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. 2021 May 17;1037:137–159. doi: 10.3897/zookeys.1037.63671

The complete mitochondrial genomes of two erythroneurine leafhoppers (Hemiptera, Cicadellidae, Typhlocybinae, Erythroneurini) with assessment of the phylogenetic status and relationships of tribes of Typhlocybinae

Xiaoxiao Chen 1, Can Li 2, Yuehua Song 1,✉
PMCID: PMC8144164  PMID: 34054318

Abstract

The number and classification of tribes in the leafhopper subfamily Typhlocybinae are not yet fully clear, and molecular data has recently been used to help resolve the problem. In this study, the mitochondrial genomes of Mitjaevia shibingensis Chen, Song & Webb, 2020 and M. dworakowskae Chen, Song & Webb, 2020 of the tribe Erythroneurini (Cicadellidae, Typhlocybinae) were sequenced. Most protein-coding genes (PCGs) start with ATN and end with TAA or TAG, and the AT content of these three codons were found differ from previous results that show that the first codon has the highest incidence. Two rRNA genes are highly conserved, and the AT content in 16S is higher than that of 12S. The nucleotide diversity and genetic distance among 13 PCGs of the four tribes from Typhlocybinae show that Empoascini nucleotide diversity is significantly less than in the other three tribes, and have the largest distance from the others, while Typhlocybini and Zyginellini have the smallest distance, indicating that the relationship between the two is the closest. The nad2, nad4, nad4L, and nad5 genes have greater nucleotide diversity, showing potential for use as the main markers for species identification. The phylogenetic analysis yielded a well-supported topology with most branches receiving maximum support and a few branches pertaining to relationships within Zyginellini and Typhlocybini receiving lower support. The species of these two tribes are intertwined, and it was impossible to resolve them into separate branches. In addition, the tribes Empoascini and Erythroneurini were recovered as monophyletic, and Alebrini was placed at the base of the tree as the most primitive. These results are broadly in line with other molecular phylogenetical studies which differ from traditional morphological classification.

Keywords: Mitjaevia dworakowskae, Mitjaevia shibingensis, mitochondrial genome, phylogenetic analysis, tribal taxonomic status

Introduction

Cicadellidae (leafhoppers) are the largest family of the order Hemiptera. Representatives are important agricultural and forestry pests that feed on a variety of plants such as cereal crops, vegetables, and fruit trees, and they are also vectors of plant pathogens (Morris 1971; Guo 2011; Roddee et al. 2018). Leafhoppers also have many interesting characteristics, such as varied lifestyles and feeding strategies (including utilizing different endosymbionts), covering their bodies with brochosomes, and producing courtship signals through the plant substrate. These characteristics make leafhoppers suitable material for studies on biological evolution and geographical research (Chen et al. 2020a, b). The subfamily of Typhlocybinae is the second largest group of Cicadellidae and is widely distributed in the six major zoogeographic regions of the world. Erythroneurini, the largest tribe of Typhlocybinae, includes ~2,000 species worldwide (Wang et al. 2012).

The traditional classification of leafhopper has attracted much research attention, including the classification of Typhlocybinae. At present, Typhlocybinae contains six tribes (Alebrini, Empoascini, Erythroneurini, Zyginellini, Typhlocybini, Dikraneurini) but this division remains controversial (Hamilton 1998; Balme 2007; Dietrich 2013). Today, the emergence of next-generation sequencing technology is a breakthrough for solving this problem enabling mitochondrial genomic data to verify and reference the existing family-level classification of Typhlocybinae. Many previous attempts have been made to estimate phylogenetic relationships among leafhoppers mostly by using either morphological data or sequence data from a few gene regions (Hamilton 1983; Dietrich et al. 2001; Zahniser and Dietrich 2013; Krishnankutty et al. 2016), but there is very little research on Typhlocybinae. So far, in the National Center for Biotechnology Information (NCBI), Typhlocybinae only has complete mitochondrial genomic data for 19 species (Table 1).

Table 1.

List of the mitochondrial genomes analyzed in the present study.

Tribe Species Length (bp) GenBank accession no.
Empoascini Empoasca flavescens 15,152 MK211224.1
Empoasca onukii 15,167 NC_037210.1
Empoasca vitis 15,154 NC_024838.1
Ghauriana sinensis 15,491 MN699874.1
Erythroneurini Empoascanara dwalata 15,271 MT350235.1
Empoascanara gracilis 14,627 MT576649
Empoascanara sipra 14,827 NC_048516.1
Empoascanara wengangensis 14,830 MT445764
Illinigina sp. 14,803 KY039129.1
Mitjaevia dworakowskae 16,399 MT981880
Mitjaevia protuberanta 15,472 NC_047465.1
Mitjaevia shibingensis 15,788 MT981879
Typhlocybini Bolanusoides shaanxiensis 15,274 MN661136.1
Eupteryx minuscula 16,944 MN910279.1
Typhlocyba sp. 15,223 KY039138.1
Zyginellini Limassolla lingchuanensis 15,716 MN605256.1
Paraahimia luodianensis 16,497 NC_047464.1
Parathailocyba orla 15,382 MN894531.1
Zyginella minuta 15,544 MT488436.1
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The insect mitochondrial genome (mtDNA) is usually a closed double-stranded DNA molecule with a molecular weight of 14–20 kb. Usually, it contains 37 genes, including 13 protein-coding genes (PCGs), NADH dehydrogenase 1-6 and 4L (nad1-6 and nad4L), cytochrome c oxidase subunits 1-3 (cox1-3), ATPase subunit 6 and 8 (atp6 and atp8), cytochrome b (cytb), two ribosomal RNAs genes (16S and 12S) and 22 transfer RNA (tRNA) genes. A region rich in A + T, the control region, is also present (Boore 1999; Wang et al. 2018). Compared with the nuclear genome, the insect mitochondrial genome has the characteristics of a simple structure, low molecular weight, stable composition, conservative arrangement, maternal inheritance, and easy detection. It is very suitable for the study of evolutionary genomics and is widely used to identify the phylogenetic relationships and population structures at different taxonomic levels (Saccone et al. 2002; Cook et al. 2005; Wilson et al. 2008).

