Xiao-Ping Yu

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 trnSAGN and trnSUCN 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.

Distribution and the origin of invasive apple snails, Pomacea canaliculata and P. maculata (Gastropoda: Ampullariidae) in China

Species of Pomacea, commonly known as apple snails, are native to South America, and have become widely distributed agricultural and environmental pests in southern China since their introduction in the 1980s. However, only since 2010 have researchers recognized that at least two species, P. canaliculata and P. maculata, are present in China. Although impacts of apple snails have been extensively documented, confusion still persists regarding current distributions and origin of the species in China. To resolve this confusion, we used phylogenetic and phylogeographic methods to analyze 1464 mitochondrial COI sequences, including 349 new sequences from samples collected in southern China and 1115 publicly available sequences from snails collected in the native and introduced ranges. Pomacea canaliculata was found atxa0all sampled localities, while P. maculata was found at only five sampled localities in the Sichuan basin and Zhejiang province. Our data indicate that Chinese populations of P. canaliculata share an Argentinian origin, consistent with multiple introductions of this species elsewhere in Asia. In addition, just axa0single lineage ofP. maculata is established in China, which shares with populations in Brazil.

The complete mitochondrial genome of the wolf spider Wadicosa fidelis (Araneae: Lycosidae)

Abstract The complete mitochondrial genome of the wolf spider Wadicosa fidelis was determined. It is a circular molecule of 14,741u2009bp in length and contains a standard set of 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs and a control region. The Au2009+u2009T content of the overall base composition of majority strand (J-strand) is 76.1% (T: 43.0%; C: 8.2%; A:33.1%; G: 15.7%). Start codons in all 13 protein-coding genes (PCGs) follow the ATN rule, except of four genes (COII, COII, ND4 and ND6), which have TTG start codon. The usual termination codons (TAA and TAG) are found from nine PCGs. However, COI, ND1, ND4L, ND5 had an incomplete termination codon (T). The control region (D-loop) is 1071u2009bp long with 67.9% Au2009+u2009T content, and contains a long tandem repeat region, which is comprising three full 215u2009bp copies and a partial fourth (87u2009bp) copy.

The mitochondrial genome of Pomacea maculata (Gastropoda: Ampullariidae).

Abstract The golden apple snail, Pomacea maculata Perry, 1810 (Gastropoda: Ampullariidae) is one of the most serious invasive alien species from the native range of South America. The mitochondrial genome of P. maculata (15u2009516u2009bp) consists of 37 genes (13 protein-coding genes, two rRNAs, and 22 tRNAs) and a non-coding region with a 16u2009bp repeat unit. Most mitochondrial genes of P. maculata are distributed on the H-strand, except eight tRNA genes, which are encoded on the L-strand. A phylogenetic analysis showed that there was a close relationship between P. maculata and another invasive golden apple snail species, Pomacea canaliculata (Lamarck, 1822).

Assessing the effectiveness of mitochondrial COI and 16S rRNA genes for DNA barcoding of farmland spiders in China

Abstract DNA barcoding has been widely used to identify and discover new species in a wide range of taxa. In order to assess the effectiveness of COI (cytochrome C oxidase subunit I) and 16S (16S ribosomal RNA) in the discrimination of spiders, we have generated 289 barcodes for a total of 56 farmland spider species from 14 different families for the first time in China. Our results reveal that the standard barcoding marker COI can be used to distinguish the farmland spiders both in species and family level by NJ tree-based method, despite the absence of a barcode gap between the intra- and inter-specific genetic divergences. 16S has a lower species identification success as compared with COI. However, almost 98% of the species can be correctly distinguished for both COI and 16S when a threshold of 3% nucleotide divergence was used for species discrimination. Our study significantly improves the barcode reference sequence library for Chinese farmland spiders, and will be very useful in pest management and eco-environmental monitoring and protection.

Characterization of the complete mitogenomes of two Neoscona spiders (Araneae: Araneidae) and its phylogenetic implications.

The complete mitogenomes of two orb-weaving spiders Neoscona doenitzi and Neoscona nautica were determined and a comparative mitogenomic analysis was performed to depict evolutionary trends of spider mitogenomes. The circular mitogenomes are 14,161bp with A+T content of 74.6% in N. doenitzi and 14,049bp with A+T content of 78.8% in N. nautica, respectively. Both mitogenomes contain a standard set of 37 genes typically presented in metazoans. Gene content and orientation are identical to all previously sequenced spider mitogenomes, while gene order is rearranged by tRNAs translocation when compared with the putative ancestral gene arrangement pattern presented by Limulus polyphemus. A comparative mitogenomic analysis reveals that the nucleotide composition bias is obviously divergent between spiders in suborder Opisthothelae and Mesothelae. The loss of D-arm in the trnS(UCN) among all of Opisthothelae spiders highly suggested that this common feature is a synapomorphy for entire suborder Opisthothelae. Moreover, the trnS(AGN) in araneoids preferred to use TCT as an anticodon rather than the typical anticodon GCT. Phylogenetic analysis based on the 13 protein-coding gene sequences consistently yields trees that nest the two Neoscona spiders within Araneidae and recover superfamily Araneoidea as a monophyletic group. The molecular information acquired from the results of this study should be very useful for future research on mitogenomic evolution and genetic diversities in spiders.

