Comparative mitogenome analysis on species of four apple snails (Ampullariidae: Pomacea)

Population genetics and genetic variation of Pomacea canaliculata (Gastropoda: Ampullariidae) in China revealed by sequence analyses of three mitochondrial genes

The Golden apple snail, Pomacea canaliculata, is one of the world's 100 worst invasive alien species that is best known for its damage to wetland agriculture. It also acts as an intermediate host of some zoonotic parasites such as Angiostrongylus cantonensis, posing threats to human public health and safety. Despite is being an important agricultural pest, the genetic information and population expansion history of this snail remains poorly understood in China. In this study, we analyzed the genetic variation and population genetics of P. canaliculata populations in seven regions of China based on molecular markers of three mitochondrial (mt) genes. A total of 15 haplotypes were recognized based on single mt cox1, nad1, and nad4, and eight haplotypes were identified using the concatenated genes. High haplotype diversity, moderate nucleotide diversity, low gene flow, and high rates of gene differentiation among the seven P. canaliculata populations were detected. Shanghai and Yunnan populations showed higher genetic flow and very low genetic differentiation. The results of Tajima's D, Fu's F s, and mismatch distribution showed that P. canaliculata did not experience population expansion in China. Genetic distance based on haplotypes suggested that nad1 gene was more conserved than cox1 gene within P. canaliculata. The phylogenetic analyses showed there may be two geographical lineages in the Chinese mainland. The present study may provide a new genetic marker to analyze P. canaliculata, and results support more evidence for studying the genetic distribution of P. canaliculata in China and contribute to a deeper understanding of its population genetics and evolutionary biology.

Comparative Mitogenome Analysis of Two Native Apple Snail Species (Ampullariidae, Pomacea) from Peruvian Amazon

Apple snails of the genus Pomacea Perry, 1810 (Mollusca: Caenogastropoda: Ampullariidae) are native to the Neotropics and exhibit high species diversity, holding cultural and ecological significance as an important protein source in Peru. However, most genetic studies in Pomacea have focused mostly on invasive species, especially in Southeast Asia, where they are considered important pests. In this study, we assembled and annotated the mitochondrial genomes of two Pomacea species native to the Peruvian Amazon: Pomacea reevei Ampuero & Ramírez, 2023 and Pomacea aulanieri (Deville & Hupé, 1850). The mitogenomes of P. reevei and P. aulanieri comprise 15,660 and 16,096 bp, respectively, and contain the typical 37 genes of the animal mitochondria with a large control region of 292 bp in P. reevei and 524 bp in P. aulanieri-which fall within the range of what is currently known in Pomacea. Comparisons with previously published mitogenomes in Pomacea revealed differences in the overlapping of adjacent genes, the size of certain protein-coding genes (PCGs) and the secondary structure of some tRNAs that are consistent with the phylogenetic relationships between these species. These findings provide valuable insights into the systematics and genomics of the genus Pomacea.

Characterization of the complete mitochondrial genome of Myrmuslateralis (Heteroptera, Rhopalidae) and its implication for phylogenetic analyses

Mitochondrial genomes (mitogenomes) are widely used in research studies on phylogenetic relationships and evolutionary history. Here, we sequenced and analyzed the mitogenome of the scentless plant bug Myrmuslateralis Hsiao, 1964 (Heteroptera, Rhopalidae). The complete 17,309 bp genome encoded 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a control region. The mitogenome revealed a high A+T content (75.8%), a positive AT-skew (0.092), and a negative GC-skew (-0.165). All 13 PCGs were found to start with ATN codons, except for cox1, in which TTG was the start codon. The Ka/Ks ratios of 13 PCGs were all lower than 1, indicating that purifying selection evolved in these genes. All tRNAs could be folded into the typical cloverleaf secondary structure, except for trnS1 and trnV, which lack dihydrouridine arms. Phylogenetic trees were constructed and analyzed based on the PCG+rRNA from 38 mitogenomes, using maximum likelihood and Bayesian inference methods, showed that M.lateralis and Chorosomamacilentum Stål, 1858 grouped together in the tribe Chorosomatini. In addition, Coreoidea and Pyrrhocoroidea were sister groups among the superfamilies of Trichophora, and Rhopalidae was a sister group to Alydidae + Coreidae.

