Chloroplast genomic data provide new and robust insights into the phylogeny and evolution of the Ranunculaceae

Zhai, Wei; Duan, Xiaoshan; Zhang, Rui; Guo, Caixia; Li, Lin; Xu, Guiyun; Shan, Hongyan; Kong, Hongzhi; Ren, Yi

doi:10.1016/j.ympev.2019.02.024

Cited by 134 publications

(135 citation statements)

References 88 publications

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“…This was consistent with a previous report of the loss or pseudogenization of rpl32 within Ranunculaceae [11]. In the tribe Isopyreae, rpl32 from the cp genome was integrated into the nuclear genome, demonstrating gene transfers from an organelle genome to the nuclear genome [11,24]. A total of 17 intron-containing genes were detected in the 3 cp genomes, including 11 protein-coding genes, 6 tRNA genes harboring a single intron and 2 genes (ycf3 and clpP) harboring 2 introns (Table S5).…”

Section: Features Of the Cp Genomes Of Three Actaea Speciessupporting

confidence: 94%

“…In all three cp genomes, rpl32 (large ribosomal protein 32) was a pseudogene, with partial deletion. This was consistent with a previous report of the loss or pseudogenization of rpl32 within Ranunculaceae [11]. In the tribe Isopyreae, rpl32 from the cp genome was integrated into the nuclear genome, demonstrating gene transfers from an organelle genome to the nuclear genome [11,24].…”

Section: Features Of the Cp Genomes Of Three Actaea Speciessupporting

confidence: 92%

“…The cp genomes of all three Actaea species showed a stable and typical quadripartite structure similar to that of other angiosperms [25][26][27]. The genome length, gene content, gene orientation, and GC content of the three Actaea cp genomes were similar to those of genera within Cimicifugeae [11]. Analysis of codon usage and anticodon recognition patterns revealed that the three Actaea cp genomes contained 26,669-26,696 codons and codons for leucine (Leu), isoleucine (Ile), and serine (Ser) were the most abundant ( Figure S2A).…”

Section: Features Of the Cp Genomes Of Three Actaea Speciesmentioning

confidence: 68%

“…The GC content of the cp genome of each species was approximately 38% (Table 1). In general, the GC content of IRs was higher than that of single copy regions in all three species [10,11]. Gene content and gene order were highly similar among the Plants 2020, 9,157 3 of 13 three Actaea species.…”

Section: Features Of the Cp Genomes Of Three Actaea Speciesmentioning

confidence: 85%

“…Moreover, cp genome sequencing represents a viable alternative to DNA barcoding, a controversial method of species identification. Recently, complete cp genomes have been reported for four Actaea species, including A. heracleifolia, A. dahurica, A. vaginata, and A. asiatica [10,11]. Genomic information available…”

Section: Introductionmentioning

confidence: 99%

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Comparative Analysis of Actaea Chloroplast Genomes and Molecular Marker Development for the Identification of Authentic Cimicifugae Rhizoma

Park

Song

Yang

et al. 2020

Plants

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Actaea (Ranunculaceae; syn. Cimicifuga) is a controversial and complex genus. Dried rhizomes of Actaea species are used as Korean traditional herbal medicine. Although Actaea species are valuable, given their taxonomic classification and medicinal properties, sequence information of Actaea species is limited. In this study, we determined the complete chloroplast (cp) genome sequences of three Actaea species, including A. simplex, A. dahurica, and A. biternata. The cp genomes of these species varied in length from 159,523 to 159,789 bp and contained 112 unique functional genes, including 78 protein-coding genes, 30 transfer RNA genes, and 4 ribosomal RNA genes. Gene order, orientation, and content were well conserved in the three cp genomes. Comparative sequence analysis revealed the presence of hotspots, including ndhC-trnV-UAC, in Actaea cp genomes. High-resolution phylogenetic relationships were established among Actaea species based on cp genome sequences. Actaea species were clustered into each Actaea section, consistent with the Angiosperm Phylogeny Group (APG) IV system of classification. We also developed a novel indel marker, based on copy number variation of tandem repeats, to facilitate the authentication of the herbal medicine Cimicifugae Rhizoma. The availability Actaea cp genomes will provide abundant information for the taxonomic and phylogenetic analyses of Actaea species, and the Actaea (ACT) indel marker will be useful for the authentication of the herbal medicine.

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Section: Features Of the Cp Genomes Of Three Actaea Speciessupporting

confidence: 94%

Section: Features Of the Cp Genomes Of Three Actaea Speciessupporting

confidence: 92%

Section: Features Of the Cp Genomes Of Three Actaea Speciesmentioning

confidence: 68%

Section: Features Of the Cp Genomes Of Three Actaea Speciesmentioning

confidence: 85%

Section: Introductionmentioning

confidence: 99%

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Comparative Analysis of Actaea Chloroplast Genomes and Molecular Marker Development for the Identification of Authentic Cimicifugae Rhizoma

Park

Song

Yang

et al. 2020

Plants

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Ontogeny and Evolution of the Hyperorgan of Delphinieae

Jabbour¹,

Zalko²,

Morel³

et al. 2021

Systematics and the Exploration of Life

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A eudicot leaf from the Lower Cretaceous (Aptian, Araripe Basin) Crato Konservat‐Lagerstätte

Pessoa

Ribeiro

Jud

2021

American J of Botany

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Premise: The Crato Konservat-Lagerstätte in Brazil preserves an exceptionally rich assemblage of plant macrofossils from the Early Cretaceous (late Aptian), including rare early angiosperm fossils related to Nymphaeales, monocots, and magnoliids, and a variety of angiosperms of uncertain affinities. Macrofossils of eudicot angiosperms have not been described previously, despite the presence of tricolpate pollen. We describe a fossil leaf with morphology characteristic of eudicot angiosperms. Methods: The fossil was collected from a quarry in the Lower Cretaceous (late Aptian) Crato Formation of northeastern Brazil in the state of Ceará. We compared the leaf architecture with that of ferns, gymnosperms, and similar living and fossil angiosperms.Results: The leaf of Baderadea pinnatissecta gen. et sp. nov. is simple and petiolate, with leaf architecture similar to that of some herbaceous Ranunculales. The blade is 5 cm long and the margin is untoothed and twice pinnately lobed with narrow lobes (pinnatisect). The primary vein framework is pinnate and there are multiple orders of reticulate venation. Conclusions: The combination of characters preserved in the fossil supports the interpretation that B. pinnatissecta was an herbaceous eudicot similar to some members of Ranunculales and distinguished from other lobate Aptian angiosperms by leaf shape, presence of multiple orders of reticulate venation, and the absence of glandular teeth. The presence of eudicots in the flora of the Crato was already supported by pollen; the discovery of macrofossils like these provides additional information about their morphology and ecological role in low-latitude Early Cretaceous plant communities.

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Chloroplast genomic data provide new and robust insights into the phylogeny and evolution of the Ranunculaceae

Cited by 134 publications

References 88 publications

Comparative Analysis of Actaea Chloroplast Genomes and Molecular Marker Development for the Identification of Authentic Cimicifugae Rhizoma

Comparative Analysis of Actaea Chloroplast Genomes and Molecular Marker Development for the Identification of Authentic Cimicifugae Rhizoma

Ontogeny and Evolution of the Hyperorgan of Delphinieae

A eudicot leaf from the Lower Cretaceous (Aptian, Araripe Basin) Crato Konservat‐Lagerstätte

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