The complete mitogenome of the hydrothermal vent crab Gandalfus yunohana (Crustacea: Decapoda: Brachyura): a link between the Bythograeoidea and Xanthoidea

Yang, J.‐S., Nagasawa, H., Fujiwara, Y., Tsuchida, S. & Yang, W.‐J. The complete mitogenome of the hydrothermal vent crab Gandalfus yunohana (Crustacea: Decapoda: Brachyura): a link between the Bythograeoidea and Xanthoidea. —Zoologica Scripta, 39, 621–630. Metazoan mitochondrial genomes (mitogenomes) are often used for all‐level phylogenetic analyses and evolution modelling. Although mitochondrial fragments facilitate studying the occurrence and dispersal of hydrothermal‐vent species, few complete mitogenomes have been determined for comprehensive analyses. We determined the complete nucleotide sequence of the bythograeid crab Gandalfus yunohana. The G. yunohana mitogenome is 15 567 bp in length and with an AT content of 69.9%. A putative control region of 625 bp was identified due to its position (between rrnS and trnI) and AT richness (72.8%), which exhibits high similarity with that of the Australian giant crab Pseudocarcinus gigas. The mitochondrial gene order is identical to the typical brachyuran mode. Codon usage, nucleotide composition and bias are well conserved as the Brachyura. Phylogenetic analyses from protein‐coding genes indicated its closest relationship with P. gigas. All the results support the close evolution distance between the Bythograeoidea and Xanthoidea, which might imply the possible origin that the only superfamily of vent crabs underwent. The G. yunohana mitogenome exhibits highly conserved characteristics with those of other decapods, especially its close relative brachyurans. A recent origin rather than the relic fauna was suggested. The present study will supply considerable data of use for both genomics and evolutionary research on hydrothermal vent ecosystems.     

Comparative population structure of two dominant species,Shinkaia crosnieri (Munidopsidae: Shinkaia) and Bathymodiolus platifrons (Mytilidae: Bathymodiolus), inhabiting both deep‐sea vent and cold seep inferred from mitochondrial multi‐genes

Deep‐sea hydrothermal vents and cold seeps, limited environments without sunlight, are two types of extreme habitat for marine organisms. The differences between vents and cold seeps may facilitate genetic isolation and produce population heterogeneity. However, information on such chemosynthetic fauna taxa is rare, especially regarding the population diversity of species inhabiting both vents and cold seeps. In this study, three mitochondrial DNA fragments (the cytochrome c oxidase submit I (COI), cytochrome b gene (Cytb), and 16S) were concatenated as a mitochondrial concatenated dataset (MCD) to examine the genetic diversity, population structure, and demographic history of Shinkaia crosnieri and Bathymodiolus platifrons. The genetic diversity differences between vent and seep populations were statistically significant for S. crosnieri but not for B. platifrons. S. crosnieri showed less gene flow and higher levels of genetic differentiation between the vent and seep populations than B. platifrons. In addition, the results suggest that all the B. platifrons populations, but only the S. crosnieri vent populations, passed through a recent expansion or bottleneck. Therefore, different population distribution patterns for the two dominant species were detected; a pattern of population differentiation for S. crosnieri and a homogeneity pattern for B. platifrons. These different population distribution patterns were related to both extrinsic restrictive factors and intrinsic factors. Based on the fact that the two species were collected in almost identical or adjacent sampling sites, we speculated that the primary factors underlying the differences in the population distribution patterns were intrinsic. The historical demographics, dispersal ability, and the tolerance level of environmental heterogeneity are most likely responsible for the different distribution patterns.     