To further enrich the mitochondrial genome data of leafhoppers and provide comparative data for closely related species, we sequenced and analyzed the complete mitochondrial genomes of Mitjaevia shibingensis and M. dworakowskae and analyzed their phylogenetic relationship with other Typhlocybinae. The new molecular data obtained will help in the identification of leafhopper species, kinship comparison, and future studies on population genetics and evolution.

Materials and methods

Mitogenome sequencing, assembly, and annotation

For this study, samples of Mitjaevia shibingensis and M. dworakowskae were collected in 100% alcohol and stored at –20 °C in the laboratory. Total DNA was extracted from the entire body without the abdomen and wings. The mitochondrial gene sequences were obtained through second-generation sequencing. Primers were designed to amplify the mtDNA sequence in PCR reactions. The PCR reaction was performed using the LA Taq polymerase. The PCR conditions were as follows: initial denaturation at 94 °C for 2 min, then 35 cycles of denaturation at 94 °C for 30 sec, annealing at 55 °C for 30 sec, and extension at 72 °C for 1 min/kb, followed by the final extension at 72 °C for 10 min. The PCR products were sequenced directly, or, if needed, first cloned into a pMD18-T vector (Takara, JAP) and then sequenced, by the dideoxynucleotide procedure, using an ABI 3730 automatic sequencer (Sanger sequencing) using the same set of primers. After quality-proofing of the obtained fragments, the complete mt genome sequence was assembled manually using DNAStar (Burland 2000), and a homology search was performed by the Blast function in NCBI to verify the amplified sequence as the target sequence (Meng et al. 2013; Yu et al. 2017). The nucleotide base composition, codon usage, and A + T content values were analyzed with MEGA 6.06 (Tamura et al. 2013). The secondary structure of tRNA genes was annotated using online tools tRNAscan-SE 1.21 and ARWEN (Lowe and Eddy 1997; Laslett and Canbäck 2008). The tandem repeat sequence in the control area was determined by the online search tool Tandem Repeats Finder (Benson 1999). The base skew values for a given strand were calculated using the formulae: AT skew = [A – T] / [A + T] and GC skew = [G – C] / [G + C] (Perna and Kocher 1995). The nucleotide diversity (Pi) and sliding window analysis (sliding window: 200 bp, step size: 20 bp) of 13 PCGs among four tribes of Typhlocybinae species were conducted with DnaSP 5.0 software (Rozas et al. 2017). And the genetic distance of the four tribes was estimated in MEGA 6.06.

Phylogenetic analysis

The phylogenetic analysis included two sets of data. First, the phylogenetic tree was constructed based on 29 cox1 data among six tribes of Typhlocybiane and two outgroups. Secondly, phylogenetic tree analysis was conducted using a dataset including the complete mitochondrial genomes of the two newly sequenced erythroneurine species, 17 typhlocybiane species, and two outgroups, of which nine sets of data were from team sequencing, while the remaining 10 were obtained from the NCBI database (Table 1).

The Gblocks Server online platform was used to eliminate poorly aligned positions and divergent regions of DNA protein alignment, and all alignments were checked and corrected in MEGA 6.06 prior to the phylogenetic analysis (Tamura et al. 2013). Five datasets were generated: (1) cox1 with 573 nucleotides (2) 13 PCGs with 10,452 nucleotides (PCGs); (3) the first and second codon positions of the 13 PCGs with 6968 nucleotides (PCG12); (4) 13 PCGs with 10,452 nucleotides and 2 rRNA with 1615 nucleotides (PCGR); (5) and amino acid sequences of the 13 PCGs with 2666 amino acids (PCGAA).

The trimmed datasets were used to estimate the phylogeny by maximum likelihood (ML) using IQ-TREE and Bayesian inference (BI) using MrBayes 3.2.7 (Zhou et al. 2011; Du et al. 2017). ML constructed with the IQ-TREE used an ultrafast bootstrap approximation approach with 10,000 replicates and calculated bootstrap scores for each node (BP). BI selected GTR + I + G as the optimal model, running 10 million generations twice, sampling once every 1000 generations, after the average standard deviation of the segmentation frequency drops below 0.01, with the first 25% of the samples are discarded burn-in, and the remaining trees used to generate a consensus tree and calculate the posterior probability (PP) of each branch.

