Contribution to the mitogenome diversity in Delphacinae: Phylogenetic and ecological implications

Huang, Yi-Xin; Ren, Fang; Bartlett, Charles R.; Wei, Yangdou; Qin, Dao‐Zheng

doi:10.1016/j.ygeno.2019.08.005

Cited by 13 publications

(17 citation statements)

References 45 publications

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“…In addition, all branches except one (see grey arrow in Figure 6) were supported by the high supportive values of both trees (Figure 1), displaying a rigid phylogenetic relationship within the family Delphacidae. This is congruent with the previous phylogenetic studies [46,100,101], supporting that the phylogenetic relationship of the 30 Delphacidae species become more supportive in comparison to the incongruent cases of molecular phylogeny based on between marker sequences and complete mitogenomes [102][103][104]. The exceptional clade displaying low supportive values of ML (52; Figure 7) was also presented lower supportive values of both ML and BI trees (Clade III) in the previous phylogenetic study [46].…”

Section: Phylogenetic Tree Of 32 Delphacidae Mitogenomes Including Three Wbph Mitogenomessupporting

confidence: 88%

A New Mitochondrial Genome of Sogatella furcifera (Horváth) (Hemiptera: Delphacidae) and Mitogenome-Wide Investigation on Polymorphisms

Park¹,

Xi²,

Park³

et al. 2021

Insects

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White-backed planthopper (WBPH), Sogatella furcifera (Horváth), is one of the major sap-sucking rice pests in East Asia. We have determined a new complete mitochondrial genome of WBPH collected in the Korean peninsula using NGS technology. Its length and GC percentages are 16,613 bp and 23.8%, respectively. We observed one polymorphic site, a non-synonymous change, in the COX3 gene with confirmation heteroplasmy phenomenon within individuals of WBPH by PCR amplification and Sanger sequencing, the first report in this species. In addition, this heteroplasmy was not observed in wild WBPH populations, suggesting that it may be uncommon in fields. We analyzed single nucleotide polymorphisms, insertion, and deletions, and simple sequence repeats among the three WBPH mitogenomes from Korea and China and found diverse intraspecific variations, which could be potential candidates for developing markers to distinguish geographical populations. Phylogenetic analysis of 32 mitogenomes of Delphacidae including the three WBPH mitogenomes suggested that Delphacinae seems to be monophyletic and Sogatella species including WBPH are clearly formed as one clade. In the future, it is expected that complete mitogenomes of individuals of geographically dispersed WBPH populations will be used for further population genetic studies to understand the migration pathway of WBPH.

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Section: Phylogenetic Tree Of 32 Delphacidae Mitogenomes Including Three Wbph Mitogenomessupporting

confidence: 88%

A New Mitochondrial Genome of Sogatella furcifera (Horváth) (Hemiptera: Delphacidae) and Mitogenome-Wide Investigation on Polymorphisms

Park¹,

Xi²,

Park³

et al. 2021

Insects

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“…Morphologically, B. citricolorata belongs to the citricolorata group, while B. furca and B. luodianensis belong to the nigropunctata group. However, molecular data suggest that B. citricolorata and B. luodianensis are more closely related (Huang et al 2017(Huang et al , 2020. The application of molecular phylogenetics has significantly benefited the systematics and taxonomy of Delphacidae.…”

Section: Discussionmentioning

confidence: 99%

Three new species of the bamboo-feeding planthopper genus Bambusiphaga Huang & Ding from China (Hemiptera: Fulgoroidea: Delphacidae)

Chen

Yang

2023

EJT

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“…The target capture sequencing methodology used in this study offers a cost advantage compared to other traditional techniques for sequencing mitochondrial genomes, such as long-range PCR, shotgun sequencing and Sanger sequencing (Feutry et al 2014;Doane et al 2018;Bao et al 2019;Huang et al 2020). We applied an 8-pool capture which, since excessive coverage was obtained for almost all of our samples, can be further multiplexed in future experiments.…”

Section: Capture Sequencing As An Efficient Means Of Obtaining Comple...mentioning

confidence: 99%

Mind the gap: a set of mitochondrial genomes to enable molecular identification of fisheries relevant to conservation and economy in the South Atlantic

ALVARENGA,

D'Elia,

Santos

et al. 2023

Preprint

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Phylogenetic gaps of publicly-available reference sequences are a major obstacle for species identification and management, particularly in the Global South, where economically important fisheries and conservation flagship species often lack closely-related references. We applied target-enrichment to obtain complete mitochondrial genomes of marine ichthyofauna from the Brazilian coast lacking phylogenetically-close references. Species were selected based on economic significance, including three sardines (Dorosomatidae and Alosidae), three mackerels (Scombridae) and nine croakers (Sciaenidae), as well as conservation status, notably groupers and snappers of the Epinephelid family. Custom baits were designed to enrich mitochondrial DNA across a broad phylogenetic range of fishes. Sequencing generated approximately 100k reads per sample, which were assembled in a total of 70 complete mitochondrial genomes and include fifty-two new additions to databases, including five species with no previous mitochondrial data. Departures from the typical gene content and order occurred in only three taxa and mostly involved tRNA gene duplications. Start-codons for all genes, except Cytochrome c Oxidase Subunit I (COI), were consistently ATG, whilst a wide range of stop-codons deviated from the prevailing TAA. Phylogenetic analysis confirmed assembly accuracy and revealed signs of cryptic diversification within the Mullus genus. Lineage delimitation methods using Sardinella aurita and S. brasiliensis mitochondrial genomes support a single Operational Taxonomic Unit. Target enrichment was highly efficient, providing complete novel mitochondrial genomes with little sequencing effort. These sequences are deposited in public databases to enable conservation and management programs in Latin America that rely on molecular data for species and genus-level identification.

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Contribution to the mitogenome diversity in Delphacinae: Phylogenetic and ecological implications

Cited by 13 publications

References 45 publications

A New Mitochondrial Genome of Sogatella furcifera (Horváth) (Hemiptera: Delphacidae) and Mitogenome-Wide Investigation on Polymorphisms

A New Mitochondrial Genome of Sogatella furcifera (Horváth) (Hemiptera: Delphacidae) and Mitogenome-Wide Investigation on Polymorphisms

Three new species of the bamboo-feeding planthopper genus Bambusiphaga Huang & Ding from China (Hemiptera: Fulgoroidea: Delphacidae)

Mind the gap: a set of mitochondrial genomes to enable molecular identification of fisheries relevant to conservation and economy in the South Atlantic

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