The complete mitochondrial genome of Tuta absoluta (Lepidoptera: Gelechiidae) and genetic variation in two newly invaded populations in China

Tuta absoluta (Meyrick) (Lepidoptera: Gelechiidae) is a devastating invasive pest worldwide, causing severe damage to tomatoes. Recently, it has been recorded in the northwestern and southwestern parts of China. Here, the mitogenomes and genetic variation of two newly invaded T. absoluta populations in Xinjiang and Yunnan, were determined. The results showed that the complete mitogenome size of T. absoluta is 15298 bp for the individual from Xinjiang and 15296 bp for the individual from Yunnan, which were both longer than the reported mitogenome from Spain (15290 bp). The mitogenome sequences of individuals collected from three locations showed high levels of sequence similarity, except for 8 polymorphic sites, which were in genes cox2 (1 site), cox3 (2 sites), cob (1 site), atp6 (1 site), nad1 (2 sites) and nad5 (1 site). Tuta absoluta mitogenomes share many features with other 6 Gelechiidae mitogenomes, except for several differences in the start and stop codons of protein-coding genes and the length of intergenic spacers. Seven partial mitochondrial genes (cox1, cox2, cox3, atp6, cob, nad1, and nad5) were used for genetic variation analysis, and significant population differentiation was found between the two populations based on cox2, atp6, nad1, and nad5. The complete mitogenomes and sensitive mitochondrial gene markers reported here provide useful data for further population genetics study of this pest.     

The complete mitogenome of the hydrothermal vent crab Xenograpsus testudinatus (Decapoda, Brachyura) and comparison with brachyuran crabs

In this study, we analyzed the complete mitochondrial (mt) genome of a hydrothermal vent crab Xenograpsus testudinatus (Decapoda: Brachyura) obtained from the hydrothermal vents off Kueishantao Island, Taiwan, which extend from the deep sea Okinawa Trench. The mitogenome of X. testudinatus was 15,796 bp in length and contained the same 37 genes (e.g. 2 rRNAs, 22 tRNAs, and 13 PCGs) found in other metazoan mitogenomes. Analysis of the structural mt gene order in X. testudinatus revealed that the 13 PCGs, excluding a translocation of ND6-Cyt b cluster, were similarly ordered when compared to the pancrustacean ground pattern; however the tRNAs were severely rearranged. Phylogenetic analysis of decapod mitogenomes showed that the molecular taxonomy of the vent crab was in accordance with its morphological systematics. Together, these findings suggest that the vent crab studied here has little mitochondrial genetic variation when compared with morphologically defined conspecifics from other marine habitats.     

Characterization of the complete mitochondrial genome of Japanagallia spinosa and Durgades nigropicta (Hemiptera: Cicadellidae: Megophthalminae)

In this study, we determined and analyzed the complete mitochondrial genomes (mitogenomes) of Japanagallia spinosa and Durgades nigropicta (Hemiptera: Megophthalminae). The circular genome were 15,655 bp long in J. spinosa (GenBank: KY123686) and 15,974 bp long in D. nigropicta (GenBank: KY123687). The J. spinosa and D. nigropicta mitogenomes both contained 37 genes and the gene order was similar to that in other leafhoppers. All of the protein-coding genes started with ATN. In the J. spinosa mitogenome, the nad3, nad4L, and cytb genes used TAG as a stop codon, the atp8 and nad1 genes used TGA, and the cox2 gene used a single T. However, in the D. nigropicta mitogenome, three genes used a single T as the stop codon, whereas the nad3 gene used TAG. We predicted the secondary structures of the rRNAs in J. spinosa and D. nigropicta. The secondary structure of rrnL comprised six domains (domain III is absent in arthropods) with 42 helices and that of rrnS comprised three structural domains with 26 helices. Comparisons of J. spinosa and D. nigropicta detected some differences in H577 and H673. We determined the structural organization of the control regions in the mitogenomes of leafhoppers, where three types of repeat regions were found in most. The phylogenetic relationships between J. spinosa and D. nigropicta with related lineages were reconstructed using Bayesian inference and maximum likelihood analyses. The monophyly of each superfamily considered in this study was confirmed by the clades in the phylogenetic tree. And in this study, Cicadellidae was resolved as monophyletic by the phylogenetic analysis. This mitogenome information for J. spinosa and D. nigropicta could facilitate future studies of mitogenomic diversity and the evolution of related insect lineages.     

