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Mitochondrial DNA B Resour
Mitochondrial DNA B Resour
Mitochondrial DNA. Part B, Resources
2380-2359
Taylor & Francis

10.1080/23802359.2024.2404210
2404210
Version of Record
Data Note
Mitogenome Report
Complete mitochondrial genome of Rhopalosiphum maidis (Hemiptera: Aphididae) and its phylogenetic implications
M. Zhang et al.
https://orcid.org/0009-0004-8801-3451
Zhang Miao a‡
https://orcid.org/0009-0000-4951-799X
Kang Chen b‡
https://orcid.org/0000-0001-8655-9662
Xing Kun a§
https://orcid.org/0000-0003-4158-3604
Zhao Fei a§
a Shanxi Key Laboratory of Integrated Pest Management in Agriculture, College of Plant Protection, Shanxi Agricultural University, Taiyuan, China
b Shennong Technology Company Limited, Taigu, China
‡ These authors contributed equally to this work.

§ These authors should be considered co-corresponding authors.

Supplemental data for this article can be accessed online at https://doi.org/10.1080/23802359.2024.2404210.

CONTACT Kun Xing xingkun1215@126.com; xingkun@sxau.edu.cn Shanxi Key Laboratory of Integrated Pest Management in Agriculture, College of Plant Protection, Shanxi Agricultural University, Taiyuan, China.
16 9 2024
2024
16 9 2024
9 9 12271231
11 9 2023
9 9 2024
KnowledgeWorks Global Ltd.16 9 2024
published online in a building issue16 9 2024
© 2024 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.
2024
The Author(s)
https://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. The terms on which this article has been published allow the posting of the Accepted Manuscript in a repository by the author(s) or with their consent.

Abstract

Rhopalosiphum maidis Fitch, 1856 is widespread in tropical and temperate regions. R. maidis can spread viral diseases in maize and harm various important crops. In the present study, we report the first complete mitochondrial genome of R. maidis. The circular genome is found to be 17,021 bp in length, includes a standard set of 22 transfer RNAs, two ribosomal RNAs, 13 protein-coding genes, and two non-coding control regions. The base composition is 84.32% AT and 15.79% GC. The phylogenetic tree of the 17 Aphidini families constructed based on the nucleotide sequences of complete mitochondrial genomes strongly supports the conclusion that R. maidis is closely related to R. rufiabdominalis.

Keywords

Rhopalosiphum maidis
phylogenetic tree
mitogenome
National Key Research and Development Program of China 10.13039/501100012166 Science and Technology Major Project of Shanxi Province, China Modern Agro-industry Technology Research System in Shanxi Province This research was financially supported by the National Key Research and Development Program of China under Grant (No. 2021YFD1901101), Science and Technology Major Project of Shanxi Province, China under Grant (No. 202101140601026), and Modern Agro-industry Technology Research System in Shanxi Province under Grant (2024CYJSTX03-29, 2024CYJSTX01-19, YMZD202403). Shanxi Agricultural University Science and Technology Project (2023QT34).
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pmcIntroduction

At present, Rhopalosiphum maidis Fitch, 1856 is widely distributed in tropical and temperate regions and cause damage to various gramineous crops, including corn, sorghum, wheat, and millet (Al-Eryan and El-Tabbakh 2020). In recent years, the damage caused by R. maidis has gradually increased. R. maidis primarily resides in the heart leaves and male flowers, and can remove photosynthates, further reducing crop growth and yield. Additionally, R. maidis transmits a variety of viruses, such as maize yellow dwarf, barley yellow dwarf, cucumber mosaic, and sugarcane mosaic viruses (Klein and Smith 2002). There have been reports that the potential harm caused by their viral transmission via R. maidis may be far greater than the loss of maize yield (Kuo et al. 2006). To the best of our knowledge, this study is the first to characterize the complete mitochondrial genome of R. maidis using Illumina Novaseq and PacBio Sequel techniques to reconstruct the phylogenetic relationships based on the published genome sequences of the Aphididae family. Our findings provide molecular information for the phylogenetic and evolutionary study of R. maidis.

Materials and methods

On February 4, 2023, 30 adult specimens of R. maidis were collected from sorghum fields in Hakjia village (109.58E, 18.28 N) in Jiyang Town, Hainan Province, China. Five specimens were stored in 95% ethanol under voucher number MgPL2023022312 at the College of Plant Protection, Shanxi Agricultural University, Taiyuan, China (X.K., xingkun1215@126.com).

The taxonomic status of the R. maidis was determined following the morphological identification reported in the literature. The wingless adult was oval, soft-bodied, 2.5 mm long and bottle green with black antennae, legs, and cornicles. The 7th segment of the abdomen was black, 8th segment had a dorsal transverse band, and body surface had a mesh. The antennae had six segments. The imbricated ventral tube was long, cylindrical, and had a contracted end. The tail was conical, with four to five hairs (Razmjou and Golizadeh 2010). The morphology of R. maidis is shown in Figure 1.