Five Mitochondrial Genomes of the Genus Eysarcoris Hahn, 1834 with Phylogenetic Implications for the Pentatominae (Hemiptera: Pentatomidae)

Simple Summary

Pentatominae is the largest subfamily in the Pentatomidae, and most of its species are considered important agricultural pests. The phylogenetic relationships of tribes within Pentatominae remain controversial despite the fact that many studies have been performed using various molecular markers. In this study, five mitogenomes of the genus Eysarcoris were sequenced and analyzed, and the phylogenetic relationships of tribes within Pentatominae were reconstructed. The gene arrangement of the five mitochondrial genomes were found to be conserved and identical to other heteropteran mitogenomes. Differences in start codon usage and tandem repeats within control regions were found between E. gibbosus and the other four Eysarcoris species. In addition, the phylogenetic analyses showed that E. gibbosus is the first diverging clade within Eysarcorini. The results support the proposal to transfer E. gibbosus to the Stagonomus, another genus of Eysarcorini. Our results clarified the phylogenetic relationships among tribes of Pentatominae and laid a foundation for the further studies of Pentatominae.

Abstract

Four complete mitogenomes of Eysarcoris rosaceus, E. montivagus, E. gibbosus, E. annamita and one near-complete mitochondrial genome of E. ventralis were sequenced and used to explore the phylogenetic relationships of tribes within the subfamily Pentatominae. The mitogenomes range from 15,422 to 16,043 base pairs (bp) in length and encode 37 genes, including 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes (21 in E. ventralis), and a control region. Similar to other heteropteran species, the AT contents of the sequenced species were higher than their GC contents. The most frequently used start/stop codon was ATN/TAA. GTG was only found in atp6 and atp8 of E. gibbosus. All transfer RNA genes (tRNAs) exhibit the typical cloverleaf secondary structure, except for the trnS1 and trnV, which lacks the stem of the DHU arm. The length and copy number of repeat units were conserved within Eysarcoris, with the exception of E. gibbosus. Phylogenetic analyses based on mitogenomes using both maximum likelihood (ML) and Bayesian inference (BI) methods strongly supported the relationship among tribes within Pentatominae and confirmed that Graphosoma should be an intermediate lineage of Pentatominae. The relationship between Eysarcoris and Carbula was strongly supported and combined with our previous geometric morphometrics and chromosomal studies, suggest the Eysarcoris should belong to the tribe Eyasrcorini. This work will help to enhance our understanding of mitochondrial genomic evolution and phylogenetic relationships in Pentatominae.

Introgressive hybridization between two non-native apple snails in China: widespread hybridization and homogenization in egg morphology

BACKGROUND

Apple snails from the genus Pomacea have spread widely in paddy fields and other wetlands of southern China since their introduction in the 1980s. Pomacea spp. are commonly identified using mitochondrial COI sequences. However, sequencing the nuclear elongation factor 1-alpha (EF1α) gene revealed genetic introgression between field populations of P. canaliculata and P. maculata, which produce surviving hybrids in laboratory crossbreeding experiments.

RESULTS

In this study, we sequenced 1054 EF1α clones to design specific primers and established a fast and accurate multiplex polymerase chain reaction (PCR) method for genotyping EF1α. Combined with genotyping P. canaliculata and P. maculata based on mitochondrial COI and nuclear EF1α, we revealed the genetic introgression patterns of 30 apple snail populations in China. Purebred and hybrid individuals of P. canaliculata were widely distributed, while pure maculata-EF1α type was detected only in a few individuals identified as P. canaliculata based on COI sequences. Each egg clutch had one to three genetic patterns, indicating multiple paternity or segregation in the progeny of hybrids. The higher percentages of hybrids in both wild populations and progeny than the homozygotes indicated a potential heterosis in the apple snail populations. Additionally, egg size and clutch size of the apple snails became homogeneous among the non-native populations exhibiting introgression hybridization.