Characterization of four mitochondrial genomes of Crambidae (Lepidoptera,Pyraloidea) and phylogenetic implications

Loxostege turbidalis, Loxostege aeruginalis, Pyrausta despicata, and Crambus perlellus belong to Crambidae, Pyraloidea. Their mitochondrial genomes (mitogenomes) were successfully sequenced. The mitogenomes of L. turbidalis, L. aeruginalis, P. despicata, and C. perlellus are 15 240 bp, 15 339 bp, 15 389 bp, and 15 440 bp. The four mitogenomes all have a typical insect mitochondrial gene order, including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and one A + T rich region (control region). The PCGs are initiated by the typical ATN codons, except CGA for the cox1 gene. Most PCGs terminate with common codon TAA or TAG, the incomplete codon T is found as the stop codon for cox2, nad4, and nad5. Most tRNA genes exhibit typical cloverleaf structure, except trnS1 (AGN) lacking the dihydrouridine (DHU) arm. The secondary structure of rRNA of four mitogenomes were predicted. Poly-T structure and micro-satellite regions are conserved in control regions. The phylogenetic analyses based on 13 PCGs showed the relationships of subfamilies in Pyraloidea. Pyralidae, and Crambidae are monophyletic, respectively. Pyralidae comprises four subfamilies, which form the following topology with high support values: (Galleriinae + ((Pyralinae + Epipaschiinae)+ Phycitinae)). Crambidae includes seven subfamilies and is divided into two lineages. Pyraustinae and Spilomelinae are sister groups of each other, and form the “PS clade.” Other five subfamilies (Crambinae, Acentropinae, Scopariinae, Schoenobiinae, and Glaphyriinae) form the “non-PS clade” in the Bayesian inference tree. However, Schoenobiinae is not grouped with the other four subfamilies and located at the base of Crambidae in two maximum likelihood trees.     

Comparative Population Structure of Two Deep-Sea Hydrothermal-Vent-Associated Decapods (Chorocaris sp. 2 and Munidopsis lauensis) from Southwestern Pacific Back-Arc Basins

Studies of genetic connectivity and population structure in deep-sea chemosynthetic ecosystems often focus on endosymbiont-hosting species that are directly dependent on chemical energy extracted from vent effluent for survival. Relatively little attention has been paid to vent-associated species that are not exclusively dependent on chemosynthetic ecosystems. Here we assess connectivity and population structure of two vent-associated invertebrates—the shrimp Chorocaris sp. 2 and the squat lobster Munidopsis lauensis—that are common at deep-sea hydrothermal vents in the western Pacific. While Chorocaris sp. 2 has only been observed at hydrothermal vent sites, M. lauensis can be found throughout the deep sea but occurs in higher abundance around the periphery of active vents We sequenced mitochondrial COI genes and deployed nuclear microsatellite markers for both species at three sites in Manus Basin and either North Fiji Basin (Chorocaris sp. 2) or Lau Basin (Munidopsis lauensis). We assessed genetic differentiation across a range of spatial scales, from approximately 2.5 km to more than 3000 km. Population structure for Chorocaris sp. 2 was comparable to that of the vent-associated snail Ifremeria nautilei, with a single seemingly well-mixed population within Manus Basin that is genetically differentiated from conspecifics in North Fiji Basin. Population structure for Munidopsis lauensis was more complex, with two genetically differentiated populations in Manus Basin and a third well-differentiated population in Lau Basin. The unexpectedly high level of genetic differentiation between M. lauensis populations in Manus Basin deserves further study since it has implications for conservation and management of diversity in deep-sea hydrothermal vent ecosystems.     

The complete mitochondrial genome of Mahanta tanyae compared with other zygaenoid moths (Lepidoptera: Zygaenoidea)

The complete mitochondrial genome (mitogenome) of Mahanta tanyae was sequenced and extensively compared with all seven additionally reported zygaenoid mitogenomes. The M. tanyae mitogenome is circular, double-stranded, and 15,323 bp long. Gene content, gene order, and orientation are all typical of Lepidoptera, despite the existence of gene rearrangements for some other zygaenoid mitogenomes. Comparative analyses further showed that the incomplete termination codon T is consistently recognized in the mitochondrial cox1, cox2 and nad4 genes of all zygaenoid species, as well as in the nad5 gene in two limacodid species. Among 13 protein-coding genes, nad6 exhibits the highest evolutionary rate. The structure for each tRNA is highly conserved, including loss of the dihydorouidine (DHU) arm in trnS1 (AGN), but remarkable nucleotide variation exists, primarily in the pseudouridine (TψC) loops. Interestingly, in four species of Zygaenidae, the anticodons for trnS1 (AGN) are consistently UCU, instead of the routinely used codon GCU, in all three species of Limacodidae. In the intergenic region between trnS2 and nad1, a short sequence before the motif “ATACTAA” is present in the M. tanyae mitogenome that is unique among reported zygaenoid mitogenomes. In the A + T-rich region between the motif “ATTTA” and the microsatellite (AT)_n element, some nucleotides were present for most zygaenoid mitogenomes, which is, to our knowledge, rare even in reported lepidopteran mitogenomes. Phylogenetic analyses based on the combined 37 mitochondrial genes confirmed the position of M. tanyae in Limacodidae of the Zygaenoidea.     

