Genetic Diversity and Endosymbiont Infection Patterns of the Greenhouse Whitefly, Trialeurodes vaporariorum, in China.

Co-overexpression of the epidermal growth factor (EGF) receptor (EGFR) and c-Src frequently occurs in human tumors and is linked to enhanced tumor growth. In experimental systems this synergistic growth requires EGF-dependent association of c-Src with the EGFR and phosphorylation of Tyr-845 of the receptor by c-Src. A search for signaling mediators of Tyr(P)-845 revealed that mitochondrial cytochrome c oxidase subunit II (CoxII) binds EGFR in a Tyr(P)-845- and EGF-dependent manner. In cells this association involves translocation of EGFR to the mitochondria, but regulation of this process is ill-defined. The current study demonstrates that c-Src translocates to the mitochondria with similar kinetics as EGFR and that the catalytic activity of EGFR and c-Src as well as endocytosis and a mitochondrial localization signal are required for these events. CoxII can be phosphorylated by EGFR and c-Src, and EGF stimulation reduces Cox activity and cellular ATP, an event that is dependent in large part on EGFR localized to the mitochondria. These findings suggest EGFR plays a novel role in modulating mitochondrial function via its association with, and modification of CoxII.

Dear Editor, Multiple infections with small liver flukes and minute intestinal flukes are the serious public health concern in the lower Mekong basin [1,2]. Although the epidemiological survey for those trematode infections are primarily carried out based on copro-parasitological examination, detection/identification of fecal eggs/worms is a tedious job and often problematic because of the morphological similarities of eggs/worms. Along with the popularization of PCR-sequencing methods, copro-DNA diagnosis and molecular phylogenetic identification/speciation have been introduced in epidemiological studies. Among various genes and non-coding lesions of nuclear and mitochondrial DNAs, mitochondrial cytochrome c oxidase subunit I (COXI) is one of the most widely used inter- and intra-species marker. Using COXI and some other markers, Lee and his colleagues performed molecular phylogenetic analyses on small liver flukes (Lee SU, Huh S. Variation of nuclear and mitochondrial DNAs in Korean and Chinese isolates of Clonorchis sinensis. Korean J Parasitol 2004; 42: 145-148) and on minute intestinal flukes (Lee SU, Huh S, Sohn WM, Chai JY. Sequence comparisons of 28S ribosomal DNA and mitochondrial cytochrome c oxidase subunit I of Metagonimus yokogawai, M. takahashii and M. miyatai. Korean J Parasitol 2004; 42: 129-135). The COX1 gene sequences appeared in those articles are; Clonorchis sinensis ({type:entrez-nucleotide,attrs:{text:AF184619,term_id:296940320,term_text:AF184619}}AF184619, {type:entrez-nucleotide,attrs:{text:AF181889,term_id:285026682,term_text:AF181889}}AF181889, {type:entrez-nucleotide,attrs:{text:AF188122,term_id:285809842,term_text:AF188122}}AF188122), Metagonimus yokogawai ({type:entrez-nucleotide,attrs:{text:AF096230,term_id:297039733,term_text:AF096230}}AF096230), Metagonimus takahashii ({type:entrez-nucleotide,attrs:{text:AF096231,term_id:297039734,term_text:AF096231}}AF096231), Metagonimus miyatai ({type:entrez-nucleotide,attrs:{text:AF096232,term_id:297039735,term_text:AF096232}}AF096232), Pygidiopsis summa ({type:entrez-nucleotide,attrs:{text:AF181884,term_id:288563287,term_text:AF181884}}AF181884), and Stellantchasmus falcatus ({type:entrez-nucleotide,attrs:{text:AF181887,term_id:285804435,term_text:AF181887}}AF181887). In addition, Park [3] compared his COXI sequence of Opisthorchis viverrini Laotian isolate (AY055 382) to those of Gymnophalloides seoi ({type:entrez-nucleotide,attrs:{text:AF096234,term_id:297039736,term_text:AF096234}}AF096234) and Neodiplostomum seoulense ({type:entrez-nucleotide,attrs:{text:AF096233,term_id:285026845,term_text:AF096233}}AF096233) registered in the DNA database (Lee et al. unpublished). For the phylogenetic analyses of COXI gene of minute intestinal flukes of our own data, we have downloaded all those above mentioned COXI of Lee et al. and aligned them including our own COXI sequence of Haplorchis taichui ({type:entrez-nucleotide,attrs:{text:EF055885,term_id:119855482,term_text:EF055885}}EF055885) [4] and Paragonimus bangkokensis ({type:entrez-nucleotide,attrs:{text:AB354227,term_id:155369203,term_text:AB354227}}AB354227) [5]. Surprisingly, those sequence data were divided into 2 distinct groups without any similarities (Fig. 1). Eventually, we realized that this astonishing result is due to the reverse complementary sequences of COXI data deposited by Lee et al. (in the bottom half of the figure). We also noticed similar mixed-up deposition of the forward and reverse sequences of COXI gene of Fasciola spp., which were also included in Fig. 1 ({type:entrez-nucleotide,attrs:{text:AJ628024,term_id:88319716,term_text:AJ628024}}AJ628024, {type:entrez-nucleotide,attrs:{text:AJ628039,term_id:88319746,term_text:AJ628039}}AJ628039, {type:entrez-nucleotide,attrs:{text:FJ469984,term_id:238631966,term_text:FJ469984}}FJ469984; Zhu XQ et al. unpublished). Fig. 1 The DNA sequence alignment of the partial COXI gene of some trematodes obtained from the GenBank. Seven sequences from the top are the forward strands with JB3 primer sequence, and 2 in the middle are the forward strands without primer. Eight sequences ... For the determination of partial COX1 sequences of Platyhelminthes, the primer set of JB3 (5'-TTT TTT GGG CAT CCT GAG GTT TAT-3') and JB4.5 (5'-TAA AGA AAG AAC ATA ATG AAA ATG-3') [6] was widely used for investigating the inter- and intra-species variations of trematodes and cestodes. We noticed the mixed-up of the forward and reverse COXI sequences by Lee et al. as well as Zhu et al. because of the presence of the characteristic feature of this primer set (boxed in Fig. 1) in the sequences. The primer sequence should be deleted from the sequence data because it is not always identical with the real DNA sequence of the gene and the inclusion of the primer sequences sometimes causes the misreading in phylogenetic analyses [7]. In 3 reverse sequences, {type:entrez-nucleotide,attrs:{text:AF181884,term_id:288563287,term_text:AF181884}}AF181884, {type:entrez-nucleotide,attrs:{text:AY055380,term_id:22203992,term_text:AY055380}}AY055380, and {type:entrez-nucleotide,attrs:{text:AF096233,term_id:285026845,term_text:AF096233}}AF096233 seems to contain also the partial sequence of the cloning vector, which should be trimmed off before deposition. In general, raw data of forward and reverse sequences obtained from the sequencer should be aligned manually by cross-checking of the wave patterns because some 10-20 bases downstream from the forward primer and upstream from the reverse primer often contain erroneous base pairs [8]. Deposition of the reverse sequence means that those sequences were not aligned against forward sequence and not quite reliable. Since each sequence data in GenBank are opened for the public use, an accuracy of the sequence data is critically important for the mutual reliability of the scientists. The scientists should aware how to deposit accurate sequence data to the DNA data base. The reappraisal and correction of those sequences mentioned above is urgently necessary.

