Abstract:Debregeasia is an economically important genus of the nettle family (Urticaceae). Previous systematic studies based on morphology, or using up to four plastome regions, have not satisfactorily resolved relationships within the genus. Here, we report 25 new plastomes for Urticaceae, including 12 plastomes from five Debregeasia species and 13 plastomes from other genera. Together with the one published plastome for Debregeasia, we analyzed plastome structure and character, identified mutation hotspots and loci u… Show more
“…However, the 3′ ends are found in the IRa and IRb regions. These results are similar to those in other species in Urticaceae [ 22 ]. Fig.…”
Section: Resultssupporting
confidence: 91%
“…Although the plastid genome is highly conserved, some interesting structural variations have been observed in some taxa, such as the rare expansion of IR regions in Strobilanthes [15], the insertion of mitochondrial DNA in the plastome of Anacardium [19], and the complete or partial loss of IR regions in some legumes [16,20,21]. In a recent study, Wang et al reported plastid genomes from 13 of 58 genera in Urticaceae, providing an abundance of plastid genome resources for the study of this group of plants [22]. Unfortunately, there have been no reports on the plastid genome of Pilea plants.…”
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.
“…However, the 3′ ends are found in the IRa and IRb regions. These results are similar to those in other species in Urticaceae [ 22 ]. Fig.…”
Section: Resultssupporting
confidence: 91%
“…Although the plastid genome is highly conserved, some interesting structural variations have been observed in some taxa, such as the rare expansion of IR regions in Strobilanthes [15], the insertion of mitochondrial DNA in the plastome of Anacardium [19], and the complete or partial loss of IR regions in some legumes [16,20,21]. In a recent study, Wang et al reported plastid genomes from 13 of 58 genera in Urticaceae, providing an abundance of plastid genome resources for the study of this group of plants [22]. Unfortunately, there have been no reports on the plastid genome of Pilea plants.…”
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.
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 Wedd., Pilea glauca 'Greizy', Pilea peperomioides Diels. 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.
“…Plastome provides sufficient information to resolve the phylogenetic relationships at generic and infrageneric level. Despite several plastid genomes of species in Urticaceae have been reported (Wu et al 2017;Wu et al 2018;Fu et al 2019;Wang et al 2020), none of them belong to Procris.…”
The complete chloroplast (cp) genome of
Procris crenata
C.B.Rob was reported. The cp genome was 154,124 bp in length and contained two inverted repeats (IRs) of 25,626 bp, which were separated by large single-copy and small single-copy of 84,599 bp and 18,273 bp, respectively. The GC content was 36.5%. A total of 113 functional genes were encoded, comprising 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. This is the first reported plastid genome in
Procris
(Urticaceae), which will be useful data for resolving the relationship within the family.
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