Deep sequencing of the Colocasia esculenta transcriptome revealed candidate genes for major metabolic pathways of starch synthesis

Liu, H.; You, Yongning; Zheng, Xianwei; Diao, Youxiang; Huang, Xiaoqiao; Hu, Zhongli

doi:10.1016/j.sajb.2014.11.008

Cited by 12 publications

(11 citation statements)

References 18 publications

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“…The reads are combined into longer fragments, with all the redundancy for subsequent analysis to be removed, and the longest sequences are defined as Unigenes. Finally, the Unigenes obtained by Trinity were submitted into protein databases, including GenBank NR, GO (gene ontology), KEGG (Kyoto Encyclopaedia of Genes and Genomes), and KOG (The Eukaryotic Clusters of Orthologous Groups) databases for comparison using the BLASTX algorithm (e-value ≤ 1e-5), and the best match was selected for the comment information [ 4 , 17 ].…”

Section: Methodsmentioning

confidence: 99%

Gene cloning of a neutral ceramidase from the sphingolipid metabolic pathway based on transcriptome analysis of Amorphophallus muelleri

et al. 2018

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Amorphophallus is a perennial herbaceous plant species mainly distributed in the tropics or subtropics of Asia and Africa. It has been used as a traditional medicine for a long time and now is utilized for the pharmaceutical, chemical and agriculture industries as a valued economic crop. Recently, Amorphophallus has attracted tremendous interest because of its high ceramide content. However, the breeding and genome studies are severely limited by the arduous whole genome sequencing of Amorphophallus. In this study, the transcriptome data of A. muelleri was obtained by utilizing the high-throughput Illumina sequencing platform. Based on this information, the majority of the significant genes involved in the proposed sphingolipid metabolic pathway were identified. Then, the full-length neutral ceramidase cDNA was obtained with the help of its candidate transcripts, which were acquired from the transcriptome data. Furthermore, we demonstrated that this neutral ceramidase was a real ceramidase by eukaryotic expression in the yeast double knockout mutant Δypc1 Δydc1, which lacks the ceramidases—dihydroCDase (YDC1p), phytoCDase (YPC1p). In addition, the biochemical characterization of purified A. muelleri ceramidase (AmCDase) exhibited classical Michaelis-Menten kinetics with an optimal activity ranging from pH 6.5 to 8.0. Based on our knowledge, this study is the first to report the related information of the neutral ceramidase in Amorphophallus. All datasets can provide significant information for related studies, such as gene expression, genetic improvement and application on breeding in Amorphophallus.

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Section: Methodsmentioning

confidence: 99%

Gene cloning of a neutral ceramidase from the sphingolipid metabolic pathway based on transcriptome analysis of Amorphophallus muelleri

et al. 2018

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“…Genomic approaches are particularly useful when dealing with complex traits such as tolerance to cold climate and yield, since these traits usually have a multi-genic nature and are greatly influenced by the environment (Ivančič & Lebot, 2000). The molecular genetic researches and genetic basic data in taro are unfortunately limited in comparison with major crops (Liu et al, 2015). Nevertheless, the first taro linkage maps were generated with mainly amplified fragment length polymorphism (AFLP) and some simple sequence repeat (SSR) markers (Quero-García et al, 2006).…”

Section: Yatsugashira (Diploid)mentioning

confidence: 99%

Taro [Colocasia esculenta (L.) Schott] production in Japan: Present state, problems and prospects

