The complete chloroplast genome and phylogenetic analysis of <i>Corydalis fangshanensis</i> W.T. Wang ex S.Y. He (Papaveraceae)

Yu, Zhiying; Zhou, Tianhua; Li, Ni-Ya; Wang, Dong

doi:10.1080/23802359.2021.1987172

Cited by 6 publications

(3 citation statements)

References 15 publications

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“…Surprisingly, limited plastomes to date are available for Corydalis species. Except for the seven plastomes from our previous studies Wang, 2020, 2021;Yu et al, 2021;Huang et al, 2022), only one Corydalis plastome was formally and trustfully reported (Wu et al, 2020). This is not only in striking contrast to a species-rich genus with more than 500 species but also to the attraction they have for scientific interest.…”

Section: Introductionmentioning

confidence: 65%

New Insights Into the Backbone Phylogeny and Character Evolution of Corydalis (Papaveraceae) Based on Plastome Data

Wang

2022

Front. Plant Sci.

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A robust backbone phylogeny is fundamental for developing a stable classification and is instructive for further research. However, it was still not available for Corydalis DC., a species-rich (> 500 species), ecologically and medically important, but taxonomically notoriously difficult genus. Here, we constructed backbone phylogeny and estimated the divergence of Corydalis based on the plastome data from 39 Corydalis species (32 newly sequenced), which represent ca. 80% of sections and series across this genus. Our phylogenetic analyses recovered six fully supported main clades (I–VI) and provided full support for the majority of lineages within Corydalis. Section Archaeocapnos was unexpectedly turned out to be sister to the rest of the subg. Corydalis s. l. (clades IV–VI), thus treating as a distinct clade (clade III) to render all the main clades monophyletic. Additionally, some unusual plastome structural rearrangements were constantly detected within Corydalis and were proven to be lineage-specific in this study, which, in turn, provided further support to our phylogeny. A segment containing five genes (trnV-UAC–rbcL) in the plastome's LSC region was either normally located downstream of the ndhC gene in clade I species or translocated downstream of the atpH gene in clade II species or translocated to downstream of the trnK-UUU gene in clade III–VI species. The unique large inversion (ca. 50 kb) in the plastome LSC region of clade III species, representing an intermediate stage of the above translocation in clades IV–VI, firmly supported clade III as a distinct and early diverged clade within this large lineage (clades III–VI). Our phylogeny contradicted substantially with the morphology-based taxonomy, rejected the treatment of tuberous species as an independent evolutionary group, and proved that some commonly used diagnostic characters (e.g., root and rhizome) were results of convergent evolution, suggestive of unreliability in Corydalis. We dated the origin of crown Corydalis to the early Eocene (crown age 49.08 Ma) and revealed possible explosive radiation around 25 Ma, coinciding with the drastic uplift of the Qinghai-Tibetan Plateau in Oligocene and Miocene. This study provided the most reliable and robust backbone phylogeny of Corydalis to date and shed some new insights on the evolution of Corydalis.

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Section: Introductionmentioning

confidence: 65%

New Insights Into the Backbone Phylogeny and Character Evolution of Corydalis (Papaveraceae) Based on Plastome Data

Wang

2022

Front. Plant Sci.

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“…The chloroplast genomes of 12 Corydalis spp. have been published to date, with most being published in China, where this genus is mainly distributed [16,23,[38][39][40][41]. In this study, we compared the chloroplast genome sequences of Corydalis spp.…”

Section: Introductionmentioning

confidence: 99%

“…and Lamprocapnos spp. have been analyzed in the subfamily Fumarioideae [16,18,23,[38][39][40][41]44]. Therefore, to explore the diverse genetic structures of Corydalis and its close relatives, we included F. officinalis in our analysis.…”

Section: Introductionmentioning

confidence: 99%

Comparative analysis of the complete chloroplast genome of Papaveraceae to identify rearrangements within the Corydalis chloroplast genome

Kim,

Ha,

Park

et al. 2023

PLoS ONE

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Chloroplast genomes are valuable for inferring evolutionary relationships. We report the complete chloroplast genomes of 36 Corydalis spp. and one Fumaria species. We compared these genomes with 22 other taxa and investigated the genome structure, gene content, and evolutionary dynamics of the chloroplast genomes of 58 species, explored the structure, size, repeat sequences, and divergent hotspots of these genomes, conducted phylogenetic analysis, and identified nine types of chloroplast genome structures among Corydalis spp. The ndh gene family suffered inversion and rearrangement or was lost or pseudogenized throughout the chloroplast genomes of various Corydalis species. Analysis of five protein-coding genes revealed simple sequence repeats and repetitive sequences that can be potential molecular markers for species identification. Phylogenetic analysis revealed three subgenera in Corydalis. Subgenera Cremnocapnos and Sophorocapnos represented the Type 2 and 3 genome structures, respectively. Subgenus Corydalis included all types except type 3, suggesting that chloroplast genome structural diversity increased during its differentiation. Despite the explosive diversification of this subgenus, most endemic species collected from the Korean Peninsula shared only one type of genome structure, suggesting recent divergence. These findings will greatly improve our understanding of the chloroplast genome of Corydalis and may help develop effective molecular markers.

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Phylogenetic analysis based on single-copy orthologous proteins in highly variable chloroplast genomes of Corydalis

Yin

Huang

Liu

et al. 2022

Sci Rep

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Corydalis is one of the few lineages that have been reported to have extensive large-scale chloroplast genome (cp-genome) rearrangements. In this study, novel cp-genome rearrangements of Corydalis pinnata, C. mucronate, and C. sheareri are described. C. pinnata is a narrow endemic species only distributed at Qingcheng Mountain in southwest China. Two independent relocations of the same four genes (trnM-CAU-rbcL) were found relocated from the typically posterior part of the large single-copy region to the front of it. A uniform inversion of an 11–14-kb segment (ndhB-trnR-ACG) was found in the inverted repeat region; and extensive losses of accD, clpP, and trnV-UAC genes were detected in all cp-genomes of all three species of Corydalis. In addition, a phylogenetic tree was reconstructed based on 31 single-copy orthologous proteins in 27 cp-genomes. This study provides insights into the evolution of cp-genomes throughout the genus Corydalis and also provides a reference for further studies on the taxonomy, identification, phylogeny, and genetic transformation of other lineages with extensive rearrangements in cp-genomes.

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The complete chloroplast genome and phylogenetic analysis of Corydalis fangshanensis W.T. Wang ex S.Y. He (Papaveraceae)

Cited by 6 publications

References 15 publications

New Insights Into the Backbone Phylogeny and Character Evolution of Corydalis (Papaveraceae) Based on Plastome Data

New Insights Into the Backbone Phylogeny and Character Evolution of Corydalis (Papaveraceae) Based on Plastome Data

Comparative analysis of the complete chloroplast genome of Papaveraceae to identify rearrangements within the Corydalis chloroplast genome

Phylogenetic analysis based on single-copy orthologous proteins in highly variable chloroplast genomes of Corydalis

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