Results and discussion

Organization and composition of the genome

The genomic organization and nucleotide composition of the two new mitogenomes sequenced in this study are similar to those of other previously reported Typhlocybina (Tan et al. 2020; Yuan et al. 2020). The complete mitogenomes of M. shibingensis and M. dworakowskae are double-stranded plasmids with 15,788 and 16,399 bp, respectively. Both species contain the usual 13 PCGs, 22 tRNA genes, 2 rRNA genes, and a control region (Fig. 1). Fourteen genes encode in the minority strand (L-strand) while the others encode in the majority strand (H-strand). Mitjaevia shibingensis has a total of 46 bp intergenic space in 12 regions ranging from 1 to 8 bp. Eleven genes were found to overlap by a total of 47 bp. Mitjaevia dworakowskae has a total of 84 bp intergenic space in 12 regions ranging from 2 to 15 bp, and seven genes were found to overlap by a total of 23 bp (Table 2).

Figure 1.

Figure 1.

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Circular maps of the mitochondrial genome of Mitjaevia shibingensis and M. dworakowskae.

Table 2.

Organization of the Mitjaevia shibingensis and M. dworakowskae mitochondrial genome.

M. shibingensis/M. dworakowskae
Gene Position Size (bp) Intergenic Start codon Stop codon Strand
tRNA-Ile 1–63 1–63 63 0 H
tRNA-Gln 61–128 61–128 68 –3 0 L
tRNA-Met 151–219 137–205 69 8 9 H
nad2 220–1191 206–1177 972 0 ATA TAA H
tRNA-Trp 1190–1253 1176–1235 64 60 –2 2 H
tRNA-Cys 1246–1307 1233–1295 62 63 –8 L
tRNA-Tyr 1307–1368 1299–1364 62 66 5 3 L
cox1 1378–2913 1374–2909 1536 1 2 ATG TAA TAG H
tRNA-Leu 2915–2980 2911–2976 66 0 2 H
cox2 2981–3659 2977–3655 679 0 ATT T H
tRNA-Lys 3660–3730 3656–3726 71 0 H
tRNA-Asp 3733–3793 3727–3789 61 63 –1 0 H
atp8 3792–3944 3799–3942 153 144 –1 –2 TTG ATA TAA H
atp6 3938–4591 3936–4589 654 –7 0 ATG TAA H
cox3 4592–5371 4590–5369 780 2 8 ATG TAA H
tRNA-Gly 5376–5437 5370–5431 62 0 H
nad3 5438–5791 5432–5785 354 0 ATT ATA TAA H
tRNA-Ala 5796–5857 5791–5855 62 65 4 –2 H
tRNA-Arg 5857–5921 5861–5922 65 62 2 15 H
tRNA-Asn 5912–5986 5922–5981 66 60 –2 0 H
tRNA-Ser 5986–6053 5986–6052 68 67 –4 –1 H
tRNA-Glu 6055–6118 6058–6123 64 66 8 11 H
tRNA-Phe 6135–6197 6128–6195 63 68 4 2 L
nad5 6200–7873 6200–7873 1674 0 TTG TAA L
tRNA-His 7874–7937 7874–7937 64 0 L
nad4 7937–9265 7937–9265 1329 –7 –1 ATG TAA L
nad4L 9259–9537 9259–9537 279 1 –7 ATG TAA L
tRNA-Thr 9540–9605 9540–9604 66 65 2 0 H
tRNA-Pro 9606–9671 9605–9671 66 67 0 7 L
nad6 9674–10159 9674–10159 486 2 5 ATT TAA H
cytb 10166–11302 10162–11298 1137 7 0 ATG TAG TAA H
tRNA-Ser 11309–11372 11298–11363 64 66 –2 9 H
nad1 11363–12304 11366–12296 942 931 –10 –2 ATT TAA T L
tRNA-Leu 12305–12370 12297–12364 66 68 0 L
16S 12371–13562 12365–13549 1192 1185 0 L
tRNA-Val 13563–13627 13550–13615 65 66 0 L
12S 13628–14359 13616–14351 732 736 0 L
D-loop 14360–15788 14352–16399 1429 2048
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The AT contents and skew statistics are shown in Table 3. The mitochondrial genomes of M. shibingensis and M. dworakowskae show heavy AT nucleotide bias, with A + T% content for the whole sequence was 78.4% and 79.0%, respectively. Similar patterns of nucleotide composition are also found in other leafhopper species (Du et al. 2017; Wang et al. 2018; Xian et al. 2020). The control region (CR) has the strongest A + T% bias, while the PCGs shows the lowest A + T% among whole genes. The whole genome has positive AT skews (0.042, 0.051) and negative GC skews (–0.074, –0.104). Analysis of 37 individual genes of the two species show that AT skews are mostly positive, while for GC skews, the genes of both species are mostly negative (Fig. 2). Positive AT skews indicates that the content of base A is higher than that of base T. However, in a few genes, although the AT skews is negative, the difference in absolute value was very small. For negative GC skew, a negative value indicates that the content of base G is lower than that of base C, while a positive value indicates the opposite. In general, the basic composition of these two species is biased towards A and C.

Table 3.

Nucleotide compositions, AT skew, and GC skew in different regions of Mitjaevia shibingensis and M. dworakowskae mitochondrial genomes.

