CO1 Gene Research Articles

A new genus Gnathospinosa (Lepidoptera: Tineidae: Euplocaminae) from China, with description of a new species and its taxonomic position.

The genus Gnathospinosa Liao Huang, gen. nov., belonging to the subfamily Euplocaminae, is described with a new species G. qinlingensis Liao Huang, sp. nov. from China as its type species. The new species was illustrated with photographs of the adults and male genitalia. A preliminary phylogenetic study based on mitochondrial cytochrome c oxidase subunit I gene (co1) sequence data of the new species and Psecadioides cuneus are presented.

Genetic diversity of the endangered species Sphyrna lewini (Griffith and Smith 1834) in Lombok based on mitochondrial DNA

Sphyrna lewini is a shark with a wide distribution and one of the most endangered species. Although The International Union for Conservation of Nature (IUCN) classified this species as endangered and the species was already protected by law in Indonesia, S. lewini are currently high exploited because of their high economic value. This study conducted to analyze the genetic diversity and phylogenetic reconstruction the S. lewini landed in Lombok (n = 30) using a molecular approach based on the mitochondrial DNA. DNA amplification with the CO1 gene successfully identified 30 individuals of S. lewini with an average 625-bp nucleotide length. The value of haplotype diversity in Lombok (Hd) = 0.40 and nu π = 0.0018. The results of phylogenetic analysis using Neighbor-Joining (NJ) by Kimura 2-parameter model with 1000 bootstrap showed the connectivity of S. lewini landed in Lombok in 1 clade of 5 haplotypes. This study showed that low genetic diversity and significant differences in genetic structure between populations made this species vulnerable to extinction in Indonesia and required special treatment.

A new synonymy, CO1 barcode, and host and distribution records of the mite Podapolipus luzoni (Acari: Podapolipidae), a subelytral parasite of the invasive beetle, Gonocephalum adpressiforme (Coleoptera, Tenebrionidae)

ABSTRACTAn unusually heavy infestation of 45 adult females and 100% prevalence of the parasitic podapolipid mite, Podapolipus luzoni, was discovered in a population of the invasive tenebrionid beetle species, Gonocephalum adpressiforme, from Japan. Previously, Podapolipus luzoni was known from a single record from the Philippines from an unidentified tenebrionid beetle. We clarify the host range and distribution of the mite species, including its occurrence on Gonocephalum adpressiforme from the Philippines, and discuss its synonymy with Podapolipus alumniae, collected from the same host species in Hawaii. Diagnostic, light microscopy pictures of Podapolipus luzoni are provided. A 1230-bp fragment of the “barcode” CO1 gene was sequenced to facilitate DNA-based identification.

Complete mitochondrial genome of the Antarctic copepod Tigriopus kingsejongenesis (Harpacticoida, Harpacticidae)

The complete mitochondrial genome was sequenced from the Antarctic harpacticoid copepod Tigriopus kingsejongensis. The sequenced genome size was 14,940 bp, possessing different gene order and contents to those of the congeneric species T. japonicus and T. californicus in the genus Tigriopus. The mitochondrial genome of T. kingsejongensis has 13 protein-coding genes (PCGs), 2 rRNAs, and 22 tRNAs. Of the 13 PCGs, CO1, ND3, ATP6, and CO3 genes had incomplete stop codons T–, T–, TA–, and T–, respectively. Furthermore, the stop codons of the remaining 11 PCGs were TAA or TAG, while the start codon of 13 PCGs was ATG (CO1, ND4, Cytb, ND2, ND1, CO2, ND6, ATP6, CO3 genes), ATT (ND5, ATP8 genes), and ATA (ND3, ND4L genes), respectively. The nucleotide of 13 PCGs of T. kingsejongensis mitogenome showed 53.42, 52.17, and 49.10% similarities to the copepods T. japonicus, T. californicus, and Amphiascoides atopus, respectively, while the amino acid similarities were 64.38, 63.86, and 62.40%, respectively.

DNA barcoding of cyprinids (Labeo rohita, Catla catla and Cirrhinus mrigala), mitochondrial CO1-based study

For DNA barcoding, the Cytochrome C Oxidase 1 gene (CO1) is a genetic marker used as uniform, testimonial authentication and reliable evidence for a universal species-level bio-cataloguing system compared with the morphological identification. The barcoding of Catla catla, Cirrhinus mrigala and Labeo rohita of family Cyprinidae was accomplished in the present study. Amplified CO1 gene through PCR was sequenced and figured out using bioinformatic tools. Conspecific and congeneric, K2P nucleotide deviation and nucleotide composition, the number of haplotypes and haplotype diversity were calculated. All three species of studied fish (C. catla, L. rohita and C. mrigala) were G-deficient (17.2, 17.8 and 18.5%) than C (28.3, 27.0, 27.3), A (25.2, 27.3, 26.8) and T (28.0, 28.5, 28.1), respectively. The mean intraspecific and intergeneric K2P genetic distance was .031% and 1.23%, respectively, with a high rate of transitional substitutions. Study revealed that C. catla followed the neutral evolution (R = .5), while C. mrigala (R = 2.01) and L. rohita (R = 2.84) deviated from it and offered very low genetic diversity (<.55).

