The (non) accuracy of mitochondrial genomes for family level phylogenetics: the case of erebid moths (Lepidoptera; Erebidae)

Hr, Ghanavi; Twort,; Tj, Hartman; Zahiri, Reza; Wahlberg, Niklas

doi:10.1101/2021.07.14.452330

Cited by 4 publications

(7 citation statements)

References 58 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Our study was performed on shallow genome short reads obtained using Illumina platform. The original purpose of this sequencing effort was to study the phylogenomics of the hosts species 46 , but a similar approach to the one we have taken here can be implemented to any publicly available genomic datasets. The popularity of genomic scale sequence data methods, such as Illumina short read approach, created a wide publicly open genomic resource for the research community to study questions that are not directly into the focus of the studies generating them.…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Exploring bycatch diversity of organisms in whole genome sequencing of Erebidae moths (Lepidoptera)

Ghanavi

Twort

Duplouy

2021

Preprint

Self Cite

View full text Add to dashboard Cite

Models estimate that up to 80% of all butterfly and moth species host vertically transmitted endosymbiotic microorganisms, which can affect the host fitness, metabolism, reproduction, population dynamics, and genetic diversity, among others. The supporting empirical data are however currently highly biased towards the generally more colourful butterflies, and include less information about moths. Additionally, studies of symbiotic partners of Lepidoptera predominantly focus on the common bacterium Wolbachia pipientis, while infections by other inherited microbial partners have more rarely been investigated. Here, we mine the whole genome sequence data of 47 species of Erebidae moths, with the aims to both inform on the diversity of symbionts potentially associated with this Lepidoptera group, and discuss the potential of metagenomic approaches to inform on their associated microbiome diversity. Based on the result of Kraken2 and MetaPhlAn2 analyses, we found clear evidence of the presence of Wolbachia in four species. Our result also suggests the presence of three other bacterial symbionts (Burkholderia spp., Sodalis spp. and Arsenophonus spp.), in three other moth species. Additionally, we recovered genomic material from bracovirus in about half of our samples. The detection of the latter, usually found in mutualistic association to braconid parasitoid wasps, may inform on host-parasite interactions that take place in the natural habitat of the Erebidae moths, suggesting either contamination with material from species of the host community network, or horizontal transfer of members of the microbiome between interacting species.

show abstract

Section: Discussionmentioning

confidence: 99%

“…We used the data produced from the whole genome sequencing project of 47 Erebidae species (see 46 ). The sampling information is shown in Table 1.…”

Section: Methodsmentioning

confidence: 99%

Exploring bycatch diversity of organisms in whole genome sequencing of Erebidae moths (Lepidoptera)

Ghanavi

Twort

Duplouy

2021

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

“…Our study was performed on shallow genome short reads obtained using Illumina platform. The original purpose of this sequencing effort was to study the phylogenomics of the hosts species 50 , but a similar approach to the one we have taken here can be implemented to any publicly available genomic datasets. The popularity of genomic scale sequence data methods, such as Illumina short read approach, created a wide publicly open genomic resource for the research community to study questions that are not directly into the focus of the studies generating them.…”

Section: Discussionmentioning

confidence: 99%

“…We used the data produced from the whole genome sequencing project of 47 Erebidae species (see 50 ). The sampling information is shown in Table 1 .…”

Section: Methodsmentioning

confidence: 99%

Exploring bycatch diversity of organisms in whole genome sequencing of Erebidae moths (Lepidoptera)