基于线粒体细胞色素c氧化酶亚基I基因序列的帘蛤科贝类分子系统发育研究

Brine shrimps Artemia (Crustacea, Anostraca) are a group of cosmopolitan extremophile microcrustaceans which are composed of a complex of six sexual species and numerous Eurasian Haplotype Complex (EHC) lineages. In the present study, we analyzed a partial sequence of the mitochondrial cytochrome c oxidase subunit I (COI) and nuclear Internal transcribed spacer1 (ITS1), as well as genomic fingerprints by ISSR-PCR (inter-simple sequence repeats) for a large set of Artemia specimens (N ~ 600) from various geographical localities (N = 102) across Eurasia and America. Asian lineages have revealed a mixture of paraphyletic and polyphyletic groups of Artemia. A. urmiana and A. tibetiana represent a species complex with multiple genetic lineages. EHC lineages (Eurasian and Africa) showed a star-like haplotype pattern, which had more genetic similarities to other sexual Asian species, except A. sinica. Bayesian analysis of COI was used to estimate the time of divergence of Asian Artemia species. The Bayesian analysis indicated that Asian taxa are relatively young, particularly EHC lineages. A. urmiana recorded as the oldest species originated in the Pleistocene and could be considered as a major source of its expansion to its modern habitats in Eurasia. Molecular dating analyses using a relaxed bayesian molecular clock depicted that A. sinica has been diverged from other Asian lineages in the Miocene, around 20 million years ago (Mya). A. urmiana was the dominant sexual species in Urmia Lake exhibiting a high genetic diversity with a low level of genetic structure in the entire lake. This species was essentially homogeneous indicative of panmixia. A correlation between population differentiation and geographical and ecological differences was not observed. The invasive A. franciscana have permanently colonized 31 geographical localities along the southern and eastern coastal regions of Asia. EHC lineages were observed in 39 inland geographical localities in Asia. Asian A. franciscana generated a signature of haplotype diversity as compared to the source population from Great Salt Lake (GSL, USA). The high genetic diversity of Asian A. franciscana is probably attributed the numerous, human-mediated, dispersal events and multiple introductions from GSL & San Francisco Bay (SFB, USA) and eventually indirect introductions from other native localities in the Americas. Our results indicate that biological invasion do not necessarily lead to reduced genetic diversity, particularly if multiple source populations, each with distinctive genetic composition, contribute to the founding populations. EHC lineages showed low genetic diversity which is in contrast to the restricted geographic distribution, strong genetic structure, and regional endemism of sexual Artemia lineages in Asia. A. franciscana in GSL revealed the same condition as observed in A. urmiana. It showed a high genetic diversity with an evidence of panmixia throughout the lake. %%%%Artemia (Crustacea, Anostraca) ist eine Gruppe kosmopolitischer, extremophiler…

Phylogenetic investigations of Lingula anatina among some northwestern Pacific populations, based on mitochondrial DNA cytochrome c oxidase subunit I gene

Spodoptera litura is a notorious leaf feeding insect pest in the Asia-Pacific region and leads to a significant economic loss in vegetable and field crop production. Entomopathogenic nematodes (EPNs), lethal parasites of insects, are used as biocontrol agents. Yunnan Province in China is a well-known region due to its rich biodiversity. In the present study, a survey of EPNs using the Galleria-baiting technique was conducted in 2017 and 2018 throughout the entire Yunnan province. In total, 789 soil samples were collected from 232 sites, of which 75 samples were positive for EPNs. Phylogenetic analyses of ITS, D2D3 expansion region of the 28S rRNA gene, as well as mitochondrial cytochrome c oxidase subunit I (COI), were performed to identify isolated nematode species and evaluate their genetic diversity. In total, 13, 3, and 58 identified populations belong to Steinernema, Heterorhabditis, and Oscheius, respectively. The phylogenetic relationships of EPN species in the three genera were analyzed with the Neighbor-Joining method. The virulence of the trapped isolates in the genera of Steinernema, Heterorhabditis, and Oscheius against S. litura was evaluated. Ten new indigenous isolates from Steinernema and Heterorhabditis showed prominent virulence to S. litura within 48 hr which is equivalent to that of commercial EPNs populations. The present study provides background information on indigenous EPN resources for S. litura control in Asia-Pacific region.

