Identification of Mitochondrial DNA (NUMTs) in the Nuclear Genome of Daphnia magna

New Insight into Nucleotide Changes on Irradiated Bactrocera dorsalis (Hendel), A Pest of Horticultural Importance

Bactrocera dorsalis (Hendel) is a major quarantine pest species infesting most of the tropical fruits. Its infestation had significantly reduced and disrupted the export market trade, thus, very crucial to be controlled during the preharvest and postharvest. One of the most sustainable control methods is by using the radiation technique to reduce the pest population, thus curbing the spread of this pest to new geographical areas. The objective of this study was to measure the nucleotide changes in B. dorsalis (larval, pupal and adult stages) which had been irradiated with 50 to 400 Gray, using Gamma Cell Biobeam GM8000 irradiator with Cesium-137 source at the Malaysian Nuclear Agency, Selangor, Malaysia. Data from the treated samples (with and without morphological changes) were analysed using cytochrome oxidase subunit I (COI). The alignment of 59 sequences resulted in 0.92% variables with only four characters that were parsimony informative, and six sites (30, 60, 234, 282, 483 and 589) which had nucleotide changes, but had not been translated to another protein. Low polymorphism was presented on the sample groups, with only four haplotypes, but with high diversity value (Hd) = 0.5885. The phylogeny trees formed soft polytomy in both trees [neighbour joining (NJ) and maximum parsimony (MP)] presenting a mixture of individuals but did not show any significant difference between treatments. This finding concluded that low mutation had occurred on the treated B. dorsalis and this information is very valuable in getting new insight on the survival of B. dorsalis in the horticulture industry.

Transcriptomic Analysis of Diethylstilbestrol in Daphnia Magna: Energy Metabolism and Growth Inhibition

With the widespread use of diethylstilbestrol (DES), it has become a common contaminant in the aquatic environment. It is toxic to a wide range of aquatic organisms, disrupting the water flea growth and further interfering with several ecosystem services. Nevertheless, the molecular mechanism of DES in water fleas is still unexplicit. In this study, the 21-day chronic test showed that a negative effect of growth and reproduction can be observed with DES exposure. Subsequently applied transcriptomic analysis illustrated the molecular mechanism in mode freshwater invertebrate Daphnia magna (D. magna) exposed to 2, 200, and 1000 μg·L^-1 of DES for 9 days. Meanwhile, exposure to DES at 200 and 1000 μg·L^-1 significantly restrains the growth (body length) and reproduction (first spawning time) of D. magna. Identified differentially expressed genes (DEGs) are majorly enriched relative to energy metabolism, lipid metabolism, the digestive system, transport and catabolism pathways which were remarkably changed. These repressed and up-regulated pathways, in relation to energy synthesis and metabolism, may be the reasons for the reduced body length and delayed first spawning time. Taken together, this study revealed that DES is a threat to D. magna in the aquatic environment and clarifies the molecular mechanism of the toxicity.

NUMTs Can Imitate Biparental Transmission of mtDNA-A Case in Drosophila melanogaster

mtDNA sequences can be incorporated into the nuclear genome and produce nuclear mitochondrial fragments (NUMTs), which resemble mtDNA in their sequence but are transmitted biparentally, like the nuclear genome. NUMTs can be mistaken as real mtDNA and may lead to the erroneous impression that mtDNA is biparentally transmitted. Here, we report a case of mtDNA heteroplasmy in a Drosophila melanogaster DGRP line, in which the one haplotype was biparentally transmitted in an autosomal manner. Given the sequence identity of this haplotype with the mtDNA, the crossing experiments led to uncertainty about whether heteroplasmy was real or an artifact due to a NUMT. More specific experiments revealed that there is a large NUMT insertion in the X chromosome of a specific DGRP line, imitating biparental inheritance of mtDNA. Our result suggests that studies on mtDNA heteroplasmy and on mtDNA inheritance should first exclude the possibility of NUMT interference in their data.

