A New Mitochondrial Genome of Sogatella furcifera (Horváth) (Hemiptera: Delphacidae) and Mitogenome-Wide Investigation on Polymorphisms
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. DNA Extraction of the WBPH Samples
2.2. Genome Sequencing and De Novo Assembly of WBPH Mitogenome
2.3. Annotation of WBPH Mitogenome
2.4. Verification of Polymorphic Sites on the WBPH Mitogenome Using PCR and Sanger Sequencing Methods
2.5. Prediction of Three-Dimensional Structure of COX3 of WBPH Mitogenome
2.6. Identification of Intraspecific Variations of WBPH Mitogenomes
2.7. Identification of Simple Sequence Repeats on the WBPH Mitogenomes
2.8. Comparison of SSRs Identified from the WBPH Mitogenomes
2.9. Construction of Phylogenetic Trees
3. Results and Discussions
3.1. Complete Mitochondrial Genome of S. furcifera
3.2. Identification and Verification of the Polymorphic Site Found from the WBPH Mitogenome
3.3. Intraspecific Mitochondrial Variations Compared with the Previously Sequenced WBPH Mitogenomes
3.4. Identification and Comparison of Simple Sequence Repeats on WBPH Mitogenomes
3.5. Phylogenetic Tree of 32 Delphacidae Mitogenomes including Three WBPH Mitogenomes
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Name | Length (bp) | GC Ratio (%) | GC Skew | AT Skew | AT-Rich Region Length (bp) | GC Ratio of AT-Rich Region (%) | GenBank Accession Number | Reference |
---|---|---|---|---|---|---|---|---|
WBPHTA | 16,613 | 23.8 | −0.14163 | 0.094715 | 2219 | 17.5 | MK907866 | This study |
WBPHHN | 16,612 | 23.8 | −0.14055 | 0.092920 | 2223 | 17.5 | NC_021417 | [8] |
WBPHYN | 16,654 | 23.8 | −0.14070 | 0.094262 | 2264 | 17.7 | KC512915 | [8] |
No | Name | SSRType | Type | Start | End | Unit Sequence | Repeat # | Genes |
---|---|---|---|---|---|---|---|---|
1 | M0000001 | Normal SSR | MonoSSR | 858 | 868 | A | 11 | ND2 |
2 | M0000002 | Normal SSR | MonoSSR | 7044 | 7053 | A | 10 | ND5 |
3 | M0000003 | Normal SSR | MonoSSR | 7725 | 7737 | A | 13 | ND5 |
4 | M0000004 | Normal SSR | MonoSSR | 7830 | 7839 | A | 10 | ND4 |
5 | M0000005 | Normal SSR | MonoSSR | 8110 | 8123 | A | 14 | ND4 |
6 | M0000006 | Normal SSR | MonoSSR | 8412 | 8421 | A | 10 | ND4 |
7 | M0000007 | Normal SSR | MonoSSR | 8717 | 8727 | A | 11 | ND4 |
8 | M0000008 | Normal SSR | MonoSSR | 9057 | 9066 | A | 10 | ND4 |
9 | M0000009 | Normal SSR | MonoSSR | 10,023 | 10,032 | T | 10 | |
10 | M0000010 | Normal SSR | MonoSSR | 10,033 | 10,064 | A | 32 | |
11 | M0000011 | Normal SSR | MonoSSR | 11,819 | 11,830 | A | 12 | ND1 |
12 | M0000012 | Normal SSR | MonoSSR | 14,555 | 14,569 | T | 15 | |
13 | M0000013 | Normal SSR | MonoSSR | 14,966 | 14,988 | T | 23 | |
14 | D0000001 | Normal SSR | DiSSR | 14,785 | 14,796 | TA | 6 | |
15 | D0000002 | Normal SSR | DiSSR | 14,862 | 14,873 | TA | 6 | |
16 | D0000003 | Normal SSR | DiSSR | 15,106 | 15,115 | AT | 5 | |
17 | D0000004 | Normal SSR | DiSSR | 15,147 | 15,160 | AT | 7 | |
18 | D0000005 | Normal SSR | DiSSR | 15,192 | 15,201 | AT | 5 | |
