnanensis: the ancestral gene arrangement in Lepidoptera

ABSTRACT: BACKGROUND: Lepidoptera encompasses more than 160,000 described species that have been classified into 45-48 superfamilies. The previously determined Lepidoptera mitochondrial genomes (mitogenomes) are limited to six superfamilies of the most derived lepidopteran lineage Ditrysia. Compared with the ancestral insect gene order, these mitogenomes all contain a tRNA rearrangement. To gain new insights into Lepidoptera mitogenome evolution, we sequenced the mitogenomes of two ghost moths that belong to primitive lepidopteran lineages and conducted a comparative mitogenomic analysis across Lepidoptera. RESULTS: The mitogenomes of Thitarodes renzhiensis and T. yunnanensis are 16,173 bp and 15,814 bp long with an A+T content of 81.28% and 82.33%, respectively. Different tandem repeats in the A+T-rich region mainly account for the size difference between the two mitogenomes. Both mitogenomes include 13 protein-coding genes, 22 transfer RNA genes, and 2 ribosomal RNA genes. The 1,584-bp sequence from rrnS to nad2 was also determined for Thitarodes sp.QL, which has no repetitive sequence in the A+T-rich region. All three Thitarodes species possess the ancestral gene order with trnI-trnQ-trnM located between the A+T-rich region and nad2, which is different from the gene order trnM-trnI-trnQ in all previously sequenced Lepidoptera species. The formerly identified conserved elements of Lepidoptera mitogenomes (i.e. the motif 'ATAGA' and poly-T stretch in the A+T-rich region and the long intergenic spacer upstream of nad2) are absent in the Thitarodes mitogenomes. The phylogenetic analysis supports that Hepialoidea, represented by T. renzhiensis and T. yunnanensis, occupies a basal position in the currently sampled seven superfamilies. The relationships of the other six superfamilies are (((((Bombycoidea + Geometroidea) + Noctuoidea) + Pyraloidea) + Papilionoidea) + Tortricoidea). CONCLUSION: The mitogenomes of T. renzhiensis and T. yunnanensis exhibit unusual features compared with the previously determined Lepidoptera mitogenomes. Their ancestral gene order indicates that the tRNA rearrangement event occurred after Lepidoptera diverged from other holometabolous insect orders. Phylogenetic analysis based on mitogenome sequences is a power tool for addressing phylogenetic relationships among major Lepidoptera superfamilies. Characterization of the two ghost moth mitogenomes has enriched our knowledge of Lepidoptera mitogenomes and contributed to our understanding of the mechanisms underlying mitogenome evolution, especially gene rearrangements.     

传粉和非传粉榕小蜂线粒体基因组进化差异(英文)

【目的】目前关于榕小蜂类群的线粒体基因组报道很少,本研究旨在探讨传粉和非传粉榕小蜂两个群体的线粒体基因组的进化差异。【方法】以15种榕小蜂的线粒体基因组(其中11种的线粒体基因组为新测定)数据为基础,采用比较线粒体基因组学方法,分析榕小蜂的线粒体基因组序列和进化特征。【结果】本研究新测定的11个榕小蜂物种的近全长线粒体基因组的长度范围为12 768~17 060 bp,AT含量均大于80%,除了非传粉榕小蜂Philotrypesis tridentata外,其余物种的AT偏斜为负,GC偏斜为正。榕小蜂线粒体基因重排事件很丰富,并且重排情况可能会对该类群的系统发育分析具有重要的价值。进一步的选择压力分析显示,榕小蜂线粒体基因组中的蛋白质编码基因的ω值均远远小于1,表明这些基因经历了纯化选择,传粉榕小蜂线粒体基因组中的大部分基因比非传粉榕小蜂积累了更多的非同义突变。此外与非传粉榕小蜂相比,传粉榕小蜂的线粒体基因组还具有更丰富的基因重排、更高的核苷酸多态性和更高的氨基酸替换率。【结论】传粉榕小蜂比非传粉榕小蜂的线粒体基因组进化更快,这可能与两个群体显著不同的生活方式或进化史有关。     

