• Characterization of the Mitoch...

Treffer: Characterization of the Mitochondrial Genome of Cavariella salicicola : Insight into the Codon Usage Bias and Phylogenetic Implications in Aphidinae.

Title:
Characterization of the Mitochondrial Genome of Cavariella salicicola : Insight into the Codon Usage Bias and Phylogenetic Implications in Aphidinae.
Authors:
Jing TX; College of Plant Protection, Yangzhou University, Yangzhou 225009, China.; Jiangsu Province Engineering Research Center of Green Pesticides, Yangzhou University, Yangzhou 225009, China., Zhang YJ; College of Plant Protection, Yangzhou University, Yangzhou 225009, China., Li PX; College of Plant Protection, Yangzhou University, Yangzhou 225009, China., Wang Q; College of Plant Protection, Yangzhou University, Yangzhou 225009, China., Yang J; College of Plant Protection, Yangzhou University, Yangzhou 225009, China., Su HH; College of Plant Protection, Yangzhou University, Yangzhou 225009, China.; Jiangsu Province Engineering Research Center of Green Pesticides, Yangzhou University, Yangzhou 225009, China., Zhang S; College of Plant Protection, Yangzhou University, Yangzhou 225009, China.; Jiangsu Province Engineering Research Center of Green Pesticides, Yangzhou University, Yangzhou 225009, China.
Source:
Genes [Genes (Basel)] 2025 Nov 29; Vol. 16 (12). Date of Electronic Publication: 2025 Nov 29.
Publication Type:
Journal Article
Language:
English
Journal Info:
Publisher: MDPI Country of Publication: Switzerland NLM ID: 101551097 Publication Model: Electronic Cited Medium: Internet ISSN: 2073-4425 (Electronic) Linking ISSN: 20734425 NLM ISO Abbreviation: Genes (Basel) Subsets: MEDLINE
Imprint Name(s):
Original Publication: Basel : MDPI
MeSH Terms:
Genome, Mitochondrial*/genetics , Codon Usage*/genetics , Aphids*/genetics , Aphids*/classification, Animals ; Phylogeny ; RNA, Transfer/genetics ; Codon/genetics ; Selection, Genetic ; RNA, Ribosomal/genetics
References:
Mol Biol Evol. 2017 Dec 1;34(12):3299-3302. (PMID: 29029172)
BMC Genomics. 2023 Nov 22;24(1):703. (PMID: 37993787)
Mol Phylogenet Evol. 2018 Apr;121:12-22. (PMID: 29253532)
Int J Mol Sci. 2015 Dec 17;16(12):30091-102. (PMID: 26694371)
Mitochondrial DNA B Resour. 2021 Jul 19;6(8):2373-2375. (PMID: 34350347)
PLoS One. 2013 Oct 17;8(10):e77511. (PMID: 24147014)
Trends Genet. 1997 Jun;13(6):240-5. (PMID: 9196330)
Gene. 1999 Sep 30;238(1):53-8. (PMID: 10570983)
Mol Biol Evol. 2018 Jun 1;35(6):1547-1549. (PMID: 29722887)
Mol Biol Evol. 2000 Apr;17(4):540-52. (PMID: 10742046)
Nature. 1981 Apr 9;290(5806):470-4. (PMID: 7219536)
Genetics. 2008 Apr;178(4):2429-32. (PMID: 18430960)
Insect Mol Biol. 1996 Aug;5(3):153-65. (PMID: 8799733)
Mol Biol Evol. 2013 Apr;30(4):772-80. (PMID: 23329690)
Mol Ecol Resour. 2008 Nov;8(6):1189-201. (PMID: 21586006)
Insects. 2024 May 27;15(6):. (PMID: 38921104)
Imeta. 2023 Feb 16;2(1):e87. (PMID: 38868339)
Int J Biol Macromol. 2019 Sep 1;136:531-539. (PMID: 31207332)
Insect Sci. 2014 Jun;21(3):374-91. (PMID: 24302699)
Int J Biol Macromol. 2020 Apr 15;149:187-206. (PMID: 31917211)
Mitochondrial DNA A DNA Mapp Seq Anal. 2016;27(2):854-5. (PMID: 24865902)
BMC Genomics. 2021 Oct 21;22(1):755. (PMID: 34674653)
Genet Res. 1999 Dec;74(3):207-14. (PMID: 10689798)
J Mol Evol. 2001 Oct-Nov;53(4-5):469-76. (PMID: 11675607)
Mol Ecol Resour. 2020 Jan;20(1):348-355. (PMID: 31599058)
Nucleic Acids Res. 1999 Apr 15;27(8):1767-80. (PMID: 10101183)
Insect Biochem Mol Biol. 2019 Oct;113:103208. (PMID: 31422150)
Gene. 1990 Mar 1;87(1):23-9. (PMID: 2110097)
PLoS One. 2011;6(9):e24749. (PMID: 21935453)
Syst Biol. 2012 May;61(3):539-42. (PMID: 22357727)
PLoS One. 2010 Sep 15;5(9):e12708. (PMID: 20856815)
Physiol Mol Biol Plants. 2024 Feb;30(2):153-166. (PMID: 38623162)
Mol Biol Evol. 2015 Jan;32(1):268-74. (PMID: 25371430)
Int J Mol Sci. 2024 Oct 22;25(21):. (PMID: 39518889)
BMC Genomics. 2010 Jul 22;11:447. (PMID: 20649981)
BMC Genomics. 2024 Oct 8;25(1):945. (PMID: 39379800)
Int J Biol Macromol. 2019 Feb 1;122:824-832. (PMID: 30389524)
Trends Ecol Evol. 1999 Oct;14(10):394-398. (PMID: 10481201)
Mitochondrial DNA B Resour. 2019 Oct 15;4(2):3567-3568. (PMID: 33366088)
C R Biol. 2010 Jun-Jul;333(6-7):474-87. (PMID: 20541159)
Nat Methods. 2017 Jun;14(6):587-589. (PMID: 28481363)
BMC Genomics. 2017 Sep 6;18(1):698. (PMID: 28874137)
Biochem Genet. 2025 Feb;63(1):483-498. (PMID: 38456973)
Genes (Basel). 2023 Apr 08;14(4):. (PMID: 37107641)
Animals (Basel). 2022 Aug 03;12(15):. (PMID: 35953959)
Mitochondrial DNA B Resour. 2021 Jan 14;6(1):62-65. (PMID: 33521268)
Mol Phylogenet Evol. 2010 Apr;55(1):305-317. (PMID: 20004730)
Grant Information:
32102192 National Natural Science Foundation of China
Contributed Indexing:
Keywords: Cavariella; codon usage bias; mitochondrial genome; phylogeny
Substance Nomenclature:
9014-25-9 (RNA, Transfer)
0 (Codon)
0 (RNA, Ribosomal)
Entry Date(s):
Date Created: 20251230 Date Completed: 20251230 Latest Revision: 20260102
Update Code:
20260102
PubMed Central ID:
PMC12732342
DOI:
10.3390/genes16121427
PMID:
41465100
Database:
MEDLINE

