Abstract
The Zygothrica genus group of Drosophilidae encompasses more than 437 species and five genera. Although knowledge regarding its diversity has increased, uncertainties about its monophyly and position within Drosophilidae remain. Genomic approaches have been widely used to address different phylogenetic questions and analyses involving the mitogenome have revealed a cost-efficient tool to these studies. Thus, this work aims to characterize mitogenomes of three species of the Zygothrica genus group (from the Hirtodrosophila, Paraliodrosophila and Zygothrica genera), while comparing them with orthologous sequences from other 23 Drosophilidae species and addressing their phylogenetic position. General content concerning gene order and overlap, nucleotide composition, start and stop codon, codon usage and tRNA structures were compared, and phylogenetic trees were constructed under different datasets. The complete mitogenomes characterized for H. subflavohalterata affinis H002 and P. antennta present the PanCrustacea gene order with 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, 13 protein coding genes and an A+T rich region with two T-stretched elements. Some peculiarities such as the almost complete overlap of genes tRNAH/ND4, tRNAF/ND5 and tRNAS2/ND1 are reported for different Drosophilidae species. Non-canonical secondary structures were encountered for tRNAS1 and tRNAY, revealing patterns that apply at different phylogenetic scales. According to the best depiction of the mitogenomes evolutionary history, the three Neotropical species of the Zygothrica genus group encompass a monophyletic lineage sister to Zaprionus, composing with this genus a clade that is sister to the Drosophila subgenus.
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Acknowledgements
We would like to thank to Dr. Antonio Bernardo de Carvalho for providing the mitogenome sequences of P. antennata and H. subflavohalterata affinis H002. M. H. B. received a Research Grant from Coordenação de Aperfeiçoamento de Pessoal de Nível Superior—CAPES (Finance Code 001). L.J.R. and E. S. L. are research fellows of CNPq – PQ (# 308371/2018-6 and 407225/2016-1, respectively).
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MHB and LJR designed the study. MHB, FCR and RDM conducted analyses under guidance of ELL and LJR. MHB wrote a first draft of the manuscript and all authors revised and approved it.
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10709_2021_132_MOESM1_ESM.pdf
Linear representation of the mitogenomes of each of the 26 species evaluated in thisstudy Supplementary file1 (PDF 471 KB)
10709_2021_132_MOESM2_ESM.pdf
Box plots presenting the distribution of %A+T (A, D and G), A-T skew (B, E and H) andG-C skew (C, F and I) among lineages for PCGs (A, B and C), tRNA genes (D, E and F), andrRNA genes (G, H and I). The asterisk above brackets indicates that the embraced lineagespresented significant differences (* for p < 0.05; ** for p < 0.01 and *** for p < 0.001) Supplementary file2 (PDF 409 KB)
10709_2021_132_MOESM3_ESM.pdf
Box plots presenting the distribution of %A+T (A, D and G), A-T skew (B, E and H) andG-C skew (C, F and I) among lineages for the first (A, B and C), second (D, E and F), and thirdcodon position (G, H and I) of PCG. The asterisk above brackets indicates that the embracedlineages presented significant differences (* for p < 0.05; ** for p < 0.01 and *** for p < 0.001) Supplementary file3 (PDF 419 KB)
10709_2021_132_MOESM4_ESM.pdf
Average relative synonymous codon usage (RSCU) patterns presented by each of theevaluated species in regard to each of the codons of (A) Phe, (B) Leu, (C) Ile, (D) Met, (E) Val,(F) Ser, (G) Pro, (H) Thr, (I) Tyr, (J) Ala, (K) His, (L) Gln, (M) Asn, (N) Lys, (O) Asp, (P) Glu, (Q)Cys, (R) Trp, (S) Arg, (T) Gly and (U) Stop codons. A set (→) depicts the codon with a perfectmatch with anticodons of the mitochondrial tRNAs Supplementary file4 (PDF 554 KB)