The Entire Mitochondrial Genome of Macrophthalmus abbreviatus Reveals Insights into the Phylogeny and Gene Rearrangements of Brachyura

Brachyuran crabs comprise the most species-rich clades among extant Decapoda and are divided into several major superfamilies. However, the phylogeny of Brachyuran remains controversial, comprehensive analysis of the overall phylogeny is still lacking. Complete mitochondrial genome (mitogenome) can indicate phylogenetic relationships, as well as useful information for gene rearrangement mechanisms and molecular evolution. In this study, we firstly sequenced and annotated the complete mitogenome of Macrophthalmus abbreviatus (Brachyura; Macrophthalmidae). The mitogenome length of M. abbreviatus is 16,322 bp, containing the entire set of 37 genes and a control region typically observed in Brachyuran mitogenomes. The genome composition of M. abbreviatus was highly A+T biased 76.3% showing positive AT-skew (0.033) and negative GC-skew (??0.351). In M. abbreviatus mitogenome, most tRNA genes were folded into the clover-leaf secondary structure except trnH, trnS1 and trnC, which was similar to the other species in Macrophthalmidae. Phylogenetic analysis showed that all families form a monophyletic, and Varunidae and Macrophthalmidae clustered into a monophyletic clade as sister groups. Comparative analyses of rearrangement among Brachyura revealed that Varunidae (Grapsoidea) and Macrophthalmidae (Ocypodoidea) had the same gene order, which reinforced the result of phylogeny. The combined results of two aspects revealed that the polyphyly of Ocypodoidea and Grapsoidea were well supported. In general, the results obtained in this research will contribute to further studies on molecular based for the classification and gene rearrangements of Macrophthalmidae or even Brachyura.

     

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.     

The first mitochondrial genome for Brahmin moths (Brahmaeidae) and implications for the higher phylogeny of Bombycoidea

Bombycoidea comprises 10 families and 4723 species, and the phylogenetic relationships among families are still in debate. In this study, we have determined the complete mitochondrial genome (mitogenome) of Brahmaea porphyria. The 15,429-bp mitogenome contains a common set of 37 mitochondrial genes including 13 protein-coding genes, 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and an inferred control region, and shares the conserved gene rearrangement (trnM-trnI-trnQ) in most ditrysian mitogenomes. Moreover, we analysed the secondary structure for all the tRNA genes of B. porphyria and the preference of codon usage in the PCGs of B. porphyria. The putative 373-bp control region (CR) possesses three types of conserved elements, including ATAGA, Ploy-T stretch, and microsatellite-like elements. A phylogenetic analysis among available Bombycoidea mitogenomes using the concatenated 37 mitochondrial genes appears to support the hypothesis of (Sphingidae+Bombycidae)+Saturniidae and the relatively basal phylogenetic position of Brahmaeidae within Bombycoidea.     

Mitogenomes of two neotropical bird species and the multiple independent origin of mitochondrial gene orders in Passeriformes

At least four mitogenome arrangements occur in Passeriformes and differences among them are derived from an initial tandem duplication involving a segment containing the control region (CR), followed by loss or reduction of some parts of this segment. However, it is still unclear how often duplication events have occurred in this bird order. In this study, the mitogenomes from two species of Neotropical passerines (Sicalis olivascens and Lepidocolaptes angustirostris) with different gene arrangements were first determined. We also estimated how often duplication events occurred in Passeriformes and if the two CR copies demonstrate a pattern of concerted evolution in Sylvioidea. One tissue sample for each species was used to obtain the mitogenomes as a byproduct using next generation sequencing. The evolutionary history of mitogenome rearrangements was reconstructed mapping these characters onto a mitogenome Bayesian phylogenetic tree of Passeriformes. Finally, we performed a Bayesian analysis for both CRs from some Sylvioidea species in order to evaluate the evolutionary process involving these two copies. Both mitogenomes described comprise 2 rRNAs, 22 tRNAs, 13 protein-codon genes and the CR. However, S. olivascens has 16,768 bp showing the ancestral avian arrangement, while L. angustirostris has 16,973 bp and the remnant CR2 arrangement. Both species showed the expected gene order compared to their closest relatives. The ancestral state reconstruction suggesting at least six independent duplication events followed by partial deletions or loss of one copy in some lineages. Our results also provide evidence that both CRs in some Sylvioidea species seem to be maintained in an apparently functional state, perhaps by concerted evolution, and that this mechanism may be important for the evolution of the bird mitogenome.     

