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Comparative Study
. 2021 Jan 7;21(1):25.
doi: 10.1186/s12870-020-02793-7.

Comparative plastid genomics of four Pilea (Urticaceae) species: insight into interspecific plastid genome diversity in Pilea

Jingling Li  1 , Jianmin Tang  2 , Siyuan Zeng  1 , Fang Han  1 , Jing Yuan  1 , Jie Yu  3   4
Affiliations
Comparative Study

Comparative plastid genomics of four Pilea (Urticaceae) species: insight into interspecific plastid genome diversity in Pilea

Jingling Li et al. BMC Plant Biol. .

Abstract

Background: Pilea is a genus of perennial herbs from the family Urticaceae, and some species are used as courtyard ornamentals or for medicinal purposes. At present, there is no information about the plastid genome of Pilea, which limits our understanding of this genus. Here, we report 4 plastid genomes of Pilea taxa (Pilea mollis, Pilea glauca 'Greizy', Pilea peperomioides and Pilea serpyllacea 'Globosa') and performed comprehensive comparative analysis.

Results: The four plastid genomes all have a typical quartile structure. The lengths of the plastid genomes ranged from 150,398 bp to 152,327 bp, and each genome contained 113 unique genes, including 79 protein-coding genes, 4 rRNA genes, and 30 tRNA genes. Comparative analysis showed a rather high level of sequence divergence in the four genomes. Moreover, eight hypervariable regions were identified (petN-psbM, psbZ-trnG-GCC, trnT-UGU-trnL-UAA, accD-psbI, ndhF-rpl32, rpl32-trnL-UAG, ndhA-intron and ycf1), which are proposed for use as DNA barcode regions. Phylogenetic relationships based on the plastid genomes of 23 species of 14 genera of Urticaceae resulted in the placement of Pilea in the middle and lower part of the phylogenetic tree, with 100% bootstrap support within Urticaceae.

Conclusion: Our results enrich the resources concerning plastid genomes. Comparative plastome analysis provides insight into the interspecific diversity of the plastid genome of Pilea. The identified hypervariable regions could be used for developing molecular markers applicable in various research areas.

Keywords: Hypervariable region; Interspecific diversity; Phylogenetic relationship; Pilea; Plastid genome.

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Conflict of interest statement

The authors declare that they have no competing interests

Figures

Fig. 1
Fig. 1
Plastid genome map of four Pilea species and image of the four plants. The genome has a conservative quartile structure that is composed of an LSC region, an SSC region and a pair of IR regions. The genes outside the circle are transcribed in the counterclockwise direction, and the genes inside the circle are transcribed in the clockwise direction. Different colors in genes represent different functions. The dark gray area and light gray area of the inner circle represent the ratio of GC content to AT content in the genome, respectively
Fig. 2
Fig. 2
Comparison of the repeats in the plastid genomes of 4 Pilea species. a. Types and numbers of SSRs detected in the 4 plastomes; b. Types and numbers of interspersed repeats in the 4 plastomes
Fig. 3
Fig. 3
Comparison of the borders among the LSC, SSC, and IR regions of 10 analyzed species. The genes around the borders are shown above or below the mainline. JLB, JSB, JSA, and JLA represent junction sites of LSC/IRb, IRb/SSC, SSC/IRa, and IRa/LSC, respectively
Fig. 4
Fig. 4
Comparison of the plastomes in the 4 Pilea species by using mVISTA. The genes are represented as gray arrows on the top of the alignments. The different regions are labeled with different colors. The pink regions are “conserved noncoding sequences” (CNS), the dark blue regions are exons, and the light-blue regions are tRNAs or rRNAs. The percentages 50 and 100% refer to the similarity among sequences. The gray arrows above the aligned sequences represent genes and their orientation
Fig. 5
Fig. 5
Nucleotide diversity (Pi) of plastomes among the 4 Pilea species. Each black dot represents the nucleotide diversity per 500 bp. Seven intergenic regions (petN-psbM, 0.06067; psbZ-trnG-GCC, 0.07067; trnT-UGU-trnL-UAA, 0.06433; accD-psbI, 0.06003; ndhF-rpl32, 0.06100; rpl32-trnL-UAG, 0.06800; ndhA-intron, 0.06533) and one protein-coding region (ycf1, 0.07367–0.17067) had Pi values greater than 0.06
Fig. 6
Fig. 6
Sequence polymorphism among 79 shared plastid genes of 4 Pilea species. b. Percentages of variable sites in 79 shared protein-coding genes. We used MEGA v6.0 to calculate the percentages of variable sites. The three genes with the highest mutation rates are labeled with an *: ycf1 (16.62%), matK (10.54%) and ccsA (8.74%). b. Estimations of nonsynonymous (dN) and synonymous (dS) substitution rates and the dN/dS of 79 shared protein-coding genes. The four genes with the highest dN/dS values are labeled with an *
Fig. 7
Fig. 7
Phylogenetic relationships of species from Urticaceae inferred using the maximum likelihood (ML) method. The phylogenetic tree was constructed using the complete plastome sequences among the 25 plastid genomes. The number at the bottom of the scale, 0.01, means that the length of the branch represents the replacement frequency of bases at each site of the genome at 0.01. The bootstrap values were calculated from 1000 replicates. Two taxa from Moraceae, nam
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