Feature A% C% G% T% A+T% AT skew GC skew Length (bp)
M. shibingensis
Whole 40.8 11.6 10.0 37.6 78.4 0.042 –0.074 15,788
PCGs 39.3 12.8 11.5 36.4 75.7 0.038 –0.053 10975
1st codon position 41.6 12.1 11.5 34.9 76.5 0.087 –0.026 3659
2nd codon position 38.3 12.2 11.7 37.8 76.1 0.007 –0.018 3658
3rd codon position 38.0 14.1 11.3 36.6 74.5 0.019 –0.111 3658
tRNA 40.6 10.9 10.1 38.4 79.0 0.028 –0.037 1427
16S 48.1 11.1 6.0 34.8 82.9 0.160 –0.294 1192
12S 48.0 12.0 6.1 33.9 81.8 0.172 –0.323 732
CR 42.7 3.5 3.8 50.0 92.7 –0.079 0.038 1429
M. dworakowskae
Whole 41.5 11.6 9.4 37.5 79.0 0.051 –0.104 16,399
PCGs 40.1 12.5 10.8 36.6 76.7 0.046 –0.073 10955
1st codon position 42.4 11.9 10.6 35.1 77.5 0.095 –0.055 3652
2nd codon position 38.0 12.9 11.7 37.3 75.4 0.009 –0.047 3652
3rd codon position 39.9 12.7 10.0 37.4 77.3 0.032 –0.119 3651
tRNA 40.6 11.6 9.9 37.9 78.5 0.034 –0.081 1435
16S 49.6 11.1 6.4 32.9 82.5 0.202 –0.266 1185
12S 47.6 11.1 6.9 34.4 81.9 0.161 –0.233 736
CR 43.1 6.9 4.2 45.8 88.9 –0.030 –0.246 2048
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Figure 2.

Figure 2.

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AT and GC skews calculated for the 37 mitochondrial genomes of Mitjaevia shibingensis and M. dworakowskae. Each point indicates an individual gene.

Protein-coding genes and codon usage

Similar to other Typhlocybinae mitochondrial genomes, of the 13 PCGs of M. shibingensis and M. dworakowskae, nine genes (cox1, cox2, cox3, atp8, atp6, nad2, nad3, nad6, and cytb) are located on the major strand (H-strand) while the other four PCGs (nad4, nad4L, nad5, and nad1) are located on the minor strand (L-strand). The largest gene was the nad5 gene, and the smallest was the atp8 gene in erythroneurine mitogenomes. The average AT content values of PCGs were 75.4% and 76.7% in M. shibingensis and M. dworakowskae, respectively. The A + T content of the first codon positions (76.5%, 77.5%) was much higher than that of the second (76.1%, 75.4%) and the third (74.5%, 77.3%) positions. This result was different from most other studies which show that the third codon has the highest AT content (Du et al. 2019; Yang et al. 2020). AT skews of all codon positions is positive while GC skews are negative. Most PCGs have the standard ATN (ATA/ATT/ATG/ATC) as the start codon, while nad5 and atp8 genes have TTG, a pattern also observed in other leafhopper mitogenomes (Wang et al. 2017; Wang et al. 2020). Conventional stop codons (TAA or TAG) appear in most PCGs, except that cox2 and nad1 use an incomplete codon (a single T--) as the stop codon (see Tables 2, 3).

Research determined the behavior of the PCG codon families and found that codon usage was very similar among Cicadellidae mitogenomes when the results of two species were calculated and summarized (see Table 4, Fig. 3). All 62 available codons (excluding TAA and TAG) are present in M. shibingensis and M. dworakowskae. Synonymous codon usage bias was observed in both mitochondrial genomes, and 22 codons were used more frequently than other codons. The four most abundant codons were AAU (Asn), AAA (Lys), AUU (Ile), and UUA (Leu2). The preferred codons all end with A or U, which contribute to the high A + T bias of the entire mitogenomes.

Table 4.

Codon and Relative Synonymous Codon Usage (RSCU) of 13 PCGs in the mt genomes of Mitjaevia shibingensis and M. dworakowskae.

