Draft genome of spinach and transcriptome diversity of 120 Spinacia accessions

22Plant endogenous small RNAs (sRNAs) are important regulators of gene expression. 23There are two broad categories of plant sRNAs: microRNAs (miRNAs) and endogenous short 24interfering RNAs (siRNAs). MicroRNA loci are relatively well-annotated but comprise only a 25 small minority of the total sRNA pool; siRNA locus annotations have lagged far behind. Here, we 26 used a large dataset of published and newly generated sRNA sequencing data (1,333 sRNA-seq 27 libraries containing over 20 billion reads) and a uniform bioinformatic pipeline to produce 28 comprehensive sRNA locus annotations of 47 diverse plants, yielding over 2.7 million sRNA loci. 29The two most numerous classes of siRNA loci produced mainly 24 nucleotide and 21 nucleotide 30 siRNAs, respectively. 24 nucleotide-dominated siRNA loci usually occurred in intergenic regions, 31 especially at the 5'-flanking regions of protein-coding genes. In contrast, 21 nucleotide-32 dominated siRNA loci were most often derived from double-stranded RNA precursors copied 33 from spliced mRNAs. Genic 21 nucleotide-dominated loci were especially common from disease 34 resistance genes, including from a large number of monocots. Individual siRNA sequences of all 35 types showed very little conservation across species, while mature miRNAs were more likely to 36 be conserved. We developed a web server where our data and several search and analysis tools 37 are freely accessible at

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“…genes have expanded that might be differentially regulated (Dohm et al 2014;Xu et al 2017;502 Funk et al 2018). 503…”

Section: Genes Containing Sirna21 and Sirna22 Loci In Monocotsmentioning

confidence: 99%

Integrated annotations and analyses of small RNA-producing loci from 47 diverse plants

Lunardon

Johnson

Hagerott

et al. 2019

Preprint

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“…Similarly, sex-specific markers have been reported (Khattak et al, 2006;Lan et al, 2006;Onodera et al, 2011) to be linked to a single sex-determining gene on chromosome 1; however, these markers have been identified in restricted accessions and do not always remain linked with sex in different accessions (Fujito et al, 2015). The most recent draft of the spinach genome (Xu et al, 2017) has not identified sex-specific chromosomal regions. Therefore, while a heterozygous/homozygous sex determination system is accepted, the question of whether such a gene or gene cluster is embedded in nonrecombining chromosomal region remains unresolved.…”

Section: Introductionmentioning

confidence: 99%

Gender‐specific expression of GIBBERELLIC ACID INSENSITIVE is critical for unisexual organ initiation in dioecious Spinacia oleracea

West

Golenberg

2017

New Phytologist

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While unisexual flowers have evolved repeatedly throughout angiosperm families, the actual identification of sex-determining genes has been elusive, and their regulation within populations remains largely undefined. Here, we tested the mechanism of the feminization pathway in cultivated spinach (Spinacia oleracea), and investigated how this pathway may regulate alternative sexual development. We tested the effect of gibberellic acid (GA) on sex determination through exogenous applications of GA and inhibitors of GA synthesis and proteasome activity. GA concentrations in multiple tissues were estimated by enzyme-linked immunosorbent assay analysis. Gene function was investigated and pathway analysis was performed through virus-induced gene silencing. Relative gene expression levels were estimated by quantitative reverse transcription-polymerase chain reaction. Inhibition of GA production and proteasome activity feminized male flowers. However, there was no difference in GA content