Genus-Wide Characterization of Nuclear Mitochondrial DNAs in Bumblebee (Hymenoptera: Apidae) Genomes.

Lele Ding,Huiling Sang,Cheng Sun

doi:10.3390/insects12110963

Lele Ding, Huiling Sang + Show 1 more

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https://doi.org/10.3390/insects12110963

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Abstract

Simple SummaryThe DNA of mitochondria can be transferred into the nucleus and form nuclear mitochondrial DNAs (NUMTs). In this study, we identified and characterized NUMTs in genus-wide bumblebee species. The number of NUMTs in bumblebee is much lower than those in its closely related taxon, honeybee. The insertion sites of NUMTs in bumblebee are not random, with AT-rich regions harboring more NUMTs. In addition, NUMTs derived from the mitochondrial COX1 gene are most abundant in the nuclear genome. While the majority of NUMTs seem unfunctional in the bumblebee, some NUMTs show functional clues, which could fuse with their flanking sequences to form novel proteins. Our results shed light on the molecular features of NUMTs and uncover their contribution to genome innovation in the bumblebee.In eukaryotes, DNA of mitochondria is transferred into the nucleus and forms nuclear mitochondrial DNAs (NUMTs). Taking advantage of the abundant genomic resources for bumblebees, in this study, we de novo generated mitochondrial genomes (mitogenomes) for 11 bumblebee species. Then, we identified and characterized NUMTs in genus-wide bumblebee species. The number of identified NUMTs varies across those species, with numbers ranging from 32 to 72, and nuclear genome size is not positively related to NUMT number. The insertion sites of NUMTs in the nuclear genome are not random, with AT-rich regions harboring more NUMTs. In addition, our results suggest that NUMTs derived from the mitochondrial COX1 gene are most abundant in the bumblebee nuclear genome. Although the majority of NUMTs are found within intergenic regions, some NUMTs do reside within genic regions. Transcripts that contain both the NUMT sequence and its flanking non-NUMT sequences could be found in the bumblebee transcriptome, suggesting a potential domestication of NUMTs in the bumblebee. Taken together, our results shed light on the molecular features of NUMTs in the bumblebee and uncover their contribution to genome innovation.

Highlights

In eukaryotes, the DNA of mitochondria can be transferred to the nuclear genome and form so-called nuclear mitochondrial DNAs (NUMTs) [1,2,3,4,5,6]
The number of NUMTs varies across species, and broadly, three reasons could underlie such variation: (1) the frequency of double-strand breaks (DSBs) is different across species; (2) the frequency of DSBs repaired by non-homologous end-joining repair (NHEJ) vary between species; and (3) the rate of NUMT loss is different across species [3,5,8]
To understand factors that contribute to the variable number of NUMTs in differen bumblebee species, firstly, we investigated the relationship between NUMT numbers and the length of mitogenomes

Summary

Introduction

The DNA of mitochondria can be transferred to the nuclear genome and form so-called nuclear mitochondrial DNAs (NUMTs) [1,2,3,4,5,6]. Bumblebees (Hymenoptera: Apidae) are a group of insects that comprise the genus Bombus, with ~250 extant species classified into 15 subgenera [13,14,15]. They are important pollinators for both wild flowers and crops [16,17]. The presence of NUMTs in the bumblebee has been implicated in a previous study [18], no detailed, genome-wide analysis has yet been conducted. Our study sheds light on the molecular features of NUMTs in bumblebee, as well as their contribution to genome innovation

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