Figure 1. Species reference image captured by Kun Xing.

Total DNA was extracted using a tissue genomic DNA extraction kit (Tiangen Biochemical Technology Co. Ltd., Beijing, China). The mitochondrial genome was sequenced by Shanghai Personalbio Biotechnology Co., Ltd. (Shanghai, China) using Illumina Novaseq PE250 (Illumina, San Diego, CA, USA) and PacBio Sequel system. The Illumina data were assembled using A5-miseq v20150522 (Coil et al. 2015) and SPAdesv3.9.0 (Bankevich et al. 2012). Contigs with a high coverage depth were annotated by BLAST against the Nucleotide database in National Center of Biotechnology Information (NCBI) using blastn (v2.2.31) to extract the mitochondrial sequences (Chen et al. 2015). The collinearity of the assembly results from different software was calculated using MUMmer v3.1 (Kurtz et al. 2004) to determine the position relationships among contigs. The gaps among contigs were filled, and the results were corrected using Pilon v1.18 (Walker et al. 2014). The repeat regions of the Illumina data were further corrected and confirmed by the PacBio Sequel system. The PacBio Sequel data were assembled using Flye v2.9.1-b1781 (Kolmogorov et al. 2019). The assembly results were annotated by mitos2 (Bernt et al. 2013), and the boundary was adjusted by referring to the genome sequence of Rhopalosiphum nymphaeae (MN943499) and Rhopalosiphum rufiabdominalis (MN876840) to obtain the complete mitochondrial genome. The CGView visualization software was used to generate a whole-genome circular map (Stothard and Wishart 2005). The PacBio Sequel data were further mapped to the complete mitochondrial genome to obtain a sam assembly file and the sam assembly file was transformed to a bam assembly file. The coverage depth of each base on the genome was also calculated using SAMtools v1.16.1 (Li et al. 2009) and the sequencing depth and coverage map was draw by ggplot2 (Ito and Murphy 2013) in R (Figure S1).

The complete mitochondrial sequences in “Aphidini” were searched from NCBI database after excluding incomplete and repeating records. The nucleotide sequences of complete mitochondrial genomes from Aphidini species and outgroup from Greenidea psidii were downloaded from NCBI for the phylogenetic analysis. The nucleotide sequences of the complete mitogenome were aligned using ClustalW (Larkin et al. 2007) in MEGA-11 (Tamura et al. 2021) with default parameters. The maximum likelihood model with the lowest Bayesian Information Criterion (BIC) score is regarded as the best model. According to BIC of 104464.25, GTR (General Reversible Mitochondrial) + a discrete Gamma distribution (G) + evolutionarily invariable (I) with 1000 replicates was selected to construct a phylogenetic tree.

Results

The complete mitogenome of R. maidis (OR148359.3) is a circular DNA molecule 17,021 bp in length. The mitogenome contains 13 protein-coding genes (PCGs), 22 transfer RNA genes, large and small ribosomal RNA unit genes (rrnL and rrnS, respectively), and two large noncoding regions (putative control regions; Figure 2).

Figure 2. Circular genome feature map of Rhopalosiphum maidis drawn by CGView. The CDS, tRNAs, rRNAs, and other are denoted by the color blocks. Genes outside the map are transcribed clockwise, whereas those inside are transcribed counterclockwise. The window size is 5 bp and step is 1 bp.

The nucleotide composition of R. maidis was significantly AT-biased, with A, G, C, and T accounting for 44.89, 5.69, 10.10, and 39.32%, respectively. In this genome, the GC and AT skews were −0.279 and 0.066, respectively. The overall length of all overlaps was 75 bp and overlaps were present at 14 gene junctions. The largest overlap (29 bp) was observed between trnY and cox1. Intergenic spacers, totaling 1,746 bp, appeared at 12 positions and ranged from 1 to 1,655 bp. The control region had an A + T content of 88.82%, was 912 bp long, and was located between rrnS and trnI.

The rrnL gene was located between trnLtag and trnV and had an A + T content of 85.15% and was 1259 bp long. The rrnS gene was 759 bp long with an A + T content of 83.79%. The first two bases of start codons were “AT,” which was the same across all the 13 PCGs, and the third base of start codons was different. The PCGs cox3, nad4l, and cob started with ATG; cox1, atp6, atp8, nad6, and nad1 started with ATT; and nad2, cox2, nad3, nad5, and nad4 started with ATA. Twelve, one, and two PCGs were terminated with TAA, TAG (cob), and an incomplete stop codon T (cox1 and nad4), respectively.

Seventeen complete mitochondrial sequences in Aphidini and outgroups from Greenidea psidii were identified for the phylogenetic analysis (Table 1).

Table 1. Accession number and reference information for 18 species.