The complete mitochondrial genome of orb-weaving spider Araneus ventricosus (Araneae: Araneidae).

Abstract The complete mitochondrial genome of an orb-weaving spider Araneus ventricosus was determined. It is a circular molecule of 14,617u2009bp in length and contains a standard set of 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs and a control region. The A + T content of the overall base composition of majority strand (J-strand) is 73.4% (T: 38.5%; C: 10.1%; A: 34.9%; G: 16.5%). Among protein-coding genes, one gene (COI) begins with TTA, two (ATP6 and ND4) start with ATA, three (COII, COIII and ND6) begin with ATT and other seven genes use ATT as initiation codon. COIII and ND3 end with an incomplete stop codon (T), and ND1, ND2 and Cytb are terminated with TAG, while all other genes end with TAA as stop codon. Two regions including tandem repeats were found in the control region (D-loop): a 106u2009bp sequence tandemly repeated twice and a 195u2009bp sequence tandemly repeated twice with a partial third (120u2009bp).

The complete mitochondrial genome of Pomacea diffusa (Gastropoda: Ampullariidae)

Abstract In this study, we analyzed the complete mitochondrial genome of the spike-topped apple snail, Pomacea diffusa Blume, 1957 (Gastropoda: Ampullariidae). The mitochondrial genome of P. diffusa was 16,373u2009bp, consisting 13 protein-coding genes, 2 rRNAs, and 22 tRNAs and a non-coding region with a 12u2009bp repeat unit. There were 29 mitochondrial genes of P. diffusa are distributed on the H-strand, and the other eight tRNA genes encoded on the L-strand. The average AT content of 13 protein-coding genes was 68.7%. A phylogenetic analysis showed that there was a close relationship between P. diffusa and invasive apple snail species, Pomacea canaliculata and Pomacea aff. maculata.

The complete mitochondrial genome of the orb-weaving spider Neoscona theisi (Walckenaer) (Araneae: Araneidae)

Abstract The complete mitochondrial genome of an orb-weaving spider Neoscona theisi (Walckenaer) is determined in this article. It is a typical circular duplex DNA molecule with a length of 14,156u2009bp, which encodes the same 37 genes as all metazoan mitogenomes and an Au2009+u2009T-rich region (D-loop). The overall Au2009+u2009T content is 75.2% (A: 35.5%; T: 39.8%; G: 15.6%; C: 9.3%). All of the protein-coding genes were initiated by ATN, with the exceptions in three genes. COI has a TTA start codon, COII, COIII and ND6 use TTG as initiation codon. Three genes (ND3, COII and ND5) end with incomplete stop codons (T or TA), while all other genes terminated with canonical stop codons (TAA or TAG). Among 22 transfer RNAs genes, six of them (tRNAAla, tRNASer(AGN), tRNASer(UCN), tRNAGly, tRNAArg and tRNAHis) lack the potential to form the cloverleaf-shaped secondary structure. The Au2009+u2009T-rich region is 559u2009bp with an Au2009+u2009T content of 79.6%.

Invisible apple snail invasions: importance of continued vigilance and rigorous taxonomic assessments: Invasive apple snails in China

BACKGROUNDnDue to the similarities of overall shell morphology among apple snail species and considerable variability within species, substantial taxonomic confusion has plagued the accurate identification of Pomacea species. Many invasive apple snails have been mistakenly identified as P. canaliculata since their introduction to Asia around 1980. In 2008, three other introduced species in addition to P. canaliculata were recognized. In 2013, a fifth, previously unrecognized lineage was reported from China, indicating that despite the taxonomic clarity brought by previous work, continued surveys and taxonomic research are necessary to prevent additional introductions and continued spread, as well as to develop effective management strategies.nnnRESULTSnPhylogenetic analysis of mitochondrial COI sequences confirmed the presence of a widespread unidentified Pomacea lineage in China. All sequences from samples of this newly documented lineage were recovered in a monophyletic clade delineated from closely related species; however, different DNA barcoding methods yielded inconsistent species boundaries. Additionally, nuclear EF1α sequences indicated incomplete lineage sorting or recent hybridization of the unidentified lineage with the other two established species.nnnCONCLUSIONnBarcoding is a valuable tool for species discovery, and a powerful approach for delineating introduced species. However, determining the identity of the newly discovered invasive lineage in China will require an integrated taxonomic approach incorporating individuals from the native range, and examination of natural history collections at museums around the world. To manage and prevent additional spread of already established species, and to stop the introduction of new taxa, continued monitoring and rigorous taxonomic assessments must be undertaken.