Weitere Informationen

Background : Cavariella salicicola (Hemiptera: Aphidinae) is a pest on Salix spp. and various Umbelliferae (Apiaceae) vegetables. However, the taxonomic status and phylogenetic relationship of the genus Cavariella within Aphidinae remain controversial due to the small body size and easily confused external morphology. Methods : The complete mitochondrial genome of C. salicicola collected from Oenanthe javanica was sequenced using the Illumina platform and compared with C . theobaldi. The codon usage bias of two Cavariella aphids was assessed through Enc plot, PR2 plot, and neutrality plot analyses. Furthermore, phylogenetic trees were constructed based on both Maximum Likelihood and Bayesian Inference analysis. Results : The C. salicicola mitochondrial genome comprises 15,720 bp and represents a typical circular DNA molecule with a high AT content of 83.8%. It contains the standard 37 genes, including 2 ribosomal RNAs (rRNAs), 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), and 2 long non-coding regions (control and repeat regions). Varying degrees of codon usage bias were found across different PCGs, and the bias was predominantly influenced by natural selection rather than mutational pressure. The ratio of nonsynonymous to synonymous substitutions (Ka/Ks) indicated that all PCGs in C. salicicola , as well as most other Aphidinae species, are under strong purifying selection. The phylogenetic analysis based on Maximum Likelihood and Bayesian Inference both strongly supported the monophyly of Aphidinae, Macrosiphini, and Aphidini. Crucially, the monophyletic genus Cavariella was resolved as a sister group to all other sampled species within the tribe Macrosiphini. Conclusions : This study provides new molecular data to support the sister relationship of the genus Cavariella to other Macrosiphini aphids. This study will enhance our understanding of phylogenetic relationships within the subfamily Aphidinae.