CONCLUSION

Our findings emphasize the value of apple snails as a model to study the mechanisms and impacts of introgressive hybridization on fitness traits. © 2020 Society of Chemical Industry.

Complete mitogenomic and phylogenetic characteristics of the speckled wood-pigeon (Columba hodgsonii)

The speckled wood-pigeon, Columba hodgsonii, is mainly distributed in Bhutan, China, India, Laos, Myanmar, Nepal, Pakistan, and Thailand. Although there are several studies on birds in the family Columbidae, no study has focused on C. hodgsonii, a member of this family. Therefore, this study aimed to clarify the phylogenetic status of C. hodgsonii. The complete mitochondrial genome (mitogenome) of C. hodgsonii was sequenced and characterized and compared with those of other Columba species. The C. hodgsonii mitogenome was found to be 17,477 bp in size and contained 13 PCGs, two rRNAs, 22 tRNAs, and one CR. Of the 37 genes encoded by the C. hodgsonii mitogenome, 28 were on the heavy strand and nine were on the light strand. Twelve PCGs were initiated by ATN codons and one PCG harbored an incomplete termination codon (T-). The base composition of C. hodgsonii PCGs was A = 29.44%, T = 24.37%, G = 12.43%, and C = 33.76%. For the whole mitogenome, including PCGs, rRNAs, tRNAs, and the control region, the AT-skew was positive, and the GC-skew was negative. Phylogenetic analysis based on the base sequences of 13 PCGs from 28 Columbidae species and one outgroup using maximum likelihood and Bayesian inference indicated that C. hodgsonii belongs to the genus Columba and that the family Columbidae is monophyletic.

Comparative Mitogenomic Analysis of the Eurydema Genus in the Context of Representative Pentatomidae (Hemiptera: Heteroptera) Taxa

The family Pentatomidae, the largest within the superfamily Pentatomoidae, comprises about 5,000 species; many of which are economically important pests. Although the phylogeny of Pentatomidae species has been studied using various molecular markers, their phylogenetic relationships remain controversial. Recently, mitochondrial genomes (mitogenomes) have been extensively employed to examine the phylogenetics and evolution of different insects, and in this study, we sequenced complete/near-complete mitochondrial genomes from five shield bug species of Eurydema to gain a better understanding of phylogenetic relationships in the Pentatomidae. The five mitogenomes ranged in length from 15,500 to 16,752 bp and comprised 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), 2 ribosomal RNAs (rRNAs), and a control region. We compared mitogenomic characteristics of the Pentatomidae and constructed phylogenetic trees using Bayesian inference and maximum likelihood methods. Our results showed that gene arrangements, base composition, start/stop codons, gene overlaps, and RNA structures were conserved within the Pentatomidae and that congeneric species shared more characteristics. Saturation and heterogeneity analyses revealed that our PCGs and PCGRNA datasets were valid for phylogenetic analysis. Phylogenetic analyses showed consistent topologies based on BI and ML methods. These analyses strongly supported that Eurydema species belong to the tribe Strachiini, and formed a sister group with Pentatomini. The relationships among Eurydema species were shown to be consistent with their morphological features. (Strachiini + Pentatomini) was found to be a stable sibling of the clade comprising Cappaeini, Graphosomini, and Carpocorini. Furthermore, our results indicated that Graphosoma rubrolineatum (Heteroptera: Pentatomidae) belongs to the Pentatominae and not the Podopinae.

