De novo and comparative transcriptome analysis of cultivated and wild spinach

Xu, Chenxi; Jiao, Chen; Zheng, Yi; Sun, Honghe; Liu, Wenli; Cai, Xiaofeng; Wang, Xiaoli; Liu, Shuang; Xu, Youqiang; Mou, Beiquan; Dai, Shaojun; Fei, Zhangjun; Wang, Quanhua

doi:10.1038/srep17706

Cited by 39 publications

(35 citation statements)

References 42 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…We validated the genome assembly using the ‘Benchmarking Universal Single‐Copy Orthologs’ (BUSCO; Simão et al ., ) gene set, and found 89% of all BUSCO plant genes being represented in the assembly (Table S4). With this proportion the genome assembly and annotation completeness in rye is comparable to other plant species (Visser et al ., ; Xu et al ., ). Previously published draft genomes, as for instance the close relative barley (Mayer et al ., ), accelerated forward genetic approaches and enabled novel strategies for genome research such as exome‐capture sequencing (Mascher et al ., , ).…”

Section: Resultsmentioning

confidence: 97%

Towards a whole‐genome sequence for rye (Secale cereale L.)

et al. 2017

View full text Add to dashboard Cite

SUMMARYWe report on a whole-genome draft sequence of rye (Secale cereale L.). Rye is a diploid Triticeae species closely related to wheat and barley, and an important crop for food and feed in Central and Eastern Europe. Through whole-genome shotgun sequencing of the 7.9-Gbp genome of the winter rye inbred line Lo7 we obtained a de novo assembly represented by 1.29 million scaffolds covering a total length of 2.8 Gbp. Our reference sequence represents nearly the entire low-copy portion of the rye genome. This genome assembly was used to predict 27 784 rye gene models based on homology to sequenced grass genomes. Through resequencing of 10 rye inbred lines and one accession of the wild relative S. vavilovii, we discovered more than 90 million single nucleotide variants and short insertions/deletions in the rye genome. From these variants, we developed the high-density Rye600k genotyping array with 600 843 markers, which enabled anchoring the sequence contigs along a high-density genetic map and establishing a synteny-based virtual gene order. Genotyping data were used to characterize the diversity of rye breeding pools and genetic resources, and to obtain a genome-wide map of selection signals differentiating the divergent gene pools. This rye whole-genome sequence closes a gap in Triticeae genome research, and will be highly valuable for comparative genomics, functional studies and genome-based breeding in rye.

show abstract

Section: Resultsmentioning

confidence: 97%

Towards a whole‐genome sequence for rye (Secale cereale L.)

et al. 2017

View full text Add to dashboard Cite

show abstract

“…The software tool BUSCO was recently developed for assessment of sequence assemblies, by comparison of gene sets or transcriptomes to a core set of single-copy orthologs, allowing the calculation of levels of completeness, duplication, and fragmentation. BUSCO-derived results have been demonstrated to be more consistent than those from previously used software packages such as CEGMA, and more accurate than the commonly used N50 statistic [30], and so BUSCO has been promoted in several recent studies [28,31] [30]) demonstrated a relatively low level of duplication in the phalaris reference set, and comparable levels of missing orthologues. When compared to an additional set of de novo-assembled transcriptomes from multiple organisms, mainly of non-plant origin [30], the level of completeness and duplication is generally superior in the phalaris dataset, while fragmentation is comparable.…”

Section: Quality Of Transcriptome Assemblymentioning

confidence: 89%

Generation and Characterisation of a Reference Transcriptome for Phalaris (Phalaris aquatica L.)

et al. 2017

View full text Add to dashboard Cite

Phalaris aquatica is a cool-season perennial grass species that is extensively cultivated in Australia, with additional usage in other areas of the world. Phalaris displays a number of desirable agronomic characteristics, although unfavourable traits include excessive seed shattering, sensitivity to aluminium toxicity, and several toxicosis syndromes. Varietal development has to date been based on traditional selection methods, but would benefit from the application of genomics-based approaches, which require the development of large-scale sequence resources. Due to a large nuclear DNA content, methods that target the expressed component of the genome and reduce the complexity of analysis are most amenable to current sequencing technologies. A reference unigene set has been developed by transcriptome sequencing of multiple tissues from a single plant belonging to the variety Landmaster. Comparisons have been made to gene complements from related species, as well as reference protein databases, and patterns of gene expression in different tissues have been evaluated. A number of candidate genes relevant to removal of undesirable attributes have been identified. The reference unigene set will provide the basis for detailed studies of differential gene expression and identification of candidate genes for potential transgenic deployment, as well as a critical resource for genotypic analysis to support future genomics-assisted breeding activities for phalaris improvement.

show abstract

“…Transcriptomic analysis also helped in understanding of phylogenetic relationship. Using transcriptome sequencing data, Xu et al (2015) identified ~320,000 high-quality SNPs in spinach and indicated that Spinacia turkestanica was more closely related to the cultivated S. oleracea than S. tetrandra. Such information will be useful for exploring wild resources for quality improvement of vegetables.…”

Section: Genome Sequencing and Transcriptome Analysis For Quality Tramentioning

confidence: 99%

Advances in vegetable breeding for nutraceuticals and quality traits

Behera¹,

Singh²

2019

IJGPB

View full text Add to dashboard Cite

Vegetable crops are rich in dietary micronutrients (minerals, vitamins), antioxidents and functional phytochemicals ‘nutraceuticals’. However, some of the elements are of public health concern such as β-carotene, iron, calcium and folic acid which attracts breeders’ interest to improve their content in food sources including vegetable crops so that their dietary intake could be increased and their deficiency problems reduced. Some nutraceutical compounds such as anthocyanin, β-carotene, lycopene and glucosinolates have been reported to play active role in health and their contents have been found more in beet root, cauliflower, carrot and broccoli, respectively. The attempts through conventional breeding methods have been slow and inadequate, hence new developments in molecular and biochemical diagnostics tools and techniques showed promise in improving the nutraceutical contents and other quality traits. Molecular markers, next generation sequencing, RNA interference (RNAi) and genetic engineering have great promise in reducing time and cost involved in quality breeding. The present review summarise attempts and potential of improving the nutraceuticals and quality traits in vegetable crops. Key words:.

show abstract

De novo and comparative transcriptome analysis of cultivated and wild spinach

Cited by 39 publications

References 42 publications

Towards a whole‐genome sequence for rye (Secale cereale L.)

Towards a whole‐genome sequence for rye (Secale cereale L.)

Generation and Characterisation of a Reference Transcriptome for Phalaris (Phalaris aquatica L.)

Advances in vegetable breeding for nutraceuticals and quality traits

Contact Info

Product

Resources

About