19 | D0000006 | Normal SSR | DiSSR | 15,208 | 15,223 | TA | 8 | |
20 | D0000007 | Normal SSR | DiSSR | 15,244 | 15,253 | TA | 5 | |
21 | D0000008 | Normal SSR | DiSSR | 15,274 | 15,285 | TA | 6 | |
22 | D0000009 | Normal SSR | DiSSR | 15,335 | 15,344 | TA | 5 | |
23 | D0000010 | Normal SSR | DiSSR | 15,387 | 15,396 | TA | 5 | |
24 | T0000001 | Normal SSR | TriSSR | 15,117 | 15,128 | ATT | 4 | |
25 | Te0000001 | Normal SSR | TetraSSR | 8443 | 8454 | ATAA | 3 | ND4 |
No | SSR Group | Mitogenome | SSR Type | Type | SSR Name | Start | End | Unit Sequence | # of Repeats | Genes |
---|---|---|---|---|---|---|---|---|---|---|
1 | SSRGroup 16 | WBPHHN | Potential SSR | PentaSSR | P0000047 | 15,346 | 15,355 | AATAA | 2 | Intergenic |
WBPHYN | Potential SSR | PentaSSR | P0000047 | 15,346 | 15,355 | AATAA | 2 | Intergenic | ||
2 | SSRGroup 34 | WBPHHN | Normal SSR | MonoSSR | M0000009 | 10,023 | 10,032 | T | 10 | Intergenic |
WBPHTA | Normal SSR | MonoSSR | M0000009 | 10,023 | 10,032 | T | 10 | Intergenic | ||
3 | SSRGroup 75 | WBPHHN | Potential SSR | PentaSSR | P0000023 | 10,333 | 10,342 | TACAC | 2 | CYTB |
WBPHYN | Potential SSR | PentaSSR | P0000023 | 10,333 | 10,342 | TACAC | 2 | CYTB | ||
4 | SSRGroup 99 | WBPHYN | Potential SSR | PentaSSR | P0000044 | 15,034 | 15,043 | ATATA | 2 | Intergenic |
WBPHTA | Potential SSR | PentaSSR | P0000044 | 15,035 | 15,044 | ATATA | 2 | Intergenic | ||
5 | SSRGroup 103 | WBPHYN | Potential SSR | HexaSSR | H0000021 | 10,498 | 10,509 | TAAAAG | 2 | CYTB |
WBPHHN | Potential SSR | HexaSSR | H0000021 | 10,498 | 10,509 | TAAAAG | 2 | CYTB | ||
6 | Singleton 1 | WBPHHN | Potential SSR | PentaSSR | P0000022 | 10,016 | 10,025 | AATTT | 2 | Intergenic |
7 | Singleton 2 | WBPHHN | Potential SSR | PetanSSR | P0000044 | 15,034 | 15,043 | ATATA | 2 | Intergenic |
8 | Singleton 3 | WBPHTA | Potential SSR | PentaSSR | P0000023 | 10,337 | 10,346 | TACAC | 2 | Intergenic |
9 | Singleton 4 | WBPHTA | Potential SSR | PentaSSR | P0000047 | 15,347 | 15,356 | AATAA | 2 | Intergenic |
10 | Singleton 5 | WBPHTA | Potential SSR | HexaSSR | H0000021 | 10,502 | 10,513 | TAAAAG | 2 | Intergenic |
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Park, J.; Xi, H.; Park, J.; Seo, B.Y. A New Mitochondrial Genome of Sogatella furcifera (Horváth) (Hemiptera: Delphacidae) and Mitogenome-Wide Investigation on Polymorphisms. Insects 2021, 12, 1066. https://doi.org/10.3390/insects12121066
Park J, Xi H, Park J, Seo BY. A New Mitochondrial Genome of Sogatella furcifera (Horváth) (Hemiptera: Delphacidae) and Mitogenome-Wide Investigation on Polymorphisms. Insects. 2021; 12(12):1066. https://doi.org/10.3390/insects12121066
Chicago/Turabian StylePark, Jongsun, Hong Xi, Jonghyun Park, and Bo Yoon Seo. 2021. "A New Mitochondrial Genome of Sogatella furcifera (Horváth) (Hemiptera: Delphacidae) and Mitogenome-Wide Investigation on Polymorphisms" Insects 12, no. 12: 1066. https://doi.org/10.3390/insects12121066