Frequent Paternal Mitochondrial Inheritance and Rapid Haplotype Frequency Shifts in Copepod Hybrids

Mitochondria are assumed to be maternally inherited in most animal species, and this foundational concept has fostered advances in phylogenetics, conservation, and population genetics. Like other animals, mitochondria were thought to be solely maternally inherited in the marine copepod Tigriopus californicus, which has served as a useful model for studying mitonuclear interactions, hybrid breakdown, and environmental tolerance. However, we present PCR, Sanger sequencing, and Illumina Nextera sequencing evidence that extensive paternal mitochondrial DNA (mtDNA) transmission is occurring in inter-population hybrids of T. californicus. PCR on four types of crosses between three populations (total sample size of 376 F1 individuals) with 20% genome-wide mitochondrial divergence showed 2% to 59% of F1 hybrids with both paternal and maternal mtDNA, where low and high paternal leakage values were found in different cross directions of the same population pairs. Sequencing methods further verified nucleotide similarities between F1 mtDNA and paternal mtDNA sequences. Interestingly, the paternal mtDNA in F1s from some crosses inherited haplotypes that were uncommon in the paternal population. Compared to some previous research on paternal leakage, we employed more rigorous methods to rule out contamination and false detection of paternal mtDNA due to non-functional nuclear mitochondrial DNA fragments. Our results raise the potential that other animal systems thought to only inherit maternal mitochondria may also have paternal leakage, which would then affect the interpretation of past and future population genetics or phylogenetic studies that rely on mitochondria as uniparental markers.

Transcriptomic analysis and transgenerational effects of ZnO nanoparticles on Daphnia magna: Endocrine-disrupting potential and energy metabolism

The widespread application of zinc oxide nanoparticles (ZnO NPs) has raised concerns over the adverse effects on aquatic species. In this study, transcriptomic analysis was applied to evaluate the chronic toxicity of ZnO NPs on the freshwater invertebrate Daphnia magna and the intergenerational effects were then further investigated. Parent daphnia (F0) were exposed to ZnO NPs at 3, 60, and 300 μg L^-1 for 21 days. ZnO NPs significantly inhibited the reproduction (first pregnancy and spawning time, total number of offspring) and growth (molting frequency and body length) of F0. Here, differentially expressed genes (DEGs) involved in lysosomal and phagosome, energy metabolism and endocrine disruption pathways were significantly downregulated. Furthermore, disruption on the transport and catabolic processes probably resulted in the particle accumulation. The inhibited pathways related to energy metabolism may partially account for the body length, molting and reproductive restriction. The suppression of growth and reproduction may attribute to the down-regulation of insulin secretion and ovarian steroidogenesis pathways, respectively. Partial recovery of growth and reproductive inhibition in F1 - F3 descended from the F0 generation exposure did not support constant transgenerational effects. This study unravels the molecular mechanisms and transgenerational consequences of the toxicity of nanoparticles on Daphnia.

Contrasting Host-Parasite Population Structure: Morphology and Mitogenomics of a Parasitic Flatworm on Pelagic Deepwater Cichlid Fishes from Lake Tanganyika

Little phylogeographic structure is presumed for highly mobile species in pelagic zones. Lake Tanganyika is a unique ecosystem with a speciose and largely endemic fauna famous for its remarkable evolutionary history. In bathybatine cichlid fishes, the pattern of lake-wide population differentiation differs among species. We assessed the congruence between the phylogeographic structure of bathybatine cichlids and their parasitic flatworm Cichlidogyrus casuarinus to test the magnifying glass hypothesis. Additionally, we evaluated the use of a PoolSeq approach to study intraspecific variation in dactylogyrid monogeneans. The lake-wide population structure of C. casuarinus ex Hemibates stenosoma was assessed based on a portion of the cox1 gene combined with morphological characterisation. Additionally, intraspecific mitogenomic variation among 80 parasite samples from one spatially constrained metapopulation was assessed using shotgun NGS. While no clear geographic genetic structure was detected in parasites, both geographic and host-related phenotypic variation was apparent. The incongruence with the genetic north-south gradient observed in H. stenosoma may be explained by the broad host range of this flatworm including eupelagic bathybatine host species that form panmictic populations across the lake. In addition, we present the first parasite mitogenome from Lake Tanganyika and propose a methodological framework for studying the intraspecific mitogenomic variation of dactylogyrid monogeneans.