The first complete mitochondrial genome of a cyclophorid land snail, with implications for architaenioglossan relationships (Mollusca, Caenogastropoda, Cyclophoroidea)

Herein, we described the complete mitochondrial genome ('mitogenome') of the Chinese land snail Cyclophorus martensianus, which is the first published mitogenome for the caenogastropod family Cyclophoridae. This mitogenome is 15,308 bp long consisting of 37 genes: 13 protein-coding genes (PCGs), 22 tRNA genes and two rRNA genes. The A + T content (69.6%) is distinctly higher than the GC content (30.4%). Most PCGs start with ATN as initiation codons, and all PCGs have the conventional stop codons TAA and TAG. Overall, the biochemical properties and gene order of the cyclophorid mitogenome are very similar to those of other documented caenogastropod mitogenomes. We corroborate the findings of earlier studies that mitochondrial gene order is rather conserved among caenogastropods. Caenogastropoda are the taxonomically, morpho-anatomically and ecologically most diverse group of living gastropods comprising lineages inhabiting marine, freshwater, and terrestrial environments. Traditionally, the three most speciose groups of non-marine caenogastropods have all been placed in a single group, the Architaenioglossa. This group contains two freshwater lineages, the Viviparoidea and Ampullaroidea, and the terrestrial Cyclophoroidea. However, architaenioglossan relationships have remained controversial with several morphology-based on molecular phylogenetic analyses supporting contradicting phylogenetic hypotheses. In order to more robustly resolve the relationships among the Architaenioglossa, we have performed phylogenetic analyses of caenogastropod mitogenomes including the new mitogenome of Cyclophorus martensianus. Our phylogenetic reconstructions are based on the amino acid sequences of all protein-coding genes and consistently recovered Architaenioglossa as non-monophyletic.

A New Species of Apple Snail in the Genus Pomacea (Gastropoda: Caenogastropoda: Ampullariidae)

Pomacea canaliculata and Pomacea maculata, two species of freshwater apple snails native to South America, have been introduced to and become invasive in many tropical wetlands around the world. Among their invaded regions in mainland China, we discovered a new species (Pomacea occulta nov. sp.), which has > 5.8% inter-specific genetic divergence with its closely-related species. The present study provides a morphological description of this new species. This new species can be distinguished from the other recognized species of Pomacea by a combination of the following features: a thick shell with generally smooth, fine axial growth lines and frequent periodic growth arrests, an angulated body whorl shoulder, and a yellow-orange-red inner pallial lip; a flexible operculum, thinning dorsally towards the edge; broad kidney anterior leaflets and posterior leaflets with a deep tapering cleft; a concave rachidian base; a penis sheath with apical and medial glands, with the medial gland located in the sheath channel; and 87 to ~1000 eggs per clutch, an average egg diameter of 2.38 mm, a mean hatching height of 2.23 mm, and a mean first whorl width of 1-day-old hatchlings of 2.11 mm.

Complete mitochondrial genomes of three Oxya grasshoppers (Orthoptera) and their implications for phylogenetic reconstruction

Oxya is a genus of grasshoppers (Orthoptera: Acridoidea) attacking rice and other gramineous plants in Africa and Asia. In the present study, we characterized complete mitochondrial genomes (mitogenomes) of three species, Oxya japonica japonica (15,427 bp), Oxya hainanensis (15,443 bp) and Oxya agavisa robusta (15,552 bp) collected from China. The three mitogenomes contained a typical gene set of metazoan mitogenomes and shared the same gene order with other Acridid grasshoppers, including the rearrangement of tRNA^Asp and tRNA^Lys. Analyses of pairwise genetic distances showed that ATP8 was the least conserved gene, while COI the most conserved. To determine the position of Oxya grasshoppers in the phylogeny of Acrididae, we reconstructed phylogenetic trees among 64 species from across 11 subfamilies using nucleotide sequences of mitogenomes. While the tree confirms traditional classifications of Acrididae at major higher-levels, it suggests a few modifications for classifications at lower-levels.