Ghanavi

Twort

Duplouy

2021

Sci Rep

Self Cite

View full text Add to dashboard Cite

Models estimate that up to 80% of all butterfly and moth species host vertically transmitted endosymbiotic microorganisms, which can affect the host fitness, metabolism, reproduction, population dynamics, and genetic diversity, among others. The supporting empirical data are however currently highly biased towards the generally more colourful butterflies, and include less information about moths. Additionally, studies of symbiotic partners of Lepidoptera predominantly focus on the common bacterium Wolbachia pipientis, while infections by other inherited microbial partners have more rarely been investigated. Here, we mine the whole genome sequence data of 47 species of Erebidae moths, with the aims to both inform on the diversity of symbionts potentially associated with this Lepidoptera group, and discuss the potential of metagenomic approaches to inform on host associated microbiome diversity. Based on the result of Kraken2 and MetaPhlAn2 analyses, we found clear evidence of the presence of Wolbachia in four species. Our result also suggests the presence of three other bacterial symbionts (Burkholderia spp., Sodalis spp. and Arsenophonus spp.) in three other moth species. Additionally, we recovered genomic material from bracovirus in about half of our samples. The detection of the latter, usually found in mutualistic association to braconid parasitoid wasps, may inform on host-parasite interactions that take place in the natural habitat of the Erebidae moths, suggesting either contamination with material from species of the host community network, or horizontal transfer of members of the microbiome between interacting species.

show abstract

“…Researches on phylogenetic relationships of moths have been carried out extensively, especially on some large families like Erebidae [ 9 , 10 ], Noctuidae [ 11 , 12 , 13 , 14 , 15 , 16 ] and Geometridae [ 17 , 18 , 19 , 20 ], among which some remarkable and fundamental works were achieved by Kristensen et al [ 21 , 22 ] and Minet et al [ 23 , 24 ] initially with the studies of morphological and anatomical characteristics. As molecular markers widely applied to phylogenetic studies, new evidence has been consistently presented based on mitochondrial genes, nuclear ribosomal DNA, nuclear protein-coding genes or a combined method [ 25 , 26 , 27 , 28 , 29 ].…”

Section: Introductionmentioning

confidence: 99%

Enhanced Resolution of Evolution and Phylogeny of the Moths Inferred from Nineteen Mitochondrial Genomes

Zheng

Zhang

Yue

et al. 2022

Genes

View full text Add to dashboard Cite

The vast majority (approximately 90%) of Lepidoptera species belong to moths whose phylogeny has been widely discussed and highly controversial. For the further understanding of phylogenetic relationships of moths, nineteen nearly complete mitochondrial genomes (mitogenomes) of moths involved in six major lineages were sequenced and characterized. These mitogenomes ranged from 15,177 bp (Cyclidia fractifasciata) to 15,749 bp (Ophthalmitis albosignaria) in length, comprising of the core 37 mitochondrial genes (13 protein-coding genes (PCGs) + 22 tRNAs + two rRNAs) and an incomplete control region. The order and orientation of genes showed the same pattern and the gene order of trnM-trnI-trnQ showed a typical rearrangement of Lepidoptera compared with the ancestral order of trnI-trnQ-trnM. Among these 13 PCGs, ATP8 exhibited the fastest evolutionary rate, and Drepanidae showed the highest average evolutionary rate among six families involved in 66 species. The phylogenetic analyses based on the dataset of 13 PCGs suggested the relationship of (Notodontidae + (Noctuidae + Erebidae)) + (Geometridae + (Sphingidae + Drepanidae)), which suggested a slightly different pattern from previous studies. Most groups were well defined in the subfamily level except Erebidae, which was not fully consistent across bayesian and maximum likelihood methods. Several formerly unassigned tribes of Geometridae were suggested based on mitogenome sequences despite a not very strong support in partial nodes. The study of mitogenomes of these moths can provide fundamental information of mitogenome architecture, and the phylogenetic position of moths, and contributes to further phylogeographical studies and the biological control of pests.

show abstract

The (non) accuracy of mitochondrial genomes for family level phylogenetics: the case of erebid moths (Lepidoptera; Erebidae)

Cited by 4 publications

References 58 publications

Exploring bycatch diversity of organisms in whole genome sequencing of Erebidae moths (Lepidoptera)

Exploring bycatch diversity of organisms in whole genome sequencing of Erebidae moths (Lepidoptera)

Exploring bycatch diversity of organisms in whole genome sequencing of Erebidae moths (Lepidoptera)

Enhanced Resolution of Evolution and Phylogeny of the Moths Inferred from Nineteen Mitochondrial Genomes

Contact Info

Product

Resources

About