GenBank accession No.	Species	Genus	Tribe	Length (bp)	References	
MN871977	Aphis aurantii	Aphis	Aphidini	15296	Pu et al. (2020)	
MK540501	Aphis citricidus	Aphis	Aphidini	16763	Wei et al. (2019)	
OM894972	Aphis coreopsidis	Aphis	Aphidini	15623	Unpublished	
MT095075	Aphis craccivora	Aphis	Aphidini	15478	Voronova et al. (2020)	
MG897128	Aphis fabae mordvilkoi	Aphis	Aphidini	15346	Voronova et al. (2020)	
KJ669654	Aphis gossypii	Aphis	Aphidini	15869	Zhang et al. (2016)	
OM894973	Aphis solanella	Aphis	Aphidini	15331	Unpublished	
MN316642	Aphis spiraecola	Aphis	Aphidini	15465	Du et al. (2019)	
MK111111	Aphis glycines	Aphis	Aphidini	17954	Unpublished	
OK641613	Hyalopterus amygdali	Hyaloptera	Aphidini	15306	Unpublished	
OK274075	Hyalopterus arundiniformis	Hyaloptera	Aphidini	15408	Unpublished	
MT898422	Hyalopterus pruni	Hyaloptera	Aphidini	15410	Unpublished	
OR148359	Rhopalosiphum maidi	Rhopalosiphum	Aphidini	17021	Unpublished	
MN943499	Rhopalosiphum nymphaeae	Rhopalosiphum	Aphidini	15594	Unpublished	
MN876840	Rhopalosiphum rufiabdominalis	Rhopalosiphum	Aphidini	15289	Thao et al. (2004)	
AY531391	Schizaphis graminum	Schizaphis	Aphidini	15721	Unpublished	
MW811104	Melanaphis sacchari	Melanaphis	Aphidini	15111	Unpublished	
MH844624	Greenidea psidii	Greenidea	Greenideinae	16202	Unpublished	

The phylogenetic tree indicated that the genome of R. maidis was similar to that of R. rufiabdominalis and there was strong support for the clustering of R. maidis with R. rufiabdominalis, Schizaphis graminum, and R. nymphaeae (Figure 3).

Figure 3. Phylogenetic relationships of 17 aphidini, including Rhopalosiphum maidis, based on the nucleotide sequences of complete mitochondrial genomes using ML methods. The sequences used for tree reconstruction are listed in Table 1. The scale bar is the distance scale. The numbers beside the nodes are bootstrap values. The bootstrap value based on 1000 replicated is represented on each node. Greenidea psidii is used as outgroup to root the tree.

Discussion and conclusion

Herein, the complete mitogenome of R. maidis was assembled and analyzed using Illumina Novaseq and PacBio Sequel techniques. The mitochondrial genome of R. maidis is 17,021 bp long, has standard, metazoan set of genes in the typical insect order (Cameron 2014). Base composition is heavily AT-biased. This is consistent with previous results for other species of Aphididae. For instance, the AT contents of Aphis aurantii is 83.5% (Pu et al. 2020), A. citricidus is 84.0% (Wei et al. 2019), A. gossypii is 83.7% (Zhang et al. 2016). Voronova et al. (2020) sequenced the complete mitochondrial genomes of A. fabae mordvilkoi, A. craccivora, and M. persicae from Aphidinae, as well as Therioaphis tenera and Appendiseta robiniae from Calaphidinae, and determined that the A + T content of all five mitogenomes is >80%.

Phylogenetic analysis suggests that Rhopalosiphum is more closely related to R. rufiabdominalis, with a bootstrap rate of 96, indicating that the two species share more recent common ancestor gene. We also found that there was strong support for the clustering of Schizaphis graminum with R. maidis. This is not consistent with traditional taxonomy. Phylogenetic trees based on genome-wide sequence data may not always represent the true evolutionary history for a variety of reasons. One process that can lead to incorrect reconstruction of species phylogenies is gene flow, especially if interspecific gene flow has affected large parts of the genome (Zhang et al. 2021). We expect that these results will provide new insights and act as a reference for future studies on the phylogenetics and genetics of R. maidis.

Supplementary Material

Supplementary Information.docx

Author contributions

CK and FZ: conceptualization, methodology, formal analysis, resources, investigation, writing-original draft, writing-review and editing, and visualization. KX: investigation, writing-review and editing. KX and FZ: resources, formal analysis, investigation, writing-review and editing, visualization, supervision, project administration, and funding acquisition.

Ethical approval

The collection of the reported sample was carried out in accordance with guidelines provided by the national regulations. The sampling site is not located in any protected area. The research was conducted with the permission of Shanxi Agricultural University.

Disclosure statement

No potential conflict of interest was reported by the authors.

Data availability statement

The genome sequence data that support the findings of this study are openly available in GenBank of NCBI at https://www.ncbi.nlm.nih.gov/genbank under the accession no. OR148359.3. Illumina reads were deposited under SRR25470088, and PacBio reads under SRR29709340. The associated BioProject and Bio-Sample numbers are PRJNA1000643 and SAMN36765787.
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