De novo chromosome-level assembly of the Centella asiatica genome

Pootakham, Wirulda; Naktang, Chaiwat; Kongkachana, Wasitthee; Sonthirod, Chutima; Yoocha, Thippawan; Sangsrakru, Duangjai; Jomchai, Nukoon; U‐thoomporn, Sonicha; Romyanon, Kanokwan; Toojinda, Theerayut; Tangphatsornruang, Sithichoke

doi:10.1016/j.ygeno.2021.05.019

Cited by 18 publications

(17 citation statements)

References 40 publications

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“…The sequenced reads were mapped to the C . asiatica reference sequence [ 19 ]. We were able to map 95–96% of the total RNA reads to the reference genome ( S3 Table ).…”

Section: Resultsmentioning

confidence: 99%

“…asiatica reference genome with HISAT2 [ 21 ]. The reference genome sequence was downloaded from the national center for biotechnology information (NCBI) database with the BioProject number PRJNA642665 [ 19 ]. StringTie2 was used to quantify RNA reads mapped to gene regions of the genome [ 22 ].…”

Section: Methodsmentioning

confidence: 99%

“…A recent report on the C . asiatica genome [ 19 ] provides a reference sequence and gene annotation that enables the genome-wide gene expression patterns to be precisely analyzed using RNA-Seq data.…”

Section: Introductionmentioning

confidence: 99%

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Transcriptome sequencing revealed the influence of blue light on the expression levels of light-stress response genes in Centella asiatica

et al. 2021

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Centella asiatica is rich in medical and cosmetic properties. While physiological responses of C. asiatica to light have been widely reported, the knowledge of the effects of light on its gene expression is sparse. In this study, we used RNA sequencing (RNA-seq) to investigate the expression of the C. asiatica genes in response to monochromatic red and blue light. Most of the differentially expressed genes (DEGs) under blue light were up-regulated but those under red light were down-regulated. The DEGs encoded for CRY-DASH and UVR3 were among up-regulated genes that play significant roles in responses under blue light. The DEGs involved in the response to photosystem II photodamages and in the biosynthesis of photoprotective xanthophylls were also up-regulated. The expression of flavonoid biosynthetic DEGs under blue light was up-regulated but that under red light was down-regulated. Correspondingly, total flavonoid content under blue light was higher than that under red light. The ABI5, MYB4, and HYH transcription factors appeared as hub nodes in the protein-protein interaction network of the DEGs under blue light while ERF38 was a hub node among the DEGs under red light. In summary, stress-responsive genes were predominantly up-regulated under blue light to respond to stresses that could be induced under high energy light. The information obtained from this study can be useful to better understand the responses of C. asiatica to different light qualities.

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“…The sequenced reads were mapped to the C . asiatica reference sequence [ 19 ]. We were able to map 95–96% of the total RNA reads to the reference genome ( S3 Table ).…”

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Transcriptome sequencing revealed the influence of blue light on the expression levels of light-stress response genes in Centella asiatica

et al. 2021

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“…= not specified). Of these, four genomes are finely assembled into pseudomolecules (i.e., chromosomes, Apium graveolens [98], Daucus carota [76], Centella asiatica [99] and Coriandrum sativum [100]); whereas the others (Angelica gigas, Oenanthe javanica, Bupleurum falcatum and Foeniculum vulgare) were incomplete and/or assembled at the scaffold level [46,96,97,101]. While the latter were obtained exclusively through short reads sequencing, the first four resulted from a combination of second-and third-generation sequencing platforms, proving to be the most suitable approach for obtaining fully assembled, highly accurate genome sequences.…”

Section: Whole Genome Sequencing Provides Powerful Tools For Marker-assisted Breedingmentioning

confidence: 99%

Impact of Genomic and Transcriptomic Resources on Apiaceae Crop Breeding Strategies

Palumbo

Vannozzi

Barcaccia

2021

IJMS

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The Apiaceae taxon is one of the most important families of flowering plants and includes thousands of species used for food, flavoring, fragrance, medical and industrial purposes. This study had the specific intent of reviewing the main genomics and transcriptomic data available for this family and their use for the constitution of new varieties. This was achieved starting from the description of the main reproductive systems and barriers, with particular reference to cytoplasmic (CMS) and nuclear (NMS) male sterility. We found that CMS and NMS systems have been discovered and successfully exploited for the development of varieties only in Foeniculum vulgare, Daucus carota, Apium graveolens and Pastinaca sativa; whereas, strategies to limit self-pollination have been poorly considered. Since the constitution of new varieties benefits from the synergistic use of marker-assisted breeding in combination with conventional breeding schemes, we also analyzed and discussed the available SNP and SSR marker datasets (20 species) and genomes (8 species). Furthermore, the RNA-seq studies aimed at elucidating key pathways in stress tolerance or biosynthesis of the metabolites of interest were limited and proportional to the economic weight of each species. Finally, by aligning 53 plastid genomes from as many species as possible, we demonstrated the precision offered by the super barcoding approach to reconstruct the phylogenetic relationships of Apiaceae species. Overall, despite the impressive size of this family, we documented an evident lack of molecular data, especially because genomic and transcriptomic resources are circumscribed to a small number of species. We believe that our contribution can help future studies aimed at developing molecular tools for boosting breeding programs in crop plants of the Apiaceae family.

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“…Plant genome sequencing development started when the first genome (Arabidopsis thaliana) was completed in 2000. The whole-genome short gun assembly of C. asiatica has a size of about 430.217 Mb and it contains nine chromosome sequence information which was performed by National Center for Genetic Engineering and Biotechnology (BIOTEC), Thailand (Pootakham et al, 2021). Medicinal Materials DNA Barcode Database (MMDBD; https://rdccm.cuhk.edu.hk/mherbsdb/) and NCBI GenBank have the DNA sequence information of C. asiatica submitted which include regions of ITS,matK,rbcL,rps16,trnG,trnL,ycf5 and genome short gun assembly.…”

Section: Sequencing Based Markers Used In C Asiaticamentioning

confidence: 99%

Genetic status of Centella asiatica (L.) Urb. (Indian pennywort): A review

Mathavaraj¹,

Sabu²

2021

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In recent years, demand for medicinal plants increased due to the rise in attraction towards herbal products which are safer compared to modern drugs. Centella asiatica (L.) Urb is known as an important medicinal plant in herbal medicinal systems. It also used as an active ingredient for many products in the pharmaceutical and cosmetic industry. So far, review on this plant concerns mainly on medicinal, cosmetology and photochemical works reported. This review presents the genetic studies conducted in this herb along with a mention on conservation. Since documenting and studying genetic variation and its composition has an important connection for the understanding of evolution and improving the conservation of this species.

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De novo chromosome-level assembly of the Centella asiatica genome

Cited by 18 publications

References 40 publications

Transcriptome sequencing revealed the influence of blue light on the expression levels of light-stress response genes in Centella asiatica

Transcriptome sequencing revealed the influence of blue light on the expression levels of light-stress response genes in Centella asiatica

Impact of Genomic and Transcriptomic Resources on Apiaceae Crop Breeding Strategies

Genetic status of Centella asiatica (L.) Urb. (Indian pennywort): A review

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