Complete chloroplast genome sequence of Amomum villosum and comparative analysis with other Zingiberaceae plants

Li, Yang; Feng, Chong; Cai, Miaomiao; Chen, Jie-hu; Ding, Ping

doi:10.1016/j.chmed.2020.05.008

Cited by 9 publications

(7 citation statements)

References 48 publications

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“…These similarities in codon choice also reveal the related relationship in the four species. The observed codon pattern is consistent with the CP genomes of Amomum [68], Panax [69], Dipterygium and Cleome [70], and various other species [71][72][73].…”

Section: S3supporting

confidence: 82%

Comparison Analysis Based on Complete Chloroplast Genomes and Insights into Plastid Phylogenomic of Four Iris Species

Feng

Wang

et al. 2022

BioMed Research International

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Iris species, commonly known as rainbow flowers because of their attractive flowers, are extensively grown in landscape gardens. A few species, including Belamcanda chinensis, the synonym of I. domestica and I. tectorum, are known for their medicinal properties. However, research on the genomes and evolutionary relationships of Iris species is scarce. In the current study, the complete chloroplast (CP) genomes of I. tectorum, I. dichotoma, I. japonica, and I. domestica were sequenced and compared for their identification and relationship. The CP genomes of the four Iris species were circular quadripartite with similar lengths, GC contents, and codon usages. A total of 113 specific genes were annotated, including the ycf1 pseudogene in all species and rps19 in I. japonica alone. All the species had mononucleotide (A/T) simple sequence repeats (SSRs) and long forward and palindromic repeats in their genomes. A comparison of the CP genomes based on mVISTA and nucleotide diversity (Pi) identified three highly variable regions (ndhF-rpl32, rps15-ycf1, and rpl16). Phylogenetic analysis based on the complete CP genomes concluded that I. tectorum is a sister of I. japonica, and the subgenus Pardanthopsis with several I. domestica clustered into one branch is a sister of I. dichotoma. These findings confirm the feasibility of superbarcodes (complete CP genomes) for Iris species authentication and could serve as a resource for further research on Iris phylogeny.

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Section: S3supporting

confidence: 82%

Comparison Analysis Based on Complete Chloroplast Genomes and Insights into Plastid Phylogenomic of Four Iris Species

Feng

Wang

et al. 2022

BioMed Research International

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“…The generation of forward repeats is usually related to the activity of transposons. These activities lead to genome structure changes that can be used as genetic markers for phylogenetic relationship studies [38]. In the same line, SSRs constitute an important part of the cp genome of higher plants and are powerful molecular markers for phylogenetic studies [39].…”

Section: Evolution Of the Chloroplast Genomementioning

confidence: 99%

Analyses of Chloroplast Genome of Eutrema japonicum Provide New Insights into the Evolution of Eutrema Species

Zhang

et al. 2021

Agronomy

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Wasabi (Eutrema japonicum) is a vegetable of Brassicaceae family, currently cultivated in Southwest Asia. It is rich in nutritional and has a spicy flavour. It is regarded as a rare condiment worldwide. Its genetic profile for yield improvement and the development of E. japonicum germplasm resources remains unknown. Cognizant of this, this study sequenced and assembled the chloroplast (cp) genome of E. japonicum to enrich our genomic information of wasabi and further understand genetic relationships within the Eutrema species. The structural characteristics, phylogeny, and evolutionary relationship of cp genomes among other Brassicaceae plants were analyzed and compared to those of Eutrema species. The cp genome of E. japonicum has 153,851 bp with a typical quadripartite structure, including 37 tRNA genes, 8 rRNA genes, and 87 protein-coding genes. It contains 290 simple sequence repeats and prefers to end their codons with an A or T, which is the same as other Brassicaceae species. Moreover, the cp genomes of the Eutrema species had a high degree of collinearity and conservation during the evolution process. Nucleotide diversity analysis revealed that genes in the IR regions had higher Pi values than those in LSC (Large single copy) and SSC (Small single copy) regions, making them potential molecular markers for wasabi diversity studies. The analysis of genetic distance between Eutrema plants and other Brassicacea plants showed that intraspecies variation was found to be low, while large differences were found between genera and species. Phylogenetic analysis based on 29 cp genomes revealed the existence of a close relationship amongst the Eutrema species. Overall, this study provides baseline information for cp genome-based molecular breeding and genetic transformation studies of Eutrema plants.

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“…At present, however, only a few Zingiberaceae genomes have been reported, e.g., Zingiber officinale and Curcuma longa ( Chakraborty et al, 2021 ; Li et al, 2021 ). Furthermore, within the Amomum genus, only a limited number of chloroplast genomes have been described ( Zhang et al, 2019 ; Yang L. et al, 2020 ). The lack of whole-genome data has severely impeded our understanding of essential oil biosynthesis in A. tsao-ko .…”

Section: Resultsmentioning

confidence: 99%

Genome Sequencing of Amomum tsao-ko Provides Novel Insight Into Its Volatile Component Biosynthesis

Sun

Yan

et al. 2022

Front. Plant Sci.

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As an important economic and medicinal crop, Amomum tsao-ko is rich in volatile oils and widely used in food additives, essential oils, and traditional Chinese medicine. However, the lack of the genome remains a limiting factor for understanding its medicinal properties at the molecular level. Here, based on 288.72 Gb of PacBio long reads and 105.45 Gb of Illumina paired-end short reads, we assembled a draft genome for A. tsao-ko (2.70 Gb in size, contig N50 of 2.45 Mb). Approximately 90.07% of the predicted genes were annotated in public databases. Based on comparative genomic analysis, genes involved in secondary metabolite biosynthesis, flavonoid metabolism, and terpenoid biosynthesis showed significant expansion. Notably, the DXS, GGPPS, and CYP450 genes, which participate in rate-limiting steps for terpenoid backbone biosynthesis and modification, may form the genetic basis for essential oil formation in A. tsao-ko. The assembled A. tsao-ko draft genome provides a valuable genetic resource for understanding the unique features of this plant and for further evolutionary and agronomic studies of Zingiberaceae species.

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Complete chloroplast genome sequence of Amomum villosum and comparative analysis with other Zingiberaceae plants

Cited by 9 publications

References 48 publications

Comparison Analysis Based on Complete Chloroplast Genomes and Insights into Plastid Phylogenomic of Four Iris Species

Comparison Analysis Based on Complete Chloroplast Genomes and Insights into Plastid Phylogenomic of Four Iris Species

Analyses of Chloroplast Genome of Eutrema japonicum Provide New Insights into the Evolution of Eutrema Species

Genome Sequencing of Amomum tsao-ko Provides Novel Insight Into Its Volatile Component Biosynthesis

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