Characterization of the complete chloroplast genome of <i>Houttuynia cordata</i> Thunb and phylogenetic relationships

Yang, Xuelian

doi:10.1080/23802359.2019.1710604

Cited by 3 publications

(5 citation statements)

References 4 publications

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“…Because of the lack of a related cp genome, we employed the combination of PacBio and Illumina sequencing platforms, an effective strategy for the assembly of cp genome without a reference [39,40] to de novo assemble the H. cordata cp genome. The complete cp genome of H. cordata reported here showed a typical quadripartite cycle of 160,226 bp in length, which was consistent with a previous report of cp genome of H. cordata [22]. However, unlike the previous study, we found one more protein-coding gene and one less tRNA were obtained in the present study.…”

Section: Discussionsupporting

confidence: 91%

“…cordata reported here showed a typical quadripartite cycle of 160,226 bp in length, which was consistent with a previous report of cp genome of H . cordata [ 22 ]. However, unlike the previous study, we found one more protein-coding gene and one less tRNA were obtained in the present study.…”

Section: Discussionmentioning

confidence: 99%

“…Already, thousands of cp genomes have been completely revealed. Recently, two short communications have reported the length and gene contents of cp genomes in H. cordata [21,22]. However, a comprehensive analysis of this cp genome has not yet been performed.…”

Section: Introductionmentioning

confidence: 99%

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Chloroplast genome features of an important medicinal and edible plant: Houttuynia cordata (Saururaceae)

Zhu

Feng

et al. 2020

PLoS ONE

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Houttuynia cordata (Saururaceae), an ancient and relic species, has been used as an important medicinal and edible plant in most parts of Asia. However, because of the lack of genome information and reliable molecular markers, studies on its population structure, or phylogenetic relationships with other related species are still rare. Here, we de novo assembled the complete chloroplast (cp) genome of H. cordata using the integration of the long PacBio and short Illumina reads. The cp genome of H. cordata showed a typical quadripartite cycle of 160,226 bp. This included a pair of inverted repeats (IRa and IRb) of 26,853 bp, separated by a large single-copy (LSC) region of 88,180 bp and a small single-copy (SSC) region of 18,340 bp. A total of 112 unique genes, including 79 protein-coding genes, 29 tRNA genes, and four rRNA genes, were identified in this cp genome. Eighty-one genes were located on the LSC region, 13 genes were located on the SSC region, and 17 twocopy genes were located on the IR region. Additionally, 48 repeat sequences and 86 SSR loci, which can be used as genomic markers for population structure analysis, were also detected. Phylogenetic analysis using 21 cp genomes of the Piperales family demonstrated that H. cordata had a close relationship with the species within the Aristolochia genus. Moreover, the results of mVISTA analysis and comparisons of IR regions demonstrated that the cp genome of H. cordata was conserved with that of the Aristolochia species. Our results provide valuable information for analyzing the genetic diversity and population structure of H. cordata, which can contribute to further its genetic improvement and breeding.

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Section: Discussionsupporting

confidence: 91%

Section: Discussionmentioning

confidence: 99%

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Chloroplast genome features of an important medicinal and edible plant: Houttuynia cordata (Saururaceae)

Zhu

Feng

et al. 2020

PLoS ONE

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“…Nevertheless, molecular resources of this ecological and cultural important H. cordata are limited to inter-simple sequence repeats 17 , chloroplast genomes [18][19][20] , and transcriptomes 21 , and the nuclear genomic resources remains limited, which hinders our understanding on their phytochemistry 22,23 and evolutionary relationships 24,25 with completeness BUSCO score of 87.6%. This high-quality H. cordata genome provides an essential resource for further investigations on their biology and ecology, such as the biosynthesis of phytochemicals as well as the evolutionary biology in Saururaceae.…”

Section: Background and Summarymentioning

confidence: 99%

Chromosomal-level genome of fish mintHouttuynia cordataThunb. (Saururaceae)

Law,

Nong,

Tsang

et al. 2024

Preprint

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Herbaceous flowering plants in the family Saururaceae, or commonly known as the lizard's tail family, are native to Southeast Asia and North America. Fish mint Houttuynia cordata is native to Southeast Asia and widely cultivated as culinary herb and medicinal plant in traditional medicine. Here, using a combination of PacBio HiFi long-read sequencing and Omni-C data, we present the chromosomal-level genome assembly of H. cordata (genome size 499.6 Mb). The genome has high sequence contiguity (scaffold N50 = 64.3 Mb) and completeness (BUSCO score of 94.6 %). 40,451 protein coding genes were also predicted using two transcriptomes generated in this study. The fish mint genome provides a valuable resource for further understanding the bioactive compounds and evolution of plants in the Saururaceae more widely.

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“…Recently, different reports based on genomics [17], transcriptomics [18], metabolomics [18], and phenomics [19] have been reported in S. glabra. Various researches for characterization of extrachromosomal (chloroplast) genome [20][21][22] and to find the evolutionary relationship of various S. glabra subspecies [23] have also been presented. Furthermore, the amplified fragmentlength polymorphism (AFLP) and microsatellite establishment [24,25] and SNP marker manipulation studies [26] have also been carried out for molecular evaluation in S. glabra.…”

Section: Introductionmentioning

confidence: 99%

Transcriptome Characterization and Identification of Molecular Markers (SNP, SSR, and Indels) in the Medicinal Plant Sarcandra glabra spp.

Tian

et al. 2021

BioMed Research International

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Sarcandra glabra has significant metabolically active bioingredients of pharmaceutical importance. The deficiency of molecular markers for S. glabra is a hindrance in molecular breeding for genetic improvement. In this study, 57.756 million pair-end reads were generated by transcriptome sequencing in S. glabra (Thunb.) Nakai and its subspecies S. glabra ssp. brachystachys. A total of 141,954 unigenes with 646.63 bp average length were assembled. A total of 25,620 simple sequence repeats, 726,476 single nucleotide polymorphisms, and 42,939 insertions and deletions were identified, and the associated unigenes and differentially expressed genes were characterized. This work enhanced the molecular marker resources and will facilitate molecular breeding and gene mining in S. glabra spp.

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Characterization of the complete chloroplast genome of Houttuynia cordata Thunb and phylogenetic relationships

Cited by 3 publications

References 4 publications

Chloroplast genome features of an important medicinal and edible plant: Houttuynia cordata (Saururaceae)

Chloroplast genome features of an important medicinal and edible plant: Houttuynia cordata (Saururaceae)

Chromosomal-level genome of fish mintHouttuynia cordataThunb. (Saururaceae)

Transcriptome Characterization and Identification of Molecular Markers (SNP, SSR, and Indels) in the Medicinal Plant Sarcandra glabra spp.

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