Amino acid Codon Count/RSCU Amino acid Codon Count/RSCU
M. shibingensis M. dworakowskae M. shibingensis M. dworakowskae
Phe UUU 190 a 1.49 200 1.5 Tyr UAU 190 1.56 185 1.57
UUC 65 0.51 66 0.5 UAC 53 0.44 51 0.43
Leu2 UUA 234 3.15 245 3.33 His CAU 57 1.37 49 1.48
UUG 63 0.85 45 0.61 CAC 26 0.63 17 0.52
Leu1 CUU 46 0.62 39 0.53 Gln CAA 56 1.58 66 1.71
CUC 28 0.38 20 0.27 CAG 15 0.42 11 0.29
CUA 56 0.75 69 0.94 Asn AAU 269 1.49 281 1.54
CUG 19 0.26 24 0.33 AAC 91 0.51 84 0.46
Ile AUU 226 1.5 225 1.55 Lys AAA 242 1.62 246 1.57
AUC 75 0.5 66 0.45 AAG 56 0.38 67 0.43
Met AUA 201 1.58 213 1.68 Asp GAU 35 1.32 35 1.52
AUG 54 0.42 40 0.32 GAC 18 0.68 11 0.48
Val GUU 52 1.66 53 1.93 Glu GAA 56 1.51 62 1.65
GUC 12 0.38 11 0.4 GAG 18 0.49 13 0.35
GUA 47 1.5 41 1.49 Cys UGU 27 1.26 37 1.42
GUG 14 0.45 5 0.18 UGC 16 0.74 15 0.58
Ser2 UCU 47 1.29 48 1.28 Trp UGA 49 1.24 54 1.33
UCC 19 0.52 11 0.29 UGG 30 0.76 27 0.67
UCA 66 1.81 81 2.15 Arg CGU 14 1.27 13 1.44
UCG 8 0.22 5 0.13 CGC 5 0.45 2 0.22
Pro CCU 26 1.11 42 1.65 CGA 20 1.82 14 1.56
CCC 30 1.28 27 1.06 CGG 5 0.45 7 0.78
CCA 34 1.45 31 1.22 Ser1 AGU 53 1.46 48 1.28
CCG 4 0.17 2 0.08 AGC 16 0.44 26 0.69
Thr ACU 49 1.26 54 1.26 AGA 53 1.46 51 1.36
ACC 42 1.08 38 0.89 AGG 29 0.8 31 0.82
ACA 55 1.41 63 1.47 Gly GGU 31 1.11 34 1.31
ACG 10 0.26 16 0.37 GGC 15 0.54 10 0.38
Ala GCU 26 1.89 23 1.74 GGA 25 0.89 31 1.19
GCC 6 0.44 9 0.68 GGG 41 1.46 29 1.12
GCA 18 1.31 19 1.43 * UAA 177 1.61 170 1.61
GCG 5 0.36 2 0.15 UAG 43 0.39 41 0.39
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a The higher values of preferentially used codons are given in bold.

Figure 3.

Figure 3.

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Relative Synonymous Codon Usage (RSCU) of mitochondrial genomes for Mitjaevia shibingensis and M. dworakowskae.

Transfer RNA and ribosomal RNA genes

All 22 typical tRNA genes are present in the M. shibingensis and M. dworakowskae mitochondrial genomes, of which 14 genes were oriented on the major strand (H-strand), whereas the others were transcribed on the minor strand (L-strand). Their nucleotide lengths are almost identical between species, ranging from 60 bp to 71 bp (Table 2). The average AT content values of tRNAs is 78.5% and 79% in each species, respectively, and the tRNA genes have negligible AT and GC skews (Table 3). Compared to the ancestral insect mitochondrial gene order, no tRNA gene rearrangements were found. All of the tRNA genes can be folded into typical clover-leaf secondary structures except for the trnS1 in both species’ mitochondrial genomes, which lacks the dihydrouridine (DHU) stem and forms a simple loop. In the metazoan mt genome, lack of the DHU arm was very common in trnS1 (Yang et al. 2020). Based on the secondary structure, a total of 24 and 22 G-U weak base pairs were found in tRNAs of M. shibingensis and M. dworakowskae, respectively (Figs 4, 5). Most mismatched nucleotides were G-U pairs, which form weak bonds in tRNA and non-classical pairs in tRNA secondary structure, similar to other Cicadellidae (Jia et al. 2010).

Figure 4.

Figure 4.

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Inferred secondary structures of 22 tRNAs from Mitjaevia shibingensis. Watson-Crick base pairings are illustrated by lines (-), whereas GU base pairings are illustrated by red lines (-). Structural elements in tRNA arms and loops are illustrated as for trnV.

Figure 5.

Figure 5.

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Inferred secondary structures of 22 tRNAs from Mitjaevia dworakowskae. Watson-Crick base pairings are illustrated by lines (-), whereas GU base pairings are illustrated by red lines (-). Structural elements in tRNA arms and loops are illustrated as for trnV.

Leafhopper ribosomal RNA (rRNA) includes 16S RNA and 12S RNA. These two genes are highly conserved and are encoded on the minor strand (L-strand). Similar to other known insects, the content of A + T% in 16S was higher than that of 12S. The 16s genes of M. shibingensis and M. dworakowskae were 1192 bp and 1852 bp in length, with AT contents of 82.90% and 82.50%, respectively, and located between trnL2 and trnV. The 12S rRNA genes of both were 732 bp and 736 bp in length, with AT contents of 81.80% and 81.90%, respectively, and located after trnV. The rRNA genes showed a positive AT skew and negative GC skew (Table 3).

Control region

Like the typical insect mitochondrial genome, the mt genomes of M. shibingensis and M. dworakowskae have a large non-coding region, which was identified as the control region and located downstream of 12S. Control regions of both species were rich in AT, with lengths of 1429 bp and 2048 bp AT contents of 92.7% and 88.9%, respectively (Table 3). The control regions in the three available Mitjaevia mitogenomes were variable and not highly conserved, and their lengths ranged from 15 and 784 bp with variable numbers of repeat sequences (Fig. 6). Mitjaevia shibingensis included 21 types of repeat unit (R), 17 kinds of repeats (R1, R2) were found in M. dworakowskae with various lengths and copy numbers, and three repeat units were present in M. protuberanta. At present, we were unable to find any correlation in repeating units in the different species, probably because of the limited number of species analyzed in this study. Further comparative studies of additional leafhopper mitogenomes are needed.

Figure 6.

Figure 6.

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Organization of the control region structure in the mitochondrial genomes of three Mitjaevia species. R: repeat unit.

