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

Overview

Journal Genes (Basel)

Publisher MDPI

Date 2023 Sep 28

PMID 37761909

Authors

Alejandro Mendivil

Rina Ramirez

Jaime Morin

Jorge L Ramirez

Raquel Siccha-Ramirez

Ricardo Britzke

Fatima Rivera

Andre Ampuero

Nilda Oliveros

Carlos Congrains

Affiliations

Soon will be listed here.

Abstract

Apple snails of the genus 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 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 species native to the Peruvian Amazon: Ampuero & Ramírez, 2023 and (Deville & Hupé, 1850). The mitogenomes of and 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 and 524 bp in -which fall within the range of what is currently known in . Comparisons with previously published mitogenomes in 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 .

Citing Articles

Comparative morphology and mitogenomics of freshwater mussels Koreosolenaia, Parvasolenaia, and Sinosolenaia (Bivalvia: Unionidae: Gonideinae).

Zhang L, Liu X, Hu X, Jia J, Liu X, Wu R BMC Genomics. 2024; 25(1):1243.

PMID: 39719563 PMC: 11668111. DOI: 10.1186/s12864-024-11164-7.

References

Rozas J, Ferrer-Mata A, Sanchez-DelBarrio J, Guirao-Rico S, Librado P, Ramos-Onsins S . DnaSP 6: DNA Sequence Polymorphism Analysis of Large Data Sets. Mol Biol Evol. 2017; 34(12):3299-3302. DOI: 10.1093/molbev/msx248. View

Yang H, Zhang J, Xia J, Yang J, Guo J, Deng Z . Comparative Characterization of the Complete Mitochondrial Genomes of the Three Apple Snails (Gastropoda: Ampullariidae) and the Phylogenetic Analyses. Int J Mol Sci. 2018; 19(11). PMC: 6274680. DOI: 10.3390/ijms19113646. View

Brauer A, Kurz A, Stockwell T, Baden-Tillson H, Heidler J, Wittig I . The mitochondrial genome of the venomous cone snail Conus consors. PLoS One. 2012; 7(12):e51528. PMC: 3517553. DOI: 10.1371/journal.pone.0051528. View

Rawlings T, Hayes K, Cowie R, Collins T . The identity, distribution, and impacts of non-native apple snails in the continental United States. BMC Evol Biol. 2007; 7:97. PMC: 1919357. DOI: 10.1186/1471-2148-7-97. View

Maynard B, Kerr L, McKiernan J, Jansen E, Hanna P . Mitochondrial DNA sequence and gene organization in the [corrected] Australian blacklip [corrected] abalone Haliotis rubra (leach). Mar Biotechnol (NY). 2005; 7(6):645-58. DOI: 10.1007/s10126-005-0013-z. View

Wuyts J, De Rijk P, Van de Peer Y, Winkelmans T, De Wachter R . The European Large Subunit Ribosomal RNA Database. Nucleic Acids Res. 2000; 29(1):175-7. PMC: 29789. DOI: 10.1093/nar/29.1.175. View

Yang H, Zhang J, Deng Z, Luo H, Guo J, He S . The complete mitochondrial genome of the golden apple snail (Gastropoda: Ampullariidae). Mitochondrial DNA B Resour. 2021; 1(1):45-47. PMC: 7800459. DOI: 10.1080/23802359.2015.1137816. View

Zhou X, Chen Y, Zhu S, Xu H, Liu Y, Chen L . The complete mitochondrial genome of Pomacea canaliculata (Gastropoda: Ampullariidae). Mitochondrial DNA A DNA Mapp Seq Anal. 2014; 27(2):884-5. DOI: 10.3109/19401736.2014.919488. View

Medina M, Collins T, Walsh P . mtDNA ribosomal gene phylogeny of sea hares in the genus Aplysia (Gastropoda, Opisthobranchia, Anaspidea): implications for comparative neurobiology. Syst Biol. 2002; 50(5):676-88. DOI: 10.1080/106351501753328802. View

10.

Edgar R . MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004; 32(5):1792-7. PMC: 390337. DOI: 10.1093/nar/gkh340. View

11.

Stothard P, Grant J, Van Domselaar G . Visualizing and comparing circular genomes using the CGView family of tools. Brief Bioinform. 2017; 20(4):1576-1582. PMC: 6781573. DOI: 10.1093/bib/bbx081. View

12.

Wick R, Schultz M, Zobel J, Holt K . Bandage: interactive visualization of de novo genome assemblies. Bioinformatics. 2015; 31(20):3350-2. PMC: 4595904. DOI: 10.1093/bioinformatics/btv383. View

13.

Lanfear R, Frandsen P, Wright A, Senfeld T, Calcott B . PartitionFinder 2: New Methods for Selecting Partitioned Models of Evolution for Molecular and Morphological Phylogenetic Analyses. Mol Biol Evol. 2016; 34(3):772-773. DOI: 10.1093/molbev/msw260. View

14.

Kumar S, Stecher G, Li M, Knyaz C, Tamura K . MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms. Mol Biol Evol. 2018; 35(6):1547-1549. PMC: 5967553. DOI: 10.1093/molbev/msy096. View

15.

Talavera G, Castresana J . Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol. 2007; 56(4):564-77. DOI: 10.1080/10635150701472164. View

16.

Donath A, Juhling F, Al-Arab M, Bernhart S, Reinhardt F, Stadler P . Improved annotation of protein-coding genes boundaries in metazoan mitochondrial genomes. Nucleic Acids Res. 2019; 47(20):10543-10552. PMC: 6847864. DOI: 10.1093/nar/gkz833. View

17.

Larsson A . AliView: a fast and lightweight alignment viewer and editor for large datasets. Bioinformatics. 2014; 30(22):3276-8. PMC: 4221126. DOI: 10.1093/bioinformatics/btu531. View

18.

Guo J, Yang H, Zhang C, Xue H, Xia Y, Zhang J . Complete mitochondrial genome of the apple snail (Gastropoda, Ampullariidae) with phylogenetic consideration. Mitochondrial DNA B Resour. 2021; 2(2):865-867. PMC: 7800437. DOI: 10.1080/23802359.2017.1407683. View

19.

Jin J, Yu W, Yang J, Song Y, dePamphilis C, Yi T . GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes. Genome Biol. 2020; 21(1):241. PMC: 7488116. DOI: 10.1186/s13059-020-02154-5. View

20.

Perna N, Kocher T . Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes. J Mol Evol. 1995; 41(3):353-8. DOI: 10.1007/BF00186547. View