Complete mitochondrial genome of the hemp borer,Grapholita delineana (Lepidoptera: Tortricidae): Gene variability and phylogeny among Grapholita

The mitochondrial genome (mitogenome) has been extensively used in phylogenetics and species-level evolutionary investigations. The lepidopteran family Tortricidae (leaf-roller moths), including the genus Grapholita, contains numerous species of economic importance, but for the majority of Grapholita species, their mitogenomes remain poorly studied. Here, we sequence and annotate the full mitogenome of Grapholita delineana, an important pest of hemp worldwide and compare it with the mitogenomes of two congeneric species available from GenBank. The G. delineana mitogenome is 15,599 bp long, including 37 typical mitochondrial genes and an A + T-rich region. Gene content, order and orientation are identical to other reported tortricid mitogenomes. Analyses of nucleotide diversity, Ka/Ks, genetic distance and number of variable sites together suggest that nad6 is the fastest-evolving gene among the mitochondrial PCGs of Grapholita. Our analyses indicate that Grapholita, as presently defined, is not monophyletic, confirming previous morphological and multiple-gene studies, using mitogenomic evidence. Our study provides information on comparative mitogenomics of Tortricidae especially Grapholita.     

Mitochondrial genome of the nematode endoparasitic fungus Hirsutella vermicola reveals a high level of synteny in the family Ophiocordycipitaceae

Ophiocordycipitaceae is a diverse fungal family comprising multiple ecologically, economically, medicinally, and culturally important fungal species; however, only four species of the family have available mitochondrial genomes (mitogenomes). In this study, the complete mitogenome of the nematode endoparasitic fungus Hirsutella vermicola in Ophiocordycipitaceae was sequenced, and a comparative mitogenomic analysis of Ophiocordycipitaceae was performed. We found that the 53,793-bp circular mitogenome of H. vermicola, except for standard fungal mitochondrial genes, harbors seven introns acquired possibly through lateral transfer from other fungi and three free-standing open reading frames (ORFs) coding for hypothetical proteins. Phylogenetic analysis based on concatenated mitochondrial protein sequences confirmed its placement in Ophiocordycipitaceae. Comparison on five mitogenomes of Ophiocordycipitaceae revealed great variation on their sizes, from 35.2 kb in Tolypocladium ophioglossoides to 157.5 kb in Ophiocordyceps sinensis, mainly due to variable numbers of introns (from 7 to 54) as well as variable lengths of intergenic regions. The five mitogenomes, however, are highly syntenic to each other in terms of gene order, the presence of an intronic ORF encoding ribosomal protein S3 within rnl, and the nad2/nad3 joining pattern. Our study is the first report of the mitogenome of H. vermicola and has facilitated the understanding of mitogenome evolution of Ophiocordycipitaceae.

     