Among the Ixodid ticks, Hyalomma anatolicum is a well-known vector that transmits various pathogens to terrestrial and semi-terrestrial vertebrates including humans, and its population differ in ecology and vector competence. Expansion of this tick to new areas changes the genetic structure, and lead to affect the vector-pathogen interaction and disease outcomes. The present study was designed to infer the haplotype diversity, demographic dynamics, gene flow and genetic differentiation, and phylogeny of H. anatolicum from different countries based on the cytochrome oxidase I (COI) and 16S rDNA sequences. A total of 320 ticks were collected from cattle, buffaloes, and sheep in five districts of Khyber Pakhtunkhwa, Pakistan, morphologically identified as H. anatolicum, and subjected to genetic analysis. A total 85 and 138 sequences for COI and 16S rDNA, including 11 and 2 sequences generated in this study, respectively, were analyzed to assess haplotype network, population structure and divergence, demographic changes, and phylogenetic analysis. Analysis based on COI sequences yielded 29 haplotypes in which haplotype 1 and 15 were the predominant consisting of 35 and 20 sequences, respectively, from Pakistan, India, China, Bangladesh, Iraq, Saudi Arabia, Kazakhstan and Egypt. The 16S rRNA yielded 30 haplotypes in which haplotype 1 was predominant consisting of total 86 sequences from Pakistan, India, China, United Arab Emirates, Tajikistan, Kazakhstan, Turkey, Egypt, and Iraq. Complete haplotype network based on COI and 16S rRNA confirmed stellate structure, together with high haplotype diversity (COI 0.77899, 16S rRNA 0.60774) and low nucleotide diversity (COI 0.00445, 16S rRNA 0.00431), which support recent population expansion. Similarly, neutrality indices for the whole dataset, Tajima’s D (COI − 2.36363**, 16S rRNA − 2.54127***), Fu and Li’s D (COI − 5.72992, 16S rRNA − 6.31313*), and Fu and Li’s F (COI − 5.04435*, 16S rRNA − 5.56085*) were negative, indicating deviation from neutrality and recent population dispersal. In the phylogenetic tree based on the COI and 16S rDNA sequences, with exception of one sequence for a single haplotypes, which appeared independently, there is a single main clade that includes the largest number of sequences for all other haplotype. Based on COI and 16S rDNA sequences, the present study provided first detail information about the population genetics and haplotype networks of H. anatolicum.

Genetic diversity and spatiotemporal population structure of Anopheles sinensis in the Republic of Korea based on the mitochondrial cytochrome c oxidase subunit I (COI) marker

The locally extinct dung beetle, Gymnopleurus mopsus Pallas, 1781 (Coleoptera: Scarabaeidae), has not been found in South Korea since the 1970s. This research was conducted to understand the genetic divergence between the South Korean and Mongolian populations of G. mopsus as a part of its reintroduction program in South Korea. The genetic distance and diversity were determined using the mitochondrial cytochrome c oxidase subunit I (COI) gene sequence (658 bp) corresponding to the DNA barcode region. The mitochondrial COI gene sequences of 64 individuals of G. mopsus collected in South Korea (7 individuals) and Mongolia (57 individuals) showed a relatively high level of genetic diversity (nucleotide diversity, 0.0078 ± 0.0007; Haplotype diversity, 0.965 ± 0.017). The genetic distances between the South Korean and Mongolian populations lay within the intraspecific level and the phylogenetic reconstruction using the neighbor‐joining (NJ) method showed that all individuals belonged to a single clade. This result indicates that the current Mongolian population of G. mopsus is a good candidate source population to restore the locally extinct population of the species in South Korea.

Sphaeroma terebrans, a wood-boring isopoda, is distributed worldwide in tropical and subtropical mangroves. The taxonomy of S. terebrans is usually based on morphological characteristics, with its molecular identification still poorly understood. The number of teeth on the uropodal exopod and the length of the propodus of the seventh pereopod are considered as the major morphological characteristics in S. terebrans, which can cause difficulty in regards to accurate identification. In this study, we identified S. terebrans via molecular and morphological data. Furthermore, the validity of the mitochondrial cytochrome c oxidase subunit I (COI) gene as a DNA barcode for the identification of genus Sphaeroma, including species S. terebrans, S. retrolaeve, and S. serratum, was examined. The mitochondrial COI gene sequences of all specimens were sequenced and analysed. The interspecific Kimura 2-parameter distances were higher than intraspecific distances and no intraspecific-interspecific distance overlaps were observed. In addition, genetic distance and nucleotide diversity (π) exhibited no differences within S. terebrans. Our results revealed that the mitochondrial COI gene can serve as a valid DNA barcode for the identification of S. terebrans. Furthermore, the number of teeth on the uropodal exopod and the length of the propodus of the seventh pereopod were found to be unreliable taxonomic characteristics for S. terebrans.

ABSTRACTThe giant jellyfish Nemopilema nomurai is a scyphozoan species well-known in East Asian Marginal Seas for its damage to fisheries. The genetic diversity and population structure of N. nomurai, collected from five geographic regions in Chinese coastal seas, were examined based on mitochondrial cytochrome c oxidase subunit I (COI) gene and nuclear internal transcribed spacer one (ITS1) sequences. A total of 26 and five unique haplotypes were recovered from the COI and ITS1 genes, respectively. The overall genetic diversity of N. nomurai calculated by the COI and ITS1 sequences was low (haplotype diversity 0.727% and 0.108%, nucleotide diversity 0.212% and 0.039%). The median-joining network analysis revealed a star-like haplotype network. The hierarchical Analysis of Molecular Variance (AMOVA) of COI haplotypes showed that N. nomurai populations form a single population, with a low FST (0.0149, p = 0.1036). The dispersal ability, together with the biological characteristics, could be important factors for the lack of a geographically structured pattern in N. nomurai in Chinese coastal waters.

利用线粒体COI和微卫星标记分析文蛤7个地理群体的遗传变异

Understanding the evolutionary history, genetic diversity and distribution patterns of terrestrial gastropods in tropical regions—especially in light of climatic fluctuations and tectonic activity—is a pivotal challenge in biogeography and evolutionary biology. This study focuses on semi-slugs of the genus Microparmarion, endemic to northern Borneo. Using mitochondrial cytochrome c oxidase subunit I (COI) and 16S ribosomal RNA (16S rRNA) gene fragment sequences, we investigated phylogenetic relationships among six Microparmarion species in the region. Our combined dataset provided a well-resolved phylogeny, confirming the monophyly of each species and clarifying previous taxonomic uncertainties. Sequence divergence analyses revealed higher divergences in COI than in 16S rRNA, both within and among populations, with substantial interspecific divergences (COI: 10–11%). Haplotype network analyses uncovered distinct population structures characterized by diverse haplotypes and limited gene flow among populations, suggesting the influence of historical isolation and restricted dispersal. Ecological niche models indicated an expanded range for Microparmarion simrothi during cooler glacial periods and a contraction of suitable habitats for M. basifixus, implying differing responses to historical climatic conditions. Our findings suggest that mountain ranges like Mount Kinabalu served as important interglacial and glacial refugia for these species, influencing their current distribution patterns and genetic diversity. This study highlights the significant roles of historical climatic events and topographical barriers in shaping the evolutionary history of Microparmarion species in northern Borneo.

Thaisella chocolata is a marine gastropod (family Muricidae) occurring from northern Peru to central Chile. It is of economic importance in these countries, where hundreds of tons are caught every year. In combination with El Niño–Southern Oscillation events, fishing activity has led to the collapse of Chilean populations, raising concerns about the state of Peruvian populations. The aim of this study is to assess the demography, genetic diversity and connectivity of T. chocolata along the Peruvian coast. This would provide important insights into the resilience of this species to anthropogenic disturbance. In this study, four locations along the coast of Peru were investigated for the first time. Mitochondrial cytochrome c oxidase subunit I (COI) sequences were obtained from 116 individuals and four microsatellites from 95 individuals. Both COI (combined with 156 publicly available sequences) and microsatellite data revealed very low genetic differentiation, despite a few significant φST and FST values between population pairs. The most likely gene flow model (MIGRATE-N) is panmixia between all locations, with gene flow occurring equally northwards and southwards. This pattern may be related to the surface currents along the Peruvian coastline combined with the high pelagic larval duration of T. chocolata. Hyperdiversity was found for the COI marker (πsyn > 5%). Microsatellite loci were also polymorphic, with a mean diversity of 12.69 alleles per locus per population. No recent population bottleneck was observed (microsatellite data), while at least one past demographic expansion was suggested (COI data). Given the high genetic diversity and connectivity, T. chocolata is expected to show high evolutionary resilience and can be considered as one management unit in terms of fisheries management. However, further studies, on, for example, the characterization of effective population size (using numerous nuclear loci), are required to confirm this hypothesis. In addition, precautionary fisheries measures should be maintained, given the recent collapse of T. chocolata stocks in Chile.

Developing a new molecular marker for aphid species identification: Evaluation of eleven candidate genes with species-level sampling