三种蚜虫的线粒体基因组数据

完整的线粒体基因组已被广泛应用于分子进化、基因组学、系统发育等方面的研究。蚜虫是一类重要的农林业害虫, 但目前公开报道的蚜虫完整线粒体基因组非常有限, 因此获得更多的基因组数据对相关研究具有重要价值。本文报道了榕毛管蚜(Greenidea ficicola)、橘二叉蚜(Aphis aurantia)和油杉纩蚜(Mindarus keteleerifoliae) 3种蚜虫的完整线粒体基因组的序列、详细注释信息、基因结构图、密码子使用情况等。该数据集可为昆虫系统发育关系、种群分化格局、害虫防治等方面的工作提供帮助。     

The Complete Mitochondrial Genome of two Tetragnatha Spiders (Araneae: Tetragnathidae): Severe Truncation of tRNAs and Novel Gene Rearrangements in Araneae

Mitogenomes can provide information for phylogenetic analysis and evolutionary biology. The Araneae is one of the largest orders of Arachnida with great economic importance. In order to develop mitogenome data for this significant group, we determined the complete mitogenomes of two long jawed spiders Tetragnatha maxillosa and T. nitens and performed the comparative analysis with previously published spider mitogenomes. The circular mitogenomes are 14578 bp long with A+T content of 74.5% in T. maxillosa and 14639 bp long with A+T content of 74.3% in T. nitens, respectively. Both the mitogenomes contain a standard set of 37 genes and an A+T-rich region with the same gene orientation as the other spider mitogenomes, with the exception of the different gene order by the rearrangement of two tRNAs (trnW and trnG). Most of the tRNAs lose TΨC arm stems and have unpaired amino acid acceptor arms. As interesting features, both trnS^AGN and trnS^UCN lack the dihydrouracil (DHU) arm and long tandem repeat units are presented in the A+T-rich region of both the spider mitogenomes. The phylogenetic relationships of 23 spider mitogenomes based on the concatenated nucleotides sequences of 13 protein-coding genes indicated that the mitogenome sequences could be useful in resolving higher-level relationship of Araneae. The molecular information acquired from the results of this study should be very useful for future researches on mitogenomic evolution and genetic diversities in spiders.     

Next‐generation sequencing workflow for assembly of nonmodel mitogenomes exemplified with North Pacific albatrosses (Phoebastria spp.)

Use of complete mitochondrial genomes (mitogenomes) can greatly increase the resolution achievable in phylogeographic and historical demographic studies. Using next‐generation sequencing methods, it is now feasible to efficiently sequence mitogenomes of large numbers of individuals once a reference mitogenome is available. However, assembling the initial mitogenomes of nonmodel organisms can present challenges, for example, in birds, where mtDNA is often subject to gene rearrangements and duplications. We developed a workflow based on Illumina paired‐end, whole‐genome shotgun sequencing, which we used to generate complete 19‐kilobase mitogenomes for each of three species of North Pacific albatross, a group of birds known to carry a tandem duplication. Although this duplication had been described previously, our procedure did not depend on this prior knowledge, nor did it require a closely related reference mitogenome (e.g. a mammalian mitogenome was sufficient). We employed an iterative process including de novo assembly, reference‐guided assembly and gap closing, which enabled us to detect duplications, determine gene order and identify sequence for primer positioning to resolve any mitogenome ambiguity (via minimal targeted Sanger sequencing). We present full mtDNA annotations, including 22 tRNAs, 2 rRNAs, 13 protein‐coding genes, a control region and a duplicated feature for all three species. Pairwise comparisons supported previous hypotheses regarding the phylogenetic relationships within this group and occurrence of a shared tandem duplication. The resulting mitogenome sequences will enable rapid, high‐throughput NGS mitogenome sequencing of North Pacific albatrosses via direct reference‐guided assembly. Moreover, our approach to assembling mitogenomes should be applicable to any taxon.     