Complete mitochondrial genome of the water flea Daphnia magna (Cladocera, Daphniidae)

The complete mitochondrial genome was sequenced from the KIT strain of the freshwater water flea (Daphnia magna). The sequenced genome size was 15,253 bp long, possessing identical gene order and contents to those of the congeneric species Daphnia galeata in the genus Daphnia, while the direction of ND2 gene in some strains of D. magna was opposite. The mitochondrial genome of D. magna has 13 protein-coding genes (PGCs), 2 rRNAs, and 22 tRNAs. Of 13 PGCs, five genes (ND2, CO1, CO2, ND4, and ND5) had incomplete stop codons. Furthermore, the stop codons of the remaining eight PGCs were TAG and TAA, while the start codon of CO1 gene was CTA. The base composition of D. magna mitogenome shows an anti-G and -C bias (17.1% and 17.2%) on 13 PCGs, respectively.

Characterization of Clinostomum metacercariae using microscopic and molecular approaches

One of the fundamental aspects in understanding the biology, diversity and epidemiology of a parasite lies in its proper identification. In the present study, morphological and molecular characterization of Clinostomum metacercariae recovered from an ornamental fish, Trichogaster fasciata, was carried out in order to ascertain its identity. To serve the purpose, scanning electron micrographs and gene sequences for two commonly used molecular markers, i.e., nuclear ribosomal internal transcribed spacer 2 (rDNA-ITS2) and mitochondrial cytochrome c oxidase subunit 1 (mtCO1) were obtained. The sequences were further used for generating similarity index matrix as well as inferring phylogenies. Light and electron microscopic observations on metacercariae of the parasite revealed that it belongs to the genus Clinostomum. Identification of the same up to the level of species was made possible through sequence and phylogenetic analyses. The ITS2 sequence analyses of our species (KX758630) showed similarity to unidentified Clinostomum sp. reported from Nigeria (KY865625) and China (KP110579), and C. tilapiae recorded from South Africa (KX034048) and Nigeria (KY649353). However, the CO1 gene analyses suggested it to be highly identical to C. philippinense and the same was also corroborated in the phylogenetic analysis. Thus, morphological and molecular characterization revealed that the recovered metacercariae belong to the species C. philippinense. Additionally, a brief description of secondary structures of ITS2 of various species of Clinostomum has also been discussed.

Qualitative real-time PCR identification of the khapra beetle, Trogoderma granarium (Coleoptera: Dermestidae)

The identification of insect species is generally achieved by analyzing the specific morphological characteristics or, in more recent years, by polymerase chain reaction (PCR) assays of DNA sequences. PCR assays, which detect specific segments of DNA, have been established as a highly sensitive method for a wide range of applications, including the verification of hereditary diseases and for criminal investigations. For the identification of insects, the CO1 (cytochrome c oxidase subunit I) gene of mitochondrial (mt) DNA is often used. However, analyses of the entire mtDNA sequence might yield more reliable regions for use in the identification of insect species. Here we developed a method for real-time PCR identification of the khapra beetle, Trogoderma granarium Everts, by comparing the whole mtDNA sequences of three species of dermestid beetle: the khapra beetle, the varied carpet beetle, Anthrenus verbasci (L.), and the black carpet beetle, Attagenus unicolor japonicus Reitter. Several khapra beetle-specific mtDNA regions were identified and selected for use in the real-time PCR identification of these beetles based on Taq-Man® chemistry. Specificity tests conducted with the DNAs of several insects, including those of the three beetles described above, revealed that the primer/probe sets designed for the real-time PCR were highly specific to their targets.

