Mitochondrial DNA sequence variation in Drosophilid species (Diptera: Drosophilidae) along altitudinal gradient from Central Himalayan region of India

Sarswat, Manisha; Dewan, Saurabh; Fartyal, Rajendra Singh

doi:10.1007/s12041-016-0646-x

Cited by 7 publications

(2 citation statements)

References 40 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…While it is possible that these dissimilarities might be due to misidentification of the species, several of the eight species are easy to identify, so this is an unlikely explanation for all of the large intraspecific variations in sequence similarity in GenBank. Studies on intraspecific variation in parts of the mitogenome typically reported identities >97% [8,39,41]. Hence, similarities below 90% are much lower than expected for intraspecific variation, and are more characteristic of interspecific or intergeneric variation.…”

Section: Discussionmentioning

confidence: 99%

Mitogenome sequence accuracy using different elucidation methods

et al. 2017

View full text Add to dashboard Cite

Mitogenome sequences are highly desired because they are used in several biological disciplines. Their elucidation has been facilitated through the development of massive parallel sequencing, accelerating their deposition in public databases. However, sequencing, assembly and annotation methods might induce variability in their quality, raising concerns about the accuracy of the sequences that have been deposited in public databases. In this work we show that different sequencing methods (number of species pooled in a library, insert size and platform) and assembly and annotation methods generated variable completeness and similarity of the resulting mitogenome sequences, using three species of predaceous ladybird beetles as models. The identity of the sequences varied considerably depending on the method used and ranged from 38.19 to 90.1% for Cycloneda sanguinea, 72.85 to 91.06% for Harmonia axyridis and 41.15 to 93.60% for Hippodamia convergens. Dissimilarities were frequently found in the non-coding A+T rich region, but were also common in coding regions, and were not associated with low coverage. Mitogenome completeness and sequence identity were affected by the sequencing and assembly/annotation methods, and high within-species variation was also found for other mitogenome depositions in GenBank. This indicates a need for methods to confirm sequence accuracy, and guidelines for verifying mitogenomes should be discussed and developed by the scientific community.

show abstract

Section: Discussionmentioning

confidence: 99%

Mitogenome sequence accuracy using different elucidation methods

et al. 2017

View full text Add to dashboard Cite

show abstract

“…In Japan, this species is widespread from May to December [12] and presents genetic variations in larval and adult activity levels and the daily rhythm of adults within a population [13]. The species clusters into two extremely divergent haplogroups in Indian populations [14].…”

Section: Materials and Methods (A) Study Speciesmentioning

confidence: 99%

Mitochondrial polymorphism shapes intrapopulation behavioural variation in wild Drosophila

Ueno

Takahashi

2021

Biol. Lett.

View full text Add to dashboard Cite

Intrapopulation variation in behaviour, including activity, boldness and aggressiveness, is becoming more widely recognized and is hypothesized to substantially affect ecological and evolutionary dynamics. Although previous studies used candidate-gene approaches and genome-wide association analyses to identify genes correlated with variations in activity and aggressiveness, behavioural variation may not be fully captured in the nuclear genome, as it does not account for mitochondrial genomes. Mitochondrial genes encode products that are key regulators of the cellular energy-producing pathways in metabolic processes and are thought to play a significant role in life-history and reproductive traits. In this study, we considered many isofemale lines of Drosophila immigrans established from two wild populations to investigate whether intrapopulation variation in the mitochondrial genome affected activity level within this species. We identified two major haplogroups in these populations, and activity levels in both larvae and adults differed significantly between the two haplogroups. This result indicated that intrapopulation variation in activity level may be partially controlled by mitochondrial genes, along with the interaction between nuclear and mitochondrial genes and the age of individual organisms.

show abstract