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Box plots presenting the distribution of RSCU values for (1) UUU (Phe), (2) UUC (Phe),(3) UUA (Leu), (4)UUG (Leu), (5) CUU (Leu), (6) CUC (Leu), (7) CUA (Leu), (8) CUG (Leu), (9)AUU (Ile), (10) AUC (Ile), (11) AUA (Met), (12) AUG (Met), (13) GUU (Val), (14) GUC (Val), (15)GUA (Val), (16) GUG (Val), (17) UCU (Ser), (18) UCC (Ser), (19) UCA (Ser), (20) UCG (Ser),(21) AGU (Ser), (22) AGC (Ser), (23) AGA (Ser), (24) AGG (Ser), (25) CCU (Pro), (26) CCC(Pro), (27) CCA (Pro), (28) CCG (Pro), (29) ACU (Thr), (30) ACC (Thr), (31) ACA (Thr), (32)ACG (Thr), (33) GCU (Ala), (34) GCC (Ala), (35) GCA (Ala), (36) GCG (Ala), (37) UAU (Tyr),(38) UAC (Tyr), (39) CAU (His), (40) CAC (His), (41) CAA (Gln), (42) CAG (Gln), (43) AAU(Asn), (44) AAC (Asn), (45) AAA (Lys), (46) AAG (Lys), (47) GAU (Asp), (48) GAC (Asp), (49)GAA (Glu), (50) GAG (Glu), (51) UGU (Cys), (52) UGC (Cys), (53) UGA (Trp), (54) UGG (Trp),(55) CGU (Arg), (56) CGC (Arg), (57) CGA (Arg), (58) CGG (Arg), (59) GGU (Gly), (60) GGC(Gly), (61) GGA (Gly), (62) GGG (Gly), (63) UAA (Stop), and (64) UAG (Stop) among lineages. Supplementary file5 (PDF 2460 KB)
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Secondary structures recovered for each of the 22 tRNAs encompassing themitogenome of P. antennata Supplementary file6 (PDF 84 KB)
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Secondary structures recovered for each of the 22 tRNAs encompassing themitogenome of H. subflavohalterata affinis H002 Supplementary file7 (PDF 86 KB)
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Comparisons among the secondary structures recovered for each of the 22 tRNAsencompassing the mitogenomes of all Drosophilidae species included in this study (to theexception of Z. vittimaculosa) Supplementary file8 (PDF 1698 KB)
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Box plots presenting the distribution of (A) average nucleotide distances and (B) dN,dS and dN/dS ratios for each of the 13 mitochondrial PCG, the two rRNA genes and all thetRNA genes. Letters above bars summarizes the results of significance obtained frompairwise comparisons performed through Tukey post-hoc tests Supplementary file9 (PDF 159 KB)
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Majority-rule consensus tree reconstructed through BI based on the mRNAs (A),rRNA+mRNA (B), tRNA+rRNA+mRNA (C), aa curated (without saturated genes) (D), mRNAcurated (E), rRNA+mRNA curated (F) and tRNA+rRNA+mRNA curated (G) mitochondrialdatasets. Branch lengths are proportional to the scale, given in substitution per site. Valuesbefore each internal node represent the posterior probability (PP) and the bootstrap value (BS)recovered through BI and ML analyses, respectively Supplementary file10 (PDF 2795 KB)
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Density plots representing the results of the saturation tests performed with the set ofmitochondrial genes as measured by R2 [at nucleotide (A) and amino acid (B) levels] and byslope values [at nucleotide (C) and amino acid (D) levels] Supplementary file11 (PDF 41 KB)
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Alignments of nucleotides sequences of each of 37 genes encompassing theDrosophilidae mitogenome Supplementary file13 (RAR 54 KB)
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Alignments of aminoacid sequences of each of 13 protein coding genesencompassing the Drosophilidae mitogenome Supplementary file14 (RAR 14 KB)
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Bessa, M., Ré, F., Moura, R. et al. Comparative mitogenomics of Drosophilidae and the evolution of the Zygothrica genus group (Diptera, Drosophilidae). Genetica 149, 267–281 (2021). https://doi.org/10.1007/s10709-021-00132-8
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DOI: https://doi.org/10.1007/s10709-021-00132-8