New synonymies in the Anagrus incarnatus Haliday ‘species complex’ (Hymenoptera: Mymaridae) including a common parasitoid of economically important planthopper (Hemiptera: Delphacidae) pests of rice in Asia

ABSTRACTAnagrus nilaparvartae Pang and Wang has been recorded frequently as an egg parasitoid of rice planthoppers in SE Asia, especially of brown planthopper Nilaparvata lugens (Stål). However, what appears to be the same species was often identified either as the morphologically similar Holarctic species Anagrus incarnatosimilis Soyka (as A. incarnatus Haliday) or misidentified as an unrelated, strictly New World species A. flaveolus Waterhouse, which, unlike A. nilaparvartae, does not belong to the A. incarnatus ‘species complex’ of Anagrus (Anagrus Haliday). Besides being mostly geographically separate from each other (except in the Eastern Palaearctic region), A. nilaparvatae and A. incarnatosimilis were not known to share any hosts. Using a combination of genetic analyses and morphometric methods, specimens of A. incarnatosimilis collected in Europe were shown to be not significantly different from those of A. nilaparvatae reared from eggs of rice planthoppers and leafhoppers mainly in Taiwan and also in Malaysia. Moreover, both A. incarnatosimilis and A. nilaparvatae as well as the morphologically very similar Nearctic species A. columbi Perkins were found to be genetically identical to the common Palaearctic species A. incarnatus Haliday based on both CO1 (mitochondrial) and ITS2 (nuclear) gene regions. Consequently, A. columbi Perkins syn. n. and A. nilaparvatae Pang and Wang syn. n. are synonymised under A. incarnatus, which is re-diagnosed and illustrated. Anagrus incarnatosimilis Soyka stat. rev. (along with its eight current synonyms) is reinstated as a synonym of A. incarnatus.http://zoobank.org/urn:lsid:zoobank.org:pub:70441879-F52B-46FD-8136-6CDAC7B76511

Morphological and molecular diagnoses of Polydora brevipalpa Zachs, 1933 (Annelida: Spionidae) from the shellfish along the coast of China

Shell-boring species Polydora brevipalpa Zachs, 1933 is redescribed based on morphological observations and molecular approach for future unambiguous identification. Genetic distance analyses showed that the interspecific polydorid variation (16.7%-25.6%) was at least 15 times higher than the intraspecific one (0.2%-0.9%) based on the cytochrome c oxidase subunit I (CO1) gene sequences of polydorids. However, 18S rDNA variation pattern demonstrated a rather narrow barcoding gap, with the interspecific polydorid variation (0.5%-5.6%) being very close to the intraspecific one (0.0%-0.4%). As such, the CO1 gene exhibited better DNA barcode for identification of polydorids than the 18S rDNA gene because of the sufficiently large barcoding gaps. Analysis of molecular variance results based on CO1 gene sequences showed that most variations in sequences (97.79%) lay within groups of adult worms and egg capsules rather than between them. This indicated that egg capsules from Crassostrea gigas (Thunberg, 1793) in Ningbo and Nantong were related to the adult worms from Patinopecten yessoensis (Jay, 1857) in Dalian, and both of them belonged to P. brevipalpa. This result was further supported by parsimony network analysis, which showed that egg capsules collected from different localities and adult worms shared a single haplotype. This study was the first to report both P. brevipalpa infestation on C. gigas and to utilise the known CO1 sequences of the adult polydorids to validate morphologically unidentified egg capsules or early larvae. P. brevipalpa was most possibly brought to Chinese waters through transportation of Pa. yessoensis brood stock from Japan.

Genetic and morphometric categorization of Taenia ovis from Sheep in Iran.

Little is known about the genetic and morphological characters of Taenia ovis. The purpose of the present study was to characterize sheep isolates of T. ovis using rostellar hook morphometry as well as mitochondrial genes sequence analysis. Ninety sheep specimens of Cysticercus ovis were collected from 18 slaughterhouses in Iran. The mean ± s.d. for total length of large and small hooks were 174.1 ± 6.4 and 116.7 ± 5.4 µm, respectively. CO1 and 12S rRNA sequence analysis showed 11 and nine haplotypes, respectively. The level of pairwise nucleotide variations between individual haplotypes of CO1 and 12S rRNA genes were 0.3-1.1 and 0.2-1.0%, respectively. Level of nucleotide variation in CO1 and 12S rRNA between T. ovis haplotypes from present study and eight other Taenia species was found to be 11.3-17.8 and 5.3-16.3%, respectively. Phylogenetic analysis clustered all T. ovis isolates into a single clade comprised of the all CO1 and 12S rRNA haplotypes. CO1 nucleotide difference between T. ovis ovis and T. asiatica was 13.6% that is lesser than the corresponding difference between T. ovis ovis and T. ovis krabbei, warranting the designation of two separate species as T. ovis and T. krabbei. Interclass correlation coefficients showed that there was no significant association between rostellar hook length variation and the variability of the mitochondrial genes.

