Contribution of the intron retained in the Nxf1 gene transcript to the phylogeny of the order Chiroptera

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Abstract

This work is devoted to the possibilities of using a specific intron-containing block of the Nxf1 gene in phylogenetic studies.

Our attention was drawn to the conservative intron of the Nxf1 (nuclear export factor) gene. This intron is a part of an evolutionarily conserved block formed with flanking 110 bp and 37 bp exons, similar in representatives of various taxonomic groups. This evolutionary conservative block in our previous works was designated “cassette intron”. The Nxf1 genes are found in all representatives of Opisthokonta, and may be a convenient object for phylogenetic studies.

The Nxf1 gene sequences of seventeen representatives of the order Chiroptera obtained from publicly available databases (ensembl, ncbi). Alignment algorithm: MUSCLE. Programs: MEGA-X version 10.1.7, IQTree, Mesquite, MrBayes, and FigTree.v1.4.4. Estimation methods: Maximum Likelihood and Bayes Inference.

The use of Nxf1 gene sequences that include only exons or only introns leads to unequal loss of accuracy in establishing evolutionary relationships in comparison with the model based on the complete gene sequence. Sequences involving all exons plus a cassette intron give the same result as the complete Nxf1 gene sequence.

The obtained results indicate the importance of the cassette intron in the evolution of the Nxf1 gene of Chiroptera.

About the authors

Dmitrii D. Bondaruk

Saint-Petersburg State University

Author for correspondence.
Email: D.D.Bondaruk@yandex.ru
ORCID iD: 0000-0003-0265-5759
SPIN-code: 8162-8441

Postgraduate student

Russian Federation, Saint-Petersburg

Elena V. Golubkova

Saint Petersburg State University

Email: elena_golubkova@mail.ru
ORCID iD: 0000-0002-9528-5760
SPIN-code: 7386-1230
Scopus Author ID: 6602650894

Cand. Sci. (Biol.), Associate Professor, Department of Genetics and Biotechnology

Russian Federation, Saint Petersburg

Lyudmila A. Mamon

Saint Petersburg State University

Email: mamon@lm2010.spb.edu
ORCID iD: 0000-0001-5338-0703
SPIN-code: 7780-6907

Dr. Sci. (Biol.), Professor, Department of Genetics and Biotechnology

Russian Federation, Saint Petersburg

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Supplementary files

Supplementary Files
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2. Fig. 1. Variants of the sequence used in the experiment. 1 — Full-gene sequence; 2 — exons only; 3 — exons and intron 10; 4 — intron 10 and exons 10, 11; 5 — intron 10 (cassette intron); 6 — exons 10, 11; 7 — excluding intron 10 (cassette intron); 8 — only introns, except intron 10 (cassette intron). Non-coding exons at the 5' and 3' ends are including in sequences

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3. Fig. 2. Phylogenetic tree based on the full-gene sequence variant of the Chiroptera’s Nxf1 gene. The tree was constructed by maximum likelihood and Bayesian methods. Support ratios are denoted as SH-Like aLTR/Bootstrap and the Bayesian posterior value. Large families are color coded. The branch order within highlighted areas remains unchanged in all considered schemes or the reasons for its violation are determined and individual nodes can be considered allowed. The above designations are common to this and all following figures

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4. Fig. 3. Phylogenetic tree based on the “only exons” sequence variant of the Chiroptera’s Nxf1 gene

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5. Fig. 4. Phylogenetic tree based on the “intron 10 and exons 10, 11” sequence variant of the Chiroptera’s Nxf1 gene

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6. Appendix 1. Phylogenetic tree based on the “exons and intron 10” sequence variant of the Chiroptera’s Nxf1 gene

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7. Appendix 2. Phylogenetic tree based on the “only intron 10 (cassette intron)” sequence variant of the Chiroptera’s Nxf1 gene

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8. Appendix 3. Phylogenetic tree based on the “exons 10, 11” sequence variant of the Chiroptera’s Nxf1 gene

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9. Appendix 4. Phylogenetic tree based on the “excluding intron 10 (cassette intron)” sequence variant of the Chiroptera’s Nxf1 gene

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10. Appendix 5. Phylogenetic tree based on the “only introns, except intron 10 (cassette intron)” sequence variant of the Chiroptera’s Nxf1 gene

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Copyright (c) 2022 Bondaruk D.D., Golubkova E.V., Mamon L.A.

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This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.
 


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