Nucleotide diversity and genetic distance analysis

The sliding window analysis shows highly variable nucleotide diversity (Pi values) among 13 PCGs sequences of the four tribes of Typhlocybinae (Fig. 7). Empoascini nucleotide diversity is significantly lower than of the other three tribes. The genes nad2, nad4, nad4L, and nad5 had higher nucleotide diversity, while the genes cox3, cox2, cytb, and cox1 had comparatively low nucleotide diversity when using MEGA 6.06 software, based on Kimura-2 Parameter, and Bootstrap resampling 1000 times to test and analyze the genetic distance of the four tribes of Typhlocybinae. The results show that the genetic distance between Empoascini and the other three tribes is the largest, and between Typhlocybini and Zyginellini are the smallest (Table 5).

Figure 7.

Figure 7.

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Nucleotide diversity (Pi) and sliding window analysis of 13 PCGs of the four tribes of Typhlocybinae.

Table 5.

The genetic distance between the four tribes of Typhlocybinae.

Empoascini Typhlocybini Zyginellini
Typhlocybini 0.3663
Zyginellini 0.3645 0.2663
Erythroneurini 0.3623 0.3288 0.3262
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Nucleotide diversity analysis, a primary method for identifying the regions with large nucleotide divergence, is especially useful for designing species-specific markers. These are useful for taxa with highly variable morphological characteristics, especially Typhlocybinae species which belong to groups that are difficult to distinguish by morphology alone (Jia et al. 2010; Ma et al. 2019). Among the four tribes, nad2, nad4, and other highly variable genes have garnered our attention. Whether they can be used as the main marker for species identification or the main related genes that control the appearance of the subfamily is worthy of further study. The genetic distance reflects the distance of the genetic relationships between each tribe. Among the four tribes, Typhlocybini and Zyginellini have the smallest genetic distance, indicating that the relationship between the two is the closest, which is consistent with the results of morphological studies (Zhang 1990; Huang 2013).

Phylogenetic relationships

Historical review

Typhlocybinae has been divided into tribes based mainly on the characteristics of the wing veins for the past 90 years. Melichar (1903), Distant (1908, 1918), and Matsumura (1931), among others, divided Typhlocybinae into Empoascaria and Typhlocybaria according to whether the hindwing apical cell is closed (Fig. 8A). McAtee (1934) further divided Typhlocybinae into four tribes, Alebrini, Dikraneurini, Jorumini, and Eupterygini (Fig. 8B), based on the wing veins. Young (1952), also using the male genitalia, recognised the tribes Alebrini, Dikraneurini, Erythroneurini, and Typhlocybini (Fig. 8C). According to whether the peripheral vein of the hind wings exceeds the end of the R+M vein, it was believed that Erythroneurini evolved from Dikraneurini but Mahmood (1967), when adding the tribe Bakerini, believed this condition to be an acquired mutation. At the same time, Mahmood (1967) postulated that Erythroneurini might be more closely related to Typhlocybini, but the relationship between Erythroneurini and the other tribes still need to be determined by studying a large number of specimens. Mahmood and Ahmed (1968a), using the characteristic of the peripheral vein of the hind wings extending to the end of the R vein, separated Empoascini from the former Typhlocybini, and Typhlocybinae was divided into six tribes (Fig. 8D). Dworakowska (1970) compared the characteristics of Bakerini, Typhlocybini, and Erythroneurini, and postulated that Bakerini may be a relatively primitive branch of Erythroneurini (Fig. 8E). Dworakowska (1977, 1990) discussed Typhlocybini with respect to other tribes, and postulated that the different connection modes of the hindwing peripheral vein and CuA represented different branches, and divided Zyginellini from Typhlocybini resulting in six tribes: Alebrini, Dikraneurini, Empoascini, Erythroneurini, Typhlocybini, and Zyginellin, while Zhang (1990) postulated that Erythroneurini evolved from Empoascini. Since then, Typhlocybinae-related research has followed Dworakowska’s six-tribe classification system (Fig. 8F). However, Dietrich (2013) found that the hind wings of leafhoppers have both Zyginellini and Typhlocybini hindwing characteristics when studying the leafhoppers in South America and postulated that the venation characters may not be a stable feature for classification. In terms of overall morphology, Zyginellini and Typhlocybini have similarities present in certain genera and species. Therefore, there is no clear and strong evidence at present to determine whether or not Zyginellini belongs to a natural monophyletic group, and its taxonomic status needs to be further clarified, probably with molecular data.

Figure 8.

Figure 8.

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The traditional classification process of tribe levels in the subfamily Typhlocybinae.

More recent studies

In recent years, molecular sequencing technology has been widely used in phylogenetic analysis, which can test and verify the results of different levels of more morphology based traditional classifications. Within Typhlocybinae, only a few studies have used the combination of morphological characteristics and molecular data to construct phylogenetic relationships. The amount of data is sparse at present and further data is needed.

Dietrich and Dmitriev (2006) used PAUP 4.0b10 to analyze the phylogeny of Typhlocybinae for the first time based on morphological characteristics and concluded that Erythroneurini and Dikraneurini are closely related. However, their analysed samples came mainly from the New World, and whether their results represent the relationship between the tribes of Typhlocybinae remains to be clarified. Balme (2007) combined morphological characteristics with molecular characteristics (16S rDNA, H3) to perform a phylogenetic analysis of Typhlocybinae, and obtained the following topological structure: Alebrini + ((Empoascini + Typhlocybini) + Dikraneurini), but due to the small sample, the results need to be verified.