Mikami

Tsutsui

2019

AAS

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Taro [Colocasia esculenta (L.) Schott] production in Japan: Present state, problems and prospectsAbstract: Taro [Colocasia esculenta (L.) Schott], a member of the family Araceae, is a vegetatively propagated crop with edible tubers (corms and cormels), petioles and leaf blades. Available evidence suggests that taro originated in South Central Asia, probably in the tropical region from India to Indonesia. The crop is considered to have reached Japan by the 10 th century B. C.. In Japan, taro was a regional staple crop before the beginning of rice cultivation, but it is nowadays grown as a root vegetable. The corms and cormels of taro are an excellent source of carbohydrates and rich in essential minerals, vitamins and dietary fiber. Additionally, Japanese people have formed socio-cultural connections to the crop since olden times; taro has been served in traditional feasting and seasonal events. Despite having so much value, taro cultivation has shown declining trends in the past several decades. It should also be noted that little attention has been devoted to the genetic improvement of taro. In this review, an attempt is made to collect information about the commercial production and uses of Japanese taros as well as agronomic characteristics of leading cultivars, with the expectation that the synthesized information will aid in understanding the problems and prospects of taro cultivation in Japan. Pridelovanje tara [Colocasia esculenta (L.) Schott] na Japonskem: trenutno stanje, problemi in perspektiveIzvleček: Taro [Colocasia esculenta (L.) Schott], predstavnik družine kačnikov (Araceae), je vegetativno razmnoževana poljščina z užitnimi čebulastimi gomolji (kormi, kormiči), listnimi peclji in listnimi ploskvami. Po razpoložljivih podatkih naj bi taro izviral iz južne centralne Azije, verjetno iz tropskih predelov med Indijo in Indonezijo. Poljščina naj bi dosegla Japonsko v 10 th stoletju pred Kristusom. Na nekaterih območjih Japonske je bil taro vsakodnevna hrana pred začetkom gojenja riža, danes se goji predvsem kot korenasta zelenjava. Čebulasti gomolji tara (kormi) so odličen vir ogljikovih hidratov in bogati na esencialnih mineralih, vitaminih in prehranskih vlakninah. Japonci so že od nekdaj stkali s poljščino socio-kulturne povezave, ko je bil taro postrežen na tradicionalnik praznikih in ob sezonskih dogodkih. Kljub tako veliki vrednosti, je gojenje tara v zadnjih desetletjih upadalo. Pripomniti je še potrebno, da je bilo genetskemu izbolšanju tara posvečeno premalo pozornosti. V tem pregledu je podan poskus zbiranja podatkov o komercialni pridelavi in uporabi tara na Japonskem kot tudi agronomske lastnosti vodilnih sort v pričakovanju, da bodo te informacije pomagale razumeti težave in prihodnost gojenja tara na Japonskem.

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“…In the absence of a reference genome, various kinds of next-generation sequencing strategies such as genotype by sequencing (GBS) ( Shintaku et al, 2016 ; Helmkampf et al, 2017 ; Soulard, Mournet & Guitton, 2017 ) and RNA-seq ( Liu et al, 2015 ; You et al, 2015 ; Wang et al., 2017b ) have been adopted for development of genome-wide molecular markers for taro. For example, using GBS, Soulard, Mournet & Guitton (2017) constructed two unprecedented genetic linkage maps of taro with filtered single nucleotide polymorphisms (SNPs) and 14 SSR markers; in turn, Helmkampf et al (2017) developed over 2400 high quality SNPs from 70 taro accessions, and uncovered the underlying phylogenetic relationships between Hawaiian and other Pacific landraces.…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity and population structure of eddoe taro in China using genome-wide SNP markers

Wang

Sun

Huang

et al. 2020

PeerJ

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Taro (Colocasia esculenta) is an important root and tuber crop cultivated worldwide. There are two main types of taro that vary in morphology of corm and cormel, ‘dasheen’ and ‘eddoe’. The eddoe type (Colocasia esculenta var. antiquorium) is predominantly distributed throughout China. Characterizing the genetic diversity present in the germplasm bank of taro is fundamental to better manage, conserve and utilize the genetic resources of this species. In this study, the genetic diversity of 234 taro accessions from 16 provinces of China was assessed using 132,869 single nucleotide polymorphism (SNP) markers identified by specific length amplified fragment-sequencing (SLAF-seq). Population structure and principal component analysis permitted the accessions to be categorized into eight groups. The genetic diversity and population differentiation of the eight groups were evaluated using the characterized SNPs. Analysis of molecular variance showed that the variation among eight inferred groups was higher than that within groups, while a relatively small variance was found among the two morphological types and 16 collection regions. Further, a core germplasm set comprising 41 taro accessions that maintained the genetic diversity of the entire collection was developed based on the genotype. This research is expected to be valuable for genetic characterization, germplasm conservation, and breeding of taro.

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Deep sequencing of the Colocasia esculenta transcriptome revealed candidate genes for major metabolic pathways of starch synthesis

Cited by 12 publications

References 18 publications

Gene cloning of a neutral ceramidase from the sphingolipid metabolic pathway based on transcriptome analysis of Amorphophallus muelleri

Gene cloning of a neutral ceramidase from the sphingolipid metabolic pathway based on transcriptome analysis of Amorphophallus muelleri

Taro [Colocasia esculenta (L.) Schott] production in Japan: Present state, problems and prospects

Genetic diversity and population structure of eddoe taro in China using genome-wide SNP markers

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