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

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.

Deep Insights Into the Plastome Evolution and Phylogenetic Relationships of the Tribe Urticeae (Family Urticaceae)

“…Generally, the GC content had no significant phylogenetic implication in our study. Moreover, consistent with previous studies ( Li et al, 2020 , 2021 ; Dong et al, 2021 ), the GC content was higher in the IR than in the SC. The GC inequality perhaps also plays a significant factor in the conservatism of the IR region compared to the SC regions ( Li et al, 2020 ).…”

“…Also, the number of PCGs in the Urticeae plastomes in our study (76–78) was comparable with the typical range for angiosperm plastomes (70–88 genes) ( Wicke et al, 2011 ). Likewise, we found congruence with the range of GC content previously reported in other plastomes of Urticaceae, e.g., Pilea mollis (36.72%; Li et al, 2021 ), Elatostema dissectum (36.2%; Fu et al, 2019 ), Droguetia iners (36.9%), and Debregeasia elliptica (36.4%) ( Wang et al, 2020b ). Generally, the GC content had no significant phylogenetic implication in our study.…”

“…All 57 Urticeae CP genomes examined are quadripartite but varied in size. The observed range was consistent with chloroplast genome sizes of angiosperms ( Zhang et al, 2021 ) and the few existing sequenced plastomes of Urticaceae ( Wang et al, 2020b ; Li et al, 2021 ), which range between 120 and 180 kb. Of the plastomes in our study, Laportea grossa had the largest genome, while Nanocnide lobata had the smallest, implying that CP genomes in Urticaceae are structurally different.…”

“…Mostly, the SC/IR borders are relatively conserved among angiosperm plastomes and usually located within the rps19 or ycf1 gene ( Downie and Jansen, 2015 ), even though it is assumed that IR expansion or contraction is accompanied by the shift of genes located in the IR/SC boundary ( Zhu et al, 2016 ). Similar IR/SC changes are also evident in other Urticaceae plastomes ( Wang et al, 2020b ; Li et al, 2021 ). Changes in the IR/SC junctions have been considered one of the main drivers of the size diversity in the CP genomes of higher plants ( Ma et al, 2013 ; Yang et al, 2016 ; Yan et al, 2018 ; Xue et al, 2019 ).…”

“…Chloroplasts are ubiquitous organelles in plants with tractable attributes that make them highly suitable for use in phylogenetic and phylogeographic studies ( Demenou et al, 2020 ; Silverio et al, 2021 ; Simmonds et al, 2021 ; Wang et al, 2021 ). In Urticaceae, whole chloroplast genomes have proven to be indispensable for sequence variation exploration ( Wang et al, 2020b ; Li et al, 2021 ). More broadly, studies of chloroplast genomes have been useful for understanding molecular evolutionary patterns of gene duplication, loss, rearrangement, and transfer across angiosperms ( Yan et al, 2018 ; Do et al, 2020 ; Liu et al, 2020a ; Oyebanji et al, 2020 ), though discordant relationships may be caused by plastid capture and other evolutionary processes.…”