Jiang (2016) used 28S rDNA D2–D3, 16S rDNA sequence and morphological characteristics to make a preliminary exploration of the phylogenetic relationships of Typhlocybinae and obtained the following topological structure: Alebrini + (Empoascini + Erythroneurini), implying that Erythroneurini is a monophyletic group. Song et al. (2020) constructed a phylogenetic tree of Typhlocybinae using 13PCGs of eight species and obtained the following topology: Empoascini+ (Typhlocybini+ (Erythroneurini+Zyginellini)). These four tribes are all monophyletic, and Erythroneurini and Zyginellini are sister groups, differing only slightly from the traditional morphological classification. Jiao (2017) used MP and NJ methods to analyze the phylogenetic relationship between Alebrini and Dikraneurini based only on morphological data. The results showed that the two tribes’ monophyly was well supported, and its position in the evolutionary tree was similar to that of Zhang (1990) and showed that Alebrini is more primitive.

Results

This study, based on 29 species of cox1, 19 species of 13 PCGs, and two rRNA mitochondrial genes data of Typhlocybinae produced a slightly different result to the traditional classification with respect to Typhlocybini and Zyginellini. Maximum Likelihood (ML) method was used with IQ-TREE using an ultrafast bootstrap approximation approach with 10,000 replicates. The Bayesian Inference (BI) analysis was performed using MrBayes 3.2.7, with the best fit model GTR+I+ G (Vogler and DeSalle 1993).

Cox1 is one of the mitochondrial protein-coding genes and its bi-terminal sequence is more conservative than cox2. It has a rapid evolution rate and large differences between species, and can provide rich phylogenetic information, hence is an ideal mitochondrial molecular marker. The gene sequences were obtained in the current study by downloading the cox1 gene sequence of 29 species of Typhlocybinae and two outgroups of Idiocerinae from NCBI to construct a phylogenetic tree. BI and ML analyses generated the same tree topology: (Alebrini + Empoascini) + (Erythroneurini + ((Zyginellini + Typhlocybini) + Dikraneurini))). Most relationships were highly supported, and a few branches pertaining to relationships within Zyginellini and Typhlocybini received lower support (Fig. 9). Also, the tree topology is different from previous research, with Alebrini + Empoascini forming sister groups, and the species of Zyginellini and Typhlocybini are interconnected and cannot be resolved into separate branches. The remaining tribes are monophyletic groups. Alebrini is placed at the base of the tree and is therefore the most primitive. The phylogenetic relationship is generally consistent with the results of previous studies based on morphology and molecules (Balme 2007; Jiang 2016).

Figure 9.

Figure 9.

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ML and BI Phylogenetic tree inferred from cox1 of Typhlocybinae. The first number at each node is a bootstrap proportion (BP) of maximum likelihood (ML) analyses, and the second number is Bayesian posterior probability (PP).

At present, the complete mitochondrial genome data of Alebrini and Dikraneurini have not been added to NCBI. Thus, the phylogenetic relationships were analyzed based on the concatenated nucleotide sequences of 13 PCGs and two rRNA from 19 Typhlocybinae (the remaining four tribes) species and two outgroups. Although ML and PB analyses produced inconsistent topologies across the different datasets and models, most relationships were highly supported and consistent in the analyses, and the main difference is the relationship of species between Zyginellini and Typhlocybini. (Figs 10, 11). In this study, Empoascini and Erythroneurini were recovered as monophyletic, always forming a clade with high support values, while Zyginellini and Typhlocybini formed a single branch in every tree, and neither tribe was ever resolved as monophyletic, which suggests that the hind wing character traditionally used to separate these two tribes is not reliable and that the tribes should probably be treated as synonyms, as was suggested previously by Dietrich (2013). Within the Typhlocybinae, the four species of Empoascini studied constituted one clade and tended to be placed at the basal position of the tree as the sister group to the other tribes. Unlike the previous analyses, the our results support the combination of Zyginellini and Typhlocybini as a tribe. As with other recent studies, our results indicate that sequence data from leafhopper mitogenomes is informative of phylogenetic relationships in the taxonomic hierarchy of this group. Also, the results of the phylogenetic tree and nucleotide diversity are consistent. Empoascini has the lowest nucleotide diversity and is clearly distinguished from the other three tribes. Therefore, we speculate that the richness of nucleotide diversity has an impact on the phylogenetic relationship of Typhlocybinae. However, data are available for only a tiny fraction of species so the addition of more species, and representatives of other major lineages, will be needed to determine the extent to which mitogenome sequence data can resolve leafhopper phylogeny.

Figure 10.

Figure 10.

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Phylogenetic trees of Typhlocybinae inferred by maximum likelihood (ML) and PhyloBayes (PB) methods based on 13 PCGs and 2 rRNA.

Figure 11.

Figure 11.

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ML and BI Phylogenetic tree inferred from 13 PCGs of Typhlocybinae. The first number at each node is a bootstrap proportion (BP) of maximum likelihood (ML) analyses, and the second number is Bayesian posterior probabilities (PP).