两种纺织娘线粒体基因组的比较分析

目前关于螽斯科昆虫的线粒体基因组全序列及其分子进化的研究报道很少。本研究利用L-PCR技术结合嵌套步移PCR扩增获得纺织娘Mecopoda elongata和日本纺织娘M. niponensis的线粒体基因组全序列, 同时对二者之间的碱基组成和结构特点进行了比较分析。结果显示： 纺织娘线粒体基因组（GenBank登录号JQ917910）序列全长15 284 bp, A+T含量71.8%; 日本纺织娘线粒体基因组（GenBank登录号 JQ917909）序列全长15 364 bp, A+T含量72.4%; 2种纺织娘序列长度差异主要是控制区长度不同引起（纺织娘控制区长294 bp, 日本纺织娘控制区长393 bp）。2种纺织娘基因组基因含量、 相对位置及转录方向均与其他已报道的螽斯科昆虫一致, 未发现基因重排现象; 基因组中均存在较长的间隔序列, 在trnA/trnR之间的间隔序列长度分别为63 bp与68 bp, 在trnQ/trnM之间的分别为55 bp和26 bp, 在trnS^UCN/nad1之间的均为21 bp。而最长的基因重叠区域在2种纺织娘trnC/trnW之间均为8 bp, 在atp8/atp6和nad4L/nad4L之间均为7 bp。蛋白质编码基因的碱基组成和密码子使用均具有明显的偏倚性; 除nad1和nad2以特殊的TTG作为起始密码子, cox1使用特殊的起始密码子ATGA外, 其余的10种蛋白质编码基因均使用典型的ATN作为起始密码子。在tRNA基因中, 除trnS^AGN外, 均能折叠形成典型的三叶草形二级结构。在这些tRNA基因中均存在一定数目的以G-U错配为主的碱基错配, 类似现象同样存在于其他已测定的六足动物线粒体基因组中, 表明G-U配对在线粒体基因组中很可能是一种完全正常的碱基配对方式。基因组中控制区的A+T含量略低于线粒体基因组的其他区域, 表明高A+T含量并不是该区域的必要特征。本研究结果为螽斯科系统发生关系重建积累了有价值的数据资料。     

Comparative analysis of mitochondrial genomes of Nirvanini and Evacanthini (Hemiptera: Cicadellidae) reveals an explicit evolutionary relationship

Mitogenomes of five leafhopper species, Chudania hellerina and Concaveplana rufolineata in Nirvanini, Carinata rufipenna, Evacanthus danmainus and E. heimianus representing Evacanthini, were sequenced. The lengths of these five mitogenomes range from 15,044 (C. hellerina) to 15,680 bp (E. heimianus). All five mitogenomes exhibit similar base composition, gene size and codon usage of protein-coding genes. All 22 tRNA genes have typical cloverleaf secondary structures, except for trnS1 (AGN) which appears to lack the dihydrouridine arm. The two included Nirvanini species employ the anticodon TCT instead of the commonly used GCT in trnS1 (AGN). Genes nad2, atp8 and nad6 were highly variable while cox1 and cob showed the lowest nucleotide diversity. Phylogenetic analyses of two concatenated nucleotide datasets, incorporating the newly sequenced taxa and other available membracoid mitogenomes, recovered each included leafhopper subfamily as monophyletic with evacanthine tribes Nirvanini and Evacanthini forming monophyletic sister clades. A relationship among Evacanthinae, Cicadellinae and Typhlocybinae received moderate branch support.     

Unveiling introgression in bumblebee (Bombus terrestris) populations through mitogenome-based markers

The bumblebee, Bombus terrestris, is an important pollinator commercially used on a global scale. The exported subspecies B. t. terrestris has colonised diverse environments, in some cases displacing wild pollinators to the verge of local extinction. In this sense, the native Iberian subspecies B. t. lusitanicus may be threatened by the subspecies B. t. terrestris, naturally distributed from the Pyrenees to Central Europe but also observed in southern Spain due to escapes from commercial nests. Mitochondrial genomes have a low recombination rate and a small effective population size owing to their maternal inheritance, thus providing an accurate approach to study hybridisation events between populations. Therefore, we present the sequences of the mitogenomes of both subspecies as a molecular framework to select suitable markers to detect possible introgression events between them. We used metagenomics to obtain approximately 17 kbp of the mitogenome from both subspecies. Their mitogenomes differed in 358 bp (excluding the AT-rich region). Four mitogenomic fragments were selected to be tested as subspecific diagnostic markers. A RFLP detected in the gene nad2 (NADH dehydrogenase subunit 2) has proven to be an efficient, quick and cost-effective tool to assess the dispersion of the non-endemic subspecies into Iberian native populations. Subspecific haplotypes were observed in both morphological subspecies, suggesting introgression events in the northern natural contact area and in the new human-mediated contact area in the south of the Iberian Peninsula.     