Round and pointed-head grenadier fishes (Actinopterygii: Gadiformes) represent a single sister group: evidence from the complete mitochondrial genome sequences

The gene order of mitochondrial genomes (mitogenomes) has been employed as a useful phylogenetic marker in various metazoan animals, because it may represent uniquely derived characters shared by members of monophyletic groups. During the course of molecular phylogenetic studies of the order Gadiformes (cods and their relatives) based on whole mitogenome sequences, we found that two deep-sea grenadiers (Squalogadus modificatus and Trachyrincus murrayi: family Macrouridae) revealed a unusually identical gene order (translocation of the tRNA(Leu (UUR))). Both are members of the same family, although their external morphologies differed so greatly (e.g., round vs. pointed head) that they have been placed in different subfamilies Macrouroidinae and Trachyrincinae, respectively. Additionally, we determined the whole mitogenome sequences of two other species, Bathygadus antrodes and Ventrifossa garmani, representing a total of four subfamilies currently recognized within Macrouridae. The latter two species also exhibited gene rearrangements, resulting in a total of three different patterns of unique gene order being observed in the four subfamilies. Partitioned Bayesian analysis was conducted using available whole mitogenome sequences from five macrourids plus five outgroups. The resultant trees clearly indicated that S. modificatus and T. murrayi formed a monophyletic group, having a sister relationship to other macrourids. Thus, monophyly of the two species with disparate head morphologies was corroborated by two different lines of evidence (nucleotide sequences and gene order). The overall topology of the present tree differed from any of the previously proposed, morphology-based phylogenetic hypotheses.     

The complete mitochondrial genome sequence of the little grebe (<Emphasis Type="Italic">Tachybaptus ruficollis</Emphasis>)

Podicipediformes comprises one family (Podicipedidae) including 6 genera, 22 species, and the phylogenetic placement of this order was still in debate. In this study, we sequenced the complete mitochondrial genome (mitogenome) of little grebe (Tachybaptus ruficollis) in Podicipediformes, and explored the phylogenetic position of this order with mitogenome sequences of 21 species from ten families in seven orders. The genome was 16,688 bp in length, and contained 37 genes typical to avian mitogenomes and one control region. The gene organization and characters were similar with other two mitogenomes available in Podicipediformes to date. Phylogenetic tree was constructed with Bayesian method based on mitogenome sequences excluding the control regions. The results supported the closest relationship between Podicipediformes and Phoenicopteriformes, and the topology of our tree was generally similar with the conclusions of previous molecular systematic investigations. Our results furtherly proved the validity of mitogenome data in taxonomic and phylogenetic studies.     

白纹方蟹线粒体基因组全序列测定及方蟹总科比较分析

为探讨该总科内部亲缘关系及其与线粒体基因排序之间的相关性,研究以方蟹科(Grapsidae)白纹方蟹(Grapsus albolineatus)为代表种,测定其线粒体基因组全序列。其全长为15577 bp,包含13个蛋白编码基因,22个tRNA基因, 2个rRNA基因和1个控制区。基因组碱基组成为33.4%A、12.0%G、20.6%C和34.0%T,具有明显的AT偏向性(67.4%)。除ATP8和ND1以GTG作为起始密码子外,其余蛋白编码基因均以ATN作为起始密码子;除COⅡ和Cyt b以T作为不完全终止密码子外,其余基因均以TAN作为终止密码子。亮氨酸(Leu)和半胱氨酸(Cys)分别是使用频率最高(15.28%)和最低(0.81%)的两种密码子。除tRNA-Ser1缺少DHU臂外,其余tRNA均能形成典型的三叶草结构。基于13个蛋白编码基因的核苷酸序列同时构建了方蟹总科的贝叶斯树(BI)和最大似然树(ML),两种方法构建的系统发育树扑拓结构一致,均显示所有方蟹科(Grapsidae)种类聚在一起,其中白纹方蟹与同属的细纹方蟹(G. tenuicrustatus)的亲缘关系最近;...     