Conclusions

This paper describes the complete mitochondrial genomes of M. shibingensis and M. dworakowskae, analyzes the basic composition, location, secondary structure, and other characteristics of PCGs, tRNA genes, rRNA genes, and control regions, and compares them to other Typhlocybinae mitochondrial genomes. The mitogenomes of these two species closely resemble those of most other sequenced leafhoppers in various structural and compositional aspects. The sliding window analysis shows a highly variable nucleotide diversity (Pi values) among 13 PCGs sequences of the four tribes of Typhlocybinae. Empoascini nucleotide diversity is significantly lower than in the other three tribes, and the other three tribes have little difference between them. The genes nad2, nad4, nad4L, and nad5 have higher nucleotide diversity, and whether they can be used as the main markers for species identification or the main related genes that control the appearance of the subfamily is worthy of further study. The genetic distance of the four tribes of Typhlocybinae shows that the Empoascini and the other three tribes are the largest while Typhlocybini and Zyginellini are the smallest and indicates that the relationship between the two is the closest, which is consistent with the results of morphological studies. Phylogenetic analysis of 31 cox1 yielded a well-supported topology with most branches receiving maximum support and a few branches pertaining to relationships within Zyginellini and Typhlocybini receiving lower support; the species of these two tribes are intertwined and cannot be resolved into separate branches, and Alebrini is placed at the base of the tree as the most primitive. Phylogenetic relationships were analyzed based on the concatenated nucleotide sequences of 13 PCGs and two rRNA show that although ML and PB analyses produced inconsistent topologies across the different datasets and models, and most relationships were highly supported and constant in the analyses. In this study, Empoascini and Erythroneurini were recovered as monophyletic while Zyginellini and Typhlocybini gathered into a single branch and Empoascini tended to be placed at the basal position of the tree as the sister group to the other tribes. This study indicated that mitochondrial genome sequences are informative for leafhopper phylogeny, but unlike the previous analysis (Zhang 1990), the results of this study relocated the taxonomic status and phylogenetic relationship of the six tribes of Typhlocybinae and supported the combination of Zyginellini and Typhlocybini as a single tribe. Also, the results of the phylogenetic tree and nucleotide diversity are consistent. Empoascini has the lowest nucleotide diversity and is clearly distinguished from the other three tribes. Therefore, we speculate that the richness of nucleotide diversity has an impact on the phylogenetic relationship of Typhlocybinae.

Based on the current and previous studies, the classification of the tribes of Typhlocybinae is not yet fully resolved with respect to Typhlocybini and Zyginellini, i.e., one or two tribes. From a molecular perspective, more sequencing data is needed to build a more complete phylogenetic tree to support or modify the traditional morphological classification. To this aim, it is hoped that the new data provided here will facilitate future comparative studies of leafhopper mitogenomes and demonstrate the need for more comparative data.

Acknowledgements

We thank Chris Dietrich for reviewing the manuscript and Mick Webb for checking and revising the manuscript. This work was funded partly by the World Top Discipline Program of Guizhou Province: Karst Ecoenvironment Sciences (No. 125 2019 Qianjiao Keyan Fa), the Guizhou Provincial Science and Technology Foundation ([2018]1411), the Guizhou Science and Technology Support Project ([2019]2855), the Science and Technology Project of Guiyang City ([2020]7-18), the Innovation Group Project of Education Department of Guizhou Province ([2021]013), the Training Program for High-level Innovative Talents of Guizhou Province ([2016]4020) and the Project for Regional Top Discipline Construction of Guizhou Province: Ecology in Guiyang University (Qianjiao Keyan Fa [2017]85).

Citation

Chen X, Li C, Song Y (2021) The complete mitochondrial genomes of two erythroneurine leafhoppers (Hemiptera, Cicadellidae, Typhlocybinae, Erythroneurini) with assessment of the phylogenetic status and relationships of tribes of Typhlocybinae. ZooKeys 1037: 137–159. https://doi.org/10.3897/zookeys.1037.63671

Funding Statement

This work was funded partly by the World Top Discipline Program of Guizhou Province: Karst Ecoenvironment Sciences (No.125 2019 Qianjiao Keyan Fa), the Guizhou Provincial Science and Technology Foundation ([2018]1411), the Guizhou Science and Technology Support Project ([2019]2855), the Science and Technology Project of Guiyang City ([2020]7-18), the Training Program for High-level Innovative Talents of Guizhou Province ([2016]4020) and the Project for Regional Top Discipline Construction of Guizhou Province: Ecology in Guiyang University (Qianjiao Keyan Fa [2017]85).

Supplementary materials

Supplementary material 1

Datasets of phylogenetic analysis

This dataset is made available under the Open Database License (http://opendatacommons.org/licenses/odbl/1.0/). The Open Database License (ODbL) is a license agreement intended to allow users to freely share, modify, and use this Dataset while maintaining this same freedom for others, provided that the original source and author(s) are credited.

Xiaoxiao Chen, Can Li, Yuehua Song

Data type

phylogenetic

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

Supplementary material 1

Datasets of phylogenetic analysis

This dataset is made available under the Open Database License (http://opendatacommons.org/licenses/odbl/1.0/). The Open Database License (ODbL) is a license agreement intended to allow users to freely share, modify, and use this Dataset while maintaining this same freedom for others, provided that the original source and author(s) are credited.

Xiaoxiao Chen, Can Li, Yuehua Song

Data type

phylogenetic

zookeys-1037-137-s001.zip (152KB, zip)

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