Complete mitochondrial genome of the black‐tailed hornet,Vespa ducalis (Hymenoptera: Vespidae): Genomic comparisons in Vespoidea

We sequenced the complete mitochondrial genome (mitogenome) of the black‐tailed hornet, Vespa ducalis (Hymenoptera: Vespidae). The genome was 15,779‐bp long and contained typical sets of genes [13 protein‐coding genes (PCGs), 22 tRNAs, and 2 rRNAs]. The V. ducalis A + T‐rich region was 166‐bp long and was the shortest of all sequenced Vespoidea genomes, including Vespa. The genome was highly biased toward A/T nucleotides—80.1 % in the whole genome, 77.8 % in PCGs, 83.4–85.6 % in RNAs, and 92.8 % in the A + T‐rich region. These values are well within the typical range for genes and regions of Vespoidea mitogenomes. Start and stop codons in several Vespa species—including V. ducalis—were diversified, despite these species belonging to the same genus. In comparison with the ancestral mitogenomes, Vespa mitogenomes—including that of V. ducalis—showed substantial gene rearrangement; however, we detected no gene rearrangement among Vespa species. We conducted phylogenetic reconstruction based on concatenated sequences of 13 PCGs and two rRNAs (12,755 bp ) in available species of Vespoidea—21 species in six subfamilies in two families (Vespidae and Formicidae). The Bayesian inference and maximum likelihood (ML) methods revealed that each family formed strong monophyletic groups [Bayesian posterior probability (BPP) = 1; ML, 100 %]. Moreover, V. ducalis and V. mandarinia formed a strong sister group (BPP = 1; ML, 94 %).     

The complete mitochondrial genome of the grand jackknife clam, Solen grandis (Bivalvia: Solenidae): a novel gene order and unusual non-coding region

Molluscs in general, and bivalves in particular, exhibit an extraordinary degree of mitochondrial gene order variation when compared with other metazoans. The complete mitochondrial genome of Solen grandis (Bivalvia: Solenidae) was determined using long-PCR and genome walking techniques. The entire mitochondrial genome sequence of S. grandis is 16,784 bp in length, and contains 36 genes including 12 protein-coding genes (atp8 is absent), 2 ribosomal RNAs, and 22 tRNAs. All genes are encoded on the same strand. Compared with other species, it bears a novel gene order. Besides these, we find a peculiar non-coding region of 435 bp with a microsatellite-like (TA)₁₂ element, poly-structures and many hairpin structures. In contrast to the available heterodont mitochondrial genomes from GenBank, the complete mtDNA of S. grandis has the shortest cox3 gene, and the longest atp6, nad4, nad5 genes.     

Analysis of the complete plastomes of three species of Membranoptera (Ceramiales,Rhodophyta) from Pacific North America

Next generation sequence data were generated and used to assemble the complete plastomes of the holotype of Membranoptera weeksiae, the neotype (designated here) of M. tenuis, and a specimen examined by Kylin in making the new combination M. platyphylla. The three plastomes were similar in gene content and length and showed high gene synteny to Calliarthron, Grateloupia, Sporolithon, and Vertebrata. Sequence variation in the plastome coding regions were 0.89% between M. weeksiae and M. tenuis, 5.14% between M. weeksiae and M. platyphylla, and 5.18% between M. tenuis and M. platyphylla. We were unable to decipher the complete mitogenomes of the three species due to low coverage and structural problems; however, we assembled and analyzed, the cytochrome oxidase I, II, and III loci and found that M. weeksiae and M. tenuis differed in sequence by 1.3%, M. weeksiae and M. platyphylla by 8.4%, and M. tenuis and M. platyphylla by 8.1%. Evaluation of standard marker genes indicated that sequences from the rbcL, RuBisCO spacer, and CO1 genes closely approximated the pair‐wise genetic distances observed between the plastomes of the three species of Membranoptera. A phylogenetic tree based on rbcL sequences showed that M. tenuis and M. weeksiae were sister taxa. Short rbcL sequences were obtained from type specimens of M. dimorpha, M. multiramosa, and M. edentata and confirmed their conspecificity with M. platyphylla. The data support the recognition of three species of Membranoptera occurring south of Alaska: M. platyphylla, M. tenuis, and M. weeksiae.     

