Parasitidae
Creators: name: Yang, Huijuan
name: Yang, Zhihua
name: Chen, Ting
name: Dong, Wenge
Publisher: name: Zenodo
Year: 2023
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Arachnida
Mesostigmata
Parasitidae

description: Sequence characteristics of Parasitidae tRNA genes
The mitochondrial tRNA genes of six species of Parasitidae ranged from 50 to 70 bp in length, with slight differences in total sequence length. Twenty-two tRNA genes were compared to obtain a tandem sequence of 1449 bp with no large deletions or insertions detected. There were 885 conserved sites, 521 variable sites, and 195 parsimony informative sites. The A + T content was significantly higher than the G + C content between species, showing a clear A + T preference (Table 1). All AT-skew values were positive, and all GC-skew values were negative, indicating a preference for A and C bases in the 22 tRNA genes. The number of conversions (129) was greater than the number of reversals (102), with more conversions between C and T than between A and G and more reversals between A and C and A and T. The ratio of conversions to reversals was 1.3.
Differences in the secondary structure of Parasitidae tRNA genes
The secondary structure of tRNA genes contains four arms: the amino acid acceptor arm (AA-arm), the DHC arm (D-arm), the anticodon arm (AC-arm) and the TΨC arm (T-arm). In the mitochondrial tRNA genes of six species of Parasitidae, trnS 1 (UCU) lacking the D arm fails to form a typical cloverleaf secondary structure in all of them. The remaining 21 tRNA genes of four species, Parasitus wangdunqingi, P. fimetorum, Pergamasus crassipes, and Parasitidae sp., all have typical secondary structures. Pergamasus sp. only has 20 tRNA genes with typical secondary structure (trnS 1 lacking the D arm, trnF lacking the T arm); Holoparasitus sp. only has 18 tRNA genes with typical secondary structure (trnC and trnS 1 lacking the D arm, trnE and trnF lacking the T arm). In Parasitidae species, AA stems contain 7–8 base pairs, the D, AC, and T stems contain 3–5 base pairs, and the T-AA, AA-D, D-AC, and AC-T stems have 0, 2, 1, and 3–5 bases. The majority of base pairs follow the Waston-Crick principle of base pairing, i.e. A and U pairing, G and C pairing; a total of 98 swing pairings (i.e. G and U pairing) and 19 base mismatches (i.e. C and U pairing, U and U pairing, U and C pairing, and A and G pairing) occurred. The anticodon of the trnS 1 gene of P. wangdunqingi and P. fimetorum is GCU, while the anticodon of the trnS 1 gene of other species is UCU.
The conserved sites for the secondary structure of the mitochondrial tRNA genes of six species of Parasitidae are shown in Figure 3. Specifically, the trnM gene has the most conserved sites, with 47 conserved bases; of these, the amino acid acceptor stems are highly conserved (length variation of 8 bp in Holoparasitus sp., Parasitidae sp. and Pergamasus sp., while 7 bp in all other species, with only 5 conserved bases), the D stems are extremely conserved (all 4 bp in length and all bases conserved), the anticodon stems are extremely conserved (all 5 bp in length and only 1 base not conserved), and the TΨC stems are more conserved (length variation of 2 bp in Pergamasus sp. and Pergamasus crassipes, while 3 bp in all other species, with only 5 conserved bases). Of the four loops of the trnM gene (D-loop, anticodon loop, variable loop, and TΨC loop), the anticodon loop is more conserved (all 7 bp in length and only one base is not conserved), the variable loop is the most conserved (all 3 bp in length and all bases are conserved), while the other two loops have more variable sites.
The trnC gene has the fewest conserved sites, with only 20 conserved bases; of these, the amino acid acceptor stems are less conserved (8 bp in length variation in Parasitidae sp. and Pergamasus sp. and 7 bp in length in all other species, with only 3 conserved bases), the D stems are extremely poorly conserved (no conserved bases due to the lack of the D arm in Holoparasitus sp.), the anticodon stems are highly conserved (all 10 bp in length with 8 conserved bases), and the TΨC stems are less conserved (variation of 2 bp in Holoparasitus sp. and Pergamasus sp. and 3 bp in all other species with only 1 conserved base). Of the four loops of the trnC gene (D-loop, anticodon loop, variable loop, and TΨC loop), only the anticodon loop is highly conserved (all 7 bp in length with 5 conserved bases), while the other three loops have no conserved sites.
tRNA gene codon usage preference of Parasitidae
From the Relative synonymous codon usage (RSCU) analysis (Table 2), it can be seen that P. fimetorum, P. wangdunqingi, Pergamasus crassipes, Holoparasitus sp., Parasitidae sp., and Pergamasus sp. use codons that end in A and U, respectively, 24, 21, 23, 21, 26, 26; and codons that end in G and C, respectively, 0, 2, 5, 7, 2, 2. A total of 32 codons had RSCU values of 0, indicating that these codons are not used in tRNA genes of Parasitidae, most of which are codons that end in C or G. The effective codon number (ENC) is an important indicator of codon preference for individual genes, ranging from 20 to 61. If the scatters are distributed above the standard curve, codon preference is mainly influenced by mutational pressure; if the scatters are distributed below the standard curve, codon preference is mainly influenced by natural selection (Zhang et al. 2022). The ENC values for the 22 tRNA genes of the Parasitidae ranged from 30 to 50 (Figure 4), with the majority of gene ENC observations distributed below the standard curve.
Phylogenetic analysis
Phylogenetic trees were constructed using the ML and BI methods (Figure 5). The results showed that the topology formed by the two methods of constructing the phylogenetic tree was completely consistent, and the support rate of each node was high; there were only slight differences in the support rates of nodes in some branches. In both ML and BI trees, the Parasitidae were shown to be monophyletic. Among them, P. fimetorum in this study was clustered with P. wangdunqingi to form a sister branch with high node support (BI = 1, PP = 100) and then clustered with other species of Parasitidae. In addition, there were species of different genera (Pergamasus crassipes and Holoparasitus sp.) clustered together.
description: Published as part of Yang, Huijuan, Yang, Zhihua, Chen, Ting & Dong, Wenge, 2022, Comparative analysis of tRNA genes in the mitochondrial genome of Parasitidae (Parasitiformes: Mesostigmata), pp. 645-653 in International Journal of Acarology 48 (8) on pages 647-648, DOI: 10.1080/01647954.2022.2164614, http://zenodo.org/record/15358864