High Contiguity de novo Genome Sequence Assembly of Trifoliate Yam (Dioscorea dumetorum) Using Long Read Sequencing

Siadjeu, Christian; Pucker, Boas; Viehöver, Prisca; Albach, Dirk C.; Weißhaar, Bernd

doi:10.3390/genes11030274

Cited by 62 publications

(75 citation statements)

References 51 publications

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“…Recently, the chloroplast genomes of six Chinese yam cultivars were compared to develop new markers for genetic studies (Cao et al 2018). Reference genome sequences have been published for D. rotundata and D. dumetorum (Tamiru et al 2017;Siadjeu et al 2020). A pre-publication genome sequence for D. alata is also available (Dioscorea alata v2.1 DOE-JGI, https ://phyto zome.jgi.…”

Section: Current Research Status and Breeding Objectivesmentioning

confidence: 99%

An underutilized orphan tuber crop—Chinese yam : a review

Epping¹,

Laibach

2020

Planta

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Main conclusion The diversification of food crops can improve our diets and address the effects of climate change, and in this context the orphan crop Chinese yam shows significant potential as a functional food. Abstract As the effects of climate change become increasingly visible even in temperate regions, there is an urgent need to diversify our crops in order to address hunger and malnutrition. This has led to the re-evaluation of neglected species such as Chinese yam (Dioscorea polystachya Turcz.), which has been cultivated for centuries in East Asia as a food crop and as a widely-used ingredient in traditional Chinese medicine. The tubers are rich in nutrients, but also contain bioactive metabolites such as resistant starches, steroidal sapogenins (like diosgenin), the storage protein dioscorin, and mucilage polysaccharides. These health-promoting products can help to prevent cardiovascular disease, diabetes, and disorders of the gut microbiome. Whereas most edible yams are tropical species, Chinese yam could be cultivated widely in Europe and other temperate regions to take advantage of its nutritional and bioactive properties. However, this is a laborious process and agronomic knowledge is fragmented. The underground tubers contain most of the starch, but are vulnerable to breaking and thus difficult to harvest. Breeding to improve tuber shape is complex given the dioecious nature of the species, the mostly vegetative reproduction via bulbils, and the presence of more than 100 chromosomes. Protocols have yet to be established for in vitro cultivation and genetic transformation, which limits the scope of research. This article summarizes the sparse research landscape and evaluates the nutritional and medical applications of Chinese yam. By highlighting the potential of Chinese yam tubers, we aim to encourage the adoption of this orphan crop as a novel functional food.

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Section: Current Research Status and Breeding Objectivesmentioning

confidence: 99%

An underutilized orphan tuber crop—Chinese yam : a review

Epping¹,

Laibach

2020

Planta

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“…This phenomenon shows that genomic data of Dioscorea species is relatively scarce in publicly database. There only D. rotundata [23], and D. dumetorum [24] genomic sequences were reported. The N50 is one of the most important indices used to evaluate the assembly quality.…”

Section: Discussionmentioning

confidence: 99%

“…Although a small number of genes from Dioscorea species are available in several public database, complete transcriptome or genomic data are scarce. Indeed, to date, only the genomic resources for D. alata [22], D. rotundata [23], and D. dumetorum [24] have been reported. Therefore, enhancing research efforts on the genome of Dioscorea species is important and the main focus of the presenr study.…”

Section: Discussionmentioning

confidence: 99%

“…The ultimate aim is often to reveal genes that are involved in the biosynthetic pathways in secondary metabolism of many species [18][19][20][21]. Until now, the genomic resources of D. alata [22], D. rotundata [23], and D. dumetorum [24] have been reported. Nevertheless, as a non-model species, there is lack of enomic resources, in particular, information on active substance metabolism of D. opposita.…”

Section: Introductionmentioning

confidence: 99%

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Transcriptome Assembly and Gene Expression Analysis of Leaf and Rhizome tissues of Dioscorea opposita

DianYun¹,

Cheng²,

Li³

et al. 2020

Preprint

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Background: Dioscorea opposita is a monocotyledonous plant in the Dioscoreaceae family. The rhizome of D. opposita, known as “dioscoreae rhiaoma” or “Chinese yam”, is not only a well-known traditional Chinese medicine, but also a popular health food.Methods:In this study, the leaf and rhizome tissues of D. opposita were collected. Their transcriptome sequenceand were obtained using an Illumina Hiseq 4000 platform. The data was analyzed by bioinformatics software. Likewise, the consistent expression pattern of DEGs was validated with qRT-PCR analysis.Results: A total of 46,982,031 and 53,689,620 clean reads from leaf and rhizome tissues were acquired, respectively (SRP: PRJNA628588). 50,765 unigenes were obtained with an average length of 1050 base pairs (bp). A total of 13,259 significant differentially expressed genes (DEGs) were obtained from leaf versus rhizome tissues, including 5536 up-regulated and 7723 down-regulated unigenes. In addition, 20,607 simple sequence repeats (SSRs) were identified in this study. Conclusions:This study not only enriched the transcriptomic data of D. opposita, but also laid a foundation for the analysis of terpenoid synthesis pathway.

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“…The study of the A. donax genome is still a demanding research topic aimed at collecting knowledge needed for A. donax genetic improvement, since the lack of a high-quality reference genome sequence. A hybrid approach combining Illumina and long-read sequencing technologies, i.e., Pac Bio or Nanopore, could be used as previously reported for de novo sequencing in other crops [95,96]. In particular, the high-quality reference genome of Oryza longistaminata has been obtained incorporating Illumina and PacBio sequencing data [95], while the de novo genome sequence assembly of trifoliate yam (Dioscorea dumetorum) was the result of Illumina and Oxford Nanopore technologies [96].…”

Section: Genetic Engineeringmentioning

confidence: 99%

Genetic Improvement of Arundo donax L.: Opportunities and Challenges

Danelli

Laura²,

Savona³

et al. 2020

Plants

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Arundo donax L., the giant reed—being a long-duration, low-cost, non-food energy crop able to grow in marginal lands—has emerged as a potential alternative to produce biomass for both energy production, with low carbon emissions, and industrial bioproducts. In recent years, pioneering efforts have been made to genetically improve this very promising energy crop. This review analyses the recent advances and challenges encountered in using clonal selection, mutagenesis/somaclonal variation and transgenesis/genome editing. Attempts to improve crop yield, in vitro propagation efficiency, salt and heavy metal tolerance by clonal selection were carried out, although limited by the species’ low genetic diversity and availability of mutants. Mutagenesis and somaclonal variation have also been attempted on this species; however, since Arundo donax is polyploid, it is very difficult to induce and select promising mutations. In more recent years, genomics and transcriptomics data are becoming available in Arundo, closing the gap to make possible the genetic manipulation of this energy crop in the near future. The challenge will regard the functional characterization of the genes/sequences generated by genomic sequencing and transcriptomic analysis in a complex polyploid genome.

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High Contiguity de novo Genome Sequence Assembly of Trifoliate Yam (Dioscorea dumetorum) Using Long Read Sequencing

Cited by 62 publications

References 51 publications

An underutilized orphan tuber crop—Chinese yam : a review

An underutilized orphan tuber crop—Chinese yam : a review

Transcriptome Assembly and Gene Expression Analysis of Leaf and Rhizome tissues of Dioscorea opposita

Genetic Improvement of Arundo donax L.: Opportunities and Challenges

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