Phylogenomics and multigene phylogenies decipher two new cryptic marine algae from California,Gelidium gabrielsonii and G. kathyanniae (Gelidiales,Rhodophyta)

Molecular surveys are leading to the discovery of many new cryptic species of marine algae. This is particularly true for red algal intertidal species, which exhibit a high degree of morphological convergence. DNA sequencing of recent collections of Gelidium along the coast of California, USA, identified two morphologically similar entities that differed in DNA sequence from existing species. To characterize the two new species of Gelidium and to determine their evolutionary relationships to other known taxa, phylogenomic, multigene analyses, and morphological observations were performed. Three complete mitogenomes and five plastid genomes were deciphered, including those from the new species candidates and the type materials of two closely related congeners. The mitogenomes contained 45 genes and had similar lengths (24,963–24,964 bp). The plastid genomes contained 232 genes and were roughly similar in size (175,499–177,099 bp). The organellar genomes showed a high level of gene synteny. The two Gelidium species are diminutive, turf‐forming, and superficially resemble several long established species from the Pacific Ocean. The phylogenomic analysis, multigene phylogeny, and morphological evidence confirms the recognition and naming of two new species, describe herein as G. gabrielsonii and G. kathyanniae. On the basis of the monophyly of G. coulteri, G. gabrielsonii, G. galapagense, and G. kathyanniae, we suggest that this lineage likely evolved in California. Organellar genomes provide a powerful tool for discovering cryptic intertidal species and they continue to improve our understanding of the evolutionary biology of red algae and the systematics of the Gelidiales.     

Mitochondrial genomes of the green macroalga Ulva pertusa (Ulvophyceae,Chlorophyta): novel insights into the evolution of mitogenomes in the Ulvophyceae

To further understand the trends in the evolution of mitochondrial genomes (mitogenomes or mtDNAs) in the Ulvophyceae, the mitogenomes of two separate thalli of Ulva pertusa were sequenced. Two U. pertusa mitogenomes (Up1 and Up2) were 69,333 bp and 64,602 bp in length. These mitogenomes shared two ribosomal RNAs (rRNAs), 28 transfer RNAs (tRNAs), 29 protein‐coding genes, and 12 open reading frames. The 4.7 kb difference in size was attributed to variation in intron content and tandem repeat regions. A total of six introns were present in the smaller U. pertusa mtDNA (Up2), while the larger mtDNA (Up1) had eight. The larger mtDNA had two additional group II introns in two genes (cox1 and cox2) and tandem duplication mutations in noncoding regions. Our results showed the first case of intraspecific variation in chlorophytan mitogenomes and provided further genomic data for the undersampled Ulvophyceae.     

Complete mitochondrial exploration of Echinococcus multilocularis from French alveolar echinococcosis patients

Alveolar echinococcosis (AE) is a parasitosis that is expanding worldwide, including in Europe. The development of genotypic markers is essential to follow its spatiotemporal evolution. Sequencing of the commonly used mitochondrial genes cob, cox1, and nad2 shows low discriminatory power, and analysis of the microsatellite marker EmsB does not allow nucleotide sequence analysis. We aimed to develop a new method for the genotyping of Echinococcus multilocularis based on whole mitochondrial genome (mitogenome) sequencing, to determine the genetic diversity among 30 human visceral samples from French patients, and compare this method with those currently in use. Sequencing of the whole mitochondrial genome was carried out after amplification by PCR, using one uniplex and two multiplex reactions to cover the 13,738 bp of the mitogenome, combined with Illumina technology. Thirty complete mitogenome sequences were obtained from AE lesions. One showed strong identity with Asian genotypes (99.98% identity) in a patient who had travelled to China. The other 29 mitogenomes could be differentiated into 13 haplotypes, showing higher haplotype and nucleotide diversity than when using the cob, cox1, and nad2 gene sequences alone. The mitochondrial genotyping data and EmsB profiles did not overlap, probably because one method uses the mitochondrial genome and the other the nuclear genome. The pairwise fixation index (F_st) value between individuals living inside and those living outside the endemic area was high (F_st = 0.222, P = 0.002). This is consistent with the hypothesis of an expansion from historical endemic areas to peripheral regions.     

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.