Sequencing the Ant fauna of a Small Island: Can Metagenomic Analysis Enable Faster Identification for Routine Ant Surveys?

All known ant species from a small Western Australian island were subjected to DNA barcoding of the CO1 gene, with a view to using the database to identify ants by Next Generation Sequencing in subsequent, routine surveys. A further aim was to evaluate whether the data could be used to see if any new species had arrived on the island since the total fauna had been inventoried. Of the 125 unique ant species then known from the island, 72 were successfully barcoded. Those that were refractory to amplification were largely the result of sample age and/or contamination. Following this base-line barcoding, ants were sampled from 14 regular sampling sites and ant sequences were obtained from the bulked ‘metagenomic soup’. Prior to doing this, a parataxonomist had identified all ant species in the samples and returned them to the ‘soup’. Successful identification for each site varied from 38% (Sites 12 and 27) to 100% of species (Site 10). Comparison of the number of species recovered with the number of sequences obtained from each sample showed a positive correlation between the two variables. When a site had &gt;1,000 sequences, the average recovery rate was 79%, which is in contrast to the lowest four recovery rates (Site samples 12, 22, 26 and 27), which had fewer than 440 amplicon sequences. The ability to detect individuals that occur at low frequencies is also important. We analysed each site individually to determine if a species was detected and how that related to the proportion of individuals in the pooled sample. Where a species was present at &lt;4% of the total sample, it was only detected 10% of the time, indicating that adequate sequencing depth is critical to species recovery. We conclude that this technique was only partially successful in replacing conventional taxonomy and that it could have limited ability to detect incursions unless the new arrival is abundant. Current barcoding is no longer limited to the CO1 gene and other genes are characterised for identification of intractable groups where CO1 does not provide appropriate levels of resolution.

Diversity of CO1 Gene of Mitochondrial DNA in Representatives of Antimora Genus (Moridae, Gadiformes, Teleostei) in the World’s Oceans

Diversity of CO1 Gene of Mitochondrial DNA in Representatives of Antimora Genus (Moridae, Gadiformes, Teleostei) in the World’s Oceans

Diversity of the CO1 Gene of Mitochondrial DNA in Representatives of Genus Antimora (Moridae, Gadiformes) in the World Oceans.

The frequency of occurrence of the COI gene of mitochondrial DNA in the Pacific flatnose Antimora microlepis and blue antimora Antimora rostrata (Moridae, Gadiformes) was analyzed in samples collected in different areas of the World Ocean. The revealed maximum haplotype diversity of COI in the blue antimora in the North Atlantics may indicate that this species emerged in this region, from which it widely distributed in the World Ocean. The Pacific flatnose Antimora microlepis originated from Antimora rostrata. Antimora might penetrate into the North Pacific by several routes: through the Panama Strait, along the coast of Antarctica, or through the Indian Ocean along the coast of Australia.

Genetic Diversity of Echinococcus granulosus Genotype G1 in Xinjiang, Northwest of China.

Cystic echinococcosis (CE) caused by E. granulosus is a serious helminthic zoonosis in humans, livestock and wildlife. Xinjiang is one of high endemic province for CE in China. A total of 55 sheep and cattle livers containing echinococcal cysts were collected from slaughterhouses in Changji and Yining City, northern region of Xinjiang. PCR was employed for cloning 2 gene fragments, 12S rRNA and CO1 for analysis of phylogenetic diversity of E. granulosus. The results showed that all the samples collected were identified as G1 genotype of E. granulosus. Interestingly, YL5 and CJ75 strains were the older branches compared to those strains from France, Argentina, Australia. CO1 gene fragment showed 20 new genotype haploids and 5 new genotype haplogroups (H1-H5) by the analysis of Network 5.0 software, and the YLY17 strain was identified as the most ancestral haplotype. The major haplotypes, such as CJ75 and YL5 strains, showed identical to the isolates from Middle East. The international and domestic trade of livestock might contribute to the dispersal of different haplotypes for E. granulosus evolution.

Labiobaetis from the Kingdom of Saudi Arabia (Insecta, Ephemeroptera, Baetidae).

Mayfly larvae and imagos were collected at approximately 50 localities of the Kingdom of Saudi Arabia (KSU). Included in this material, three species of Labiobaetis Novikova & Kluge, 1987 are recorded, two of them being new to science. Labiobaetis potamoticus Gattolliat & Al Dhafer, sp. n. is described from both larvae and adults, whereas Labiobaetis alahmadii Gattolliat & Al Dhafer, sp. n. is only known from the larval stage. The two species are compared morphologically with Palearctic and Afrotropical species of Labiobaetis. A third species, Labiobaetis glaucus (Agnew, 1961) is reported for the first time from the Arabian Peninsula. The species was originally described from South Africa and subsequently reported from the east and northeast of Africa. A molecular reconstruction including 18 Afrotropical and Palearctic species of Labiobaetis was performed using 658 bp of the mitochondrial gene CO1. The reconstruction highly supported the validity of the two new species and confirmed the occurrence of L. glaucus in KSU.

Characterization of the complete mitochondrial genome of the medical pipefish Doryichthys boaja Bleeker 1850

In the present study, we reported the complete mitochondrial genome of medical pipefish Doryichthys boaja Bleeker 1850. The complete mitochondrial genome of D. boaja was 16,562 bp in length and had a base composition of A (31.10%), C (24.14%), G (14.36%), and T (30.40%). Similar to other Syngnathidae species, it contained a typically conserved structure, including 13 protein-coding genes, 2 rRNA genes, 1 control region (D-loop), and 22 tRNA genes. The 13 protein-coding genes encoded 3800 amino acids in total, most of which used the initiation codon ATG except CO1 gene started with GTG. For the stop codon, 6 genes applied TAA as the stop codon, while the other 7 genes used an incomplete stop codon T or TA. The lengths of 12S rRNA and 16S rRNA were 941 bp and 1671 bp, respectively. The control region of D. boaja ranged from 15,615 bp to 16,562 bp, which was 948 bp in length. The complete mitochondrial genome of D. boaja provided essential and important molecular data for phylogeography and evolutionary analysis of Syngnathidae Family.

Dario neela, a new species of badid fish from the Western Ghats of India (Teleostei: Percomorpha: Badidae)

Dario neela, is described from a small tributary stream of the Kabini River in northern Kerala, India. It can be distinguished from congeners by the male colouration in life, which shows wide rims of iridescent blue in all median fins and the pelvic fin. It is further distinguished from all species of Dario, except D. urops by the number of abdominal vertebrae (14 vs. 11-13), and from all Dario species except D. urops and D. huli by the presence of a conspicuous black blotch on the caudal-fin base. Dario neela is distinguished from D. urops by the absence of the horizontal suborbital stripe and presence of a series of up to eight black bars on the body; and from D. huli by 27-28 vertebrae and 27 scales in a lateral row and the absence of teeth from hypobranchial 3. Dario neela is genetically divergent from both Western Ghats congeners in the mitochondrial CO1 gene, showing an uncorrected p-distance of 5.9% with D. urops and 13.1% to D. huli.

A new species of Amolops (Anura: Ranidae) from southwestern Guangdong, China.

A new species, Amolops yunkaiensis sp. nov. is described based on a series of specimens from Ehuangzhang Nature Reserve and Yunkaishan Nature Reserve, southwestern Guangdong Province, China. The new species can be distinguished from all known congeners by molecular divergence in the mitochondrial 16S rRNA, 12S rRNA and CO1 genes, and a combination of the following characters: relatively small body size, SVL 31.8-34.1 mm in adult males, 35.2-39.0 mm in adult females; numerous raised large warts on dorsum and flanks; dorsal body olive-brown or light brown with dark brown blotches; absence of vomerine teeth; absence of tarsal glands; presence of a pair of subgular vocal sacs, nuptial spines on the first finger, and sparse translucent tubercles on the lower jaw, forechest, posterior belly and ventral thigh in male. Hence, the genus Amolops contains 52 species, 29 of which occur in China.

New contributions to Gruberia lanceolata (Gruber, 1884) Kahl, 1932 based on analyses of multiple populations and genes (Ciliophora, Heterotrichea, Gruberiidae)

Gruberia Kahl, 1932 is a species-poor genus comprising only seven named species. Most of these species have not been reinvestigated since the original reports. In the present work, we investigated the taxonomy and phylogeny of Gruberia lanceolata (Gruber, 1884) Kahl, 1932 based on analyses of morphology and multiple gene sequences from four South Korean populations. This species is mainly characterized by a well-developed peristome region, segmented paroral membrane, and moniliform macronucleus. Some morphological features were not stable among the four populations investigated, such as body shape and size, cell color, and the ratio of oral length to body length. However, our molecular analyses of four different genetic markers – three nuclear DNA markers (18S rDNA, ITS1-5.8S-ITS2 region, D1D2 of 28S rDNA) and one mitochondrial (mt) marker (CO1 gene) – indicated that all Korean populations examined were the same species. Based on our present findings and historic works, we propose that G. calkinsi, G. aculeata, and G. beninensis are junior synonyms of G. lanceolata.