The mitogenomes of three beetles (Coleoptera: Polyphaga: Cucujiformia): New gene rearrangement and phylogeny

The mitochondrial genome (mitogenome) has been extensively used for studying phylogenetic relationships at different taxonomic levels. Several molecular analyses have been performed, but the phylogenetic relationships among infraorders in Polyphaga have not been well resolved. In this work, three nearly complete mitogenomes of Coleoptera, Sitophilus oryzae, Oryzaephilus surinamensis and Callosobruchus chinensis, were determined. The O. surinamensis and S. oryzae mitogenomes harbor gene content typical of other Polyphaga mitogenomes, while a gene rearrangement (trnQ) was found in the C. chinensis mitogenome. The mitogenomes of these three Coleoptera species each consist of approximately 13 protein-coding genes, 22 tRNA genes, two rRNA genes and one A + T-rich region. Phylogenetic analysis within Polyphaga was carried out based on mitochondrial data. The phylogenetic results within Polyphaga support the basal position of Cyphon sp., which belonged to Scirtoidea, Elateriformia. Within Cucujiformia, monophyletic Curculionoidea, Chrysomeloidea and Tenebrionoidea were confirmed.     

The complete mitochondrial genome of Eterusia aedea (Lepidoptera,Zygaenidae) and comparison with other zygaenid moths

Zygaenidae comprises >1036 species, including many folivorous pests in agriculture. In the present study, the complete mitochondrial genome (mitogenome) of a major pest of tea trees, Eterusia aedea was determined. The 15,196-bp circular genome contained the common set of 37 mitochondrial genes (including 13 protein-coding genes, two rRNA genes, and 22 tRNA genes) and exhibited the similar genomic features to reported Zygaenidae mitogenome. Comparative analyses of Zygaenidae mitogenomes showed a typical evolutionary trend of lepidopteran mitogenomes. In addition, we also investigated the gene order of lepidopteran mitogenomes and proposed that the novel gene order trnA-trnR-trnN-trnE-trnS-trnF from Zygaenidae and Gelechiidae and most other gene rearrangements of this tRNA cluster evolved independently. Finally, the mitogenomic phylogeny of Lepidoptera was reconstructed based on multiple mitochondrial datasets. And all the phylogenetic results revealed the sister relationships of Cossoidea and Zygaenoidea with both BI and ML methods, which is the first stable mitogenomic evidence for this clade.     

Prospects on the evolutionary mitogenomics of plants: A case study on the olive family (Oleaceae)

The mitogenome is rarely used to reconstruct the evolutionary history of plants, contrary to nuclear and plastid markers. Here, we evaluate the usefulness of mitochondrial DNA for molecular evolutionary studies in Oleaceae, in which cases of cytoplasmic male sterility (CMS) and of potentially contrasted organelle inheritance are known. We compare the diversity and the evolution of mitochondrial and chloroplast genomes by focusing on the olive complex and related genera. Using high‐throughput techniques, we reconstructed complete mitogenomes (ca. 0.7 Mb) and plastomes (ca. 156 kb) for six olive accessions and one Chionanthus. A highly variable organization of mitogenomes was observed at the species level. In olive, two specific chimeric genes were identified in the mitogenome of lineage E3 and may be involved in CMS. Plastid‐derived regions (mtpt) were observed in all reconstructed mitogenomes. Through phylogenetic reconstruction, we demonstrate that multiple integrations of mtpt regions have occurred in Oleaceae, but mtpt regions shared by all members of the olive complex derive from a common ancestor. We then assembled 52 conserved mitochondrial gene regions and complete plastomes of ten additional accessions belonging to tribes Oleeae, Fontanesieae and Forsythieae. Phylogenetic congruence between topologies based on mitochondrial regions and plastomes suggests a strong disequilibrium linkage between both organellar genomes. Finally, while phylogenetic reconstruction based on plastomes fails to resolve the evolutionary history of maternal olive lineages in the Mediterranean area, their phylogenetic relationships were successfully resolved with complete mitogenomes. Overall, our study demonstrates the great potential of using mitochondrial DNA in plant phylogeographic and metagenomic studies.     

Tandem Duplication and Random Loss for mitogenome rearrangement in Symphurus (Teleost: Pleuronectiformes)

Background

The mitochondrial genomes (mitogenomes) of flatfishes (Pleuronectiformes) exhibit highly diversified types of large-scale gene rearrangements. We have reported that the mitogenomes of Crossorhombus azureus (Bothidae), Samariscus latus (Samaridae) and Cynoglossus fishes (Cynoglossidae) show different types of gene rearrangements.

Results

In the present study, the complete mitogenomes of two Symphurus species (Cynoglossidae), Symphurus plagiusa and Symphurus orientalis, were determined. The gene order in the S. plagiusa mitogenome is the same as that of a typical vertebrate (without any gene rearrangements). Surprisingly, large-scale gene rearrangements have occurred in S. orientalis. In the rearranged fragment from the control region (CR) to the WANCY tRNA cluster (tRNA cluster of tRNA-W, tRNA-A, tRNA-N, tRNA-C and tRNA-Y) in the S. orientalis mitogenome, tRNA-V and tRNA-M have been translocated to the 3’ end of the 16S rRNA gene, with six large intergenic spacers over 20 bp in length. In addition, an origin for light-strand replication (O_L) structure that is typically located in the WANCY region was absent in both the S. plagiusa and S. orientalis mitogenomes. It is generally recognized that a sequence in the WANCY region that encodes tRNAs forms a hairpin structure (O_L-like structure) and can act as the O_L when the typical locus is lost. Moreover, an additional O_L-like structure was identified near the control region in the S. plagiusa mitogenome.

Conclusions

The positions of the intergenic spacers and the rearranged genes of the S. orientalis mitogenome strongly indicate that the mechanism underlying the rearrangement of this mitogenome was Tandem Duplication and Random Loss. Additionally, two O_L-like regions substituting for the typical locus were found in the S. plagiusa mitogenome. We speculate that the ancestral mitogenomes of S. plagiusa and S. orientalis also had this characteristic, such that if both O_L-like structures functioned during mitochondrial replication, they could initiate duplicate replications of the light strand (L-strand), leading to duplication of the region between the two structures. We consider that this mechanism may account for the gene duplication that occurred during the gene rearrangement process in the evolution of the ancestral mitogenome to the S. orientalis mitogenome.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1581-6) contains supplementary material, which is available to authorized users.     

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.     

Comparative mitochondrial genomic analysis of Macrophthalmus pacificus and insights into the phylogeny of the Ocypodoidea & Grapsoidea

Grapsoidea and Ocypodoidea, two of the most abundant and economically important groups in Brachyura, are of great commercial value to fisheries and aquaculture. However, the taxonomy of Ocypodoidea and Grapsoidea has long been highly disputed. Previous studies have investigated this problem through phylogenetic analysis based on limited taxonomic sampling, with different reports proposing either monophyly or paraphyly, but no definitive conclusion has been reached. In this study, the complete mitogenome of Macrophthalmus pacificus (Ocypodoidea, Macrophthalmidae) is reported on and the relationship between Ocypodoidea and Grapsoidea is further investigated. Sequencing the M. pacificus mitogenome, which is a closed circular molecule containing a typical 37 genes, preliminarily determined the ancestral gene order of Macrophthalmidae, which is consistent with previous studies. Comparative analyses of gene order among Ocypodoidea and Grapsoidea revealed that Varunidae (Grapsoidea) and Macrophthalmidae (Ocypodoidea) have the same rearrangement, which confirms previous research. Larger data analysis revealed that these two families (Varunidae and Macrophthalmidae) cluster into a monophyletic clade as sister groups. Rearrangement and phylogeny lines of evidence is concluded that Varunidae and Macrophthalmidae may be of common origin. Furthermore, the remaining Ocypodoidea and Grapsoidea families mix paraphyletically in the phylogenetic tree. Therefore, both gene rearrangement and phylogenetic analysis support the paraphyly of Ocypodoidea and Grapsoidea, which reinforces this view. These findings provide important information regarding Brachyura's phylogenetic relationships, which demonstrates the advantage of mitogenome sequence data in phylogenetic studies.