Abstract
The control region of mitochondrial genome is the main non-coding region. There is no details about Geospiza magnirostris’s control region, who is the only species of Geospiza in Darwin finches whose mitochondrial genome has been sequenced. In this study, the control region mitochondrial genome of G. magnirostris was analyzed. Compare research for 15 Passerine species, belonging to 4 families (Darwin ground finch, Thraupidae, Icteridae, Emberizidae), was also been done. The result showed the length was 1202 bp and it could been divided into three parts, domainI, domainII and domainIII. Genetic distances showed average divergence of different family ranged from 0.36% (Darwin ground finch) to 9.20% (Emberizidae), indicated that the Darwin ground finch may be a very conservative single-source species. Some specific sequence fragments such as conservative sequence box, boxes C, D, F and E, HSP/LSP, CSB-1, TAS-1 were also found in the control region of G. magnirostris, while B-box, CSB-2 and CSB-3 were not found in it. The F-box was detected in all selected 15 species and was 29 bp in length with no variant sites. In the E-box, 20 of the 21 nucleotide positions were identical as conserved among the selected species. There are two variant sites in the D-box, and five variant sites in the C-box. Basing the phylogenetic tree, it can be clearly seen that the relationship of G. magnirostris and family Thraupidae is the closest in all selected family. Through this study, the structure characteristics of G. magnirostris control region were explored and understood. This study provided more basic information for in-depth research of G. magnirostris. It’s also reminded us that we should pay more attention to explore the characteristics of the control region of Darwin’s finches.
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Abbreviations
- CSB-1:
-
Conserved Sequence Blocks
- F E D C boxes:
-
Conserved Sequence Blocks of DomainII
- HSP:
-
Heavy-strand Transcription Promoter
- IUCN:
-
International Union for Conservation of Nature
- LC:
-
Least Concern
- LSP:
-
Light-strand Transcription Promoter
- ML:
-
Maximum Likehood
- NCBI:
-
National Center for Biotechnology Information
- OH:
-
origin of H-strand replication
- TAS:
-
Termination Associated Sequence
- VNTR:
-
Variable Number of Tandem Repeats
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Acknowledgements
We thank Wang Shuangye and Yang Nan for participating in some data analysis during the experiment. We also thank them for reviewing the first draft of the manuscript.
Funding
The study was supported by Natural Science Foundation of Hunan Province (2019JJ50027, 2019JJ40012), Key Technology R&D Program of Hunan Province (2016TP2007; 2016TP1014; 2017TP2014) and Scientific Innovation Fund for Graduate of Central South University of Forestry and Technology (20183023).
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Z. Y. and H. T. providing the funding. X. Z. and W. L. conceived and designed the experiments. W. L. and H. S. performed the experiments and analyzed the data. H. C., W. L., and X. Z. contributed analysis tools. W. L. and X. Z. wrote the paper. All co-authors have read and approved the manuscript.
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Zhenggang, X., Liang, W., Sihan, H. et al. Structural variation and phylogenetic relationship of Geospiza magnirostris based on mitochondrial control region. Biologia 76, 1367–1373 (2021). https://doi.org/10.2478/s11756-020-00669-7
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DOI: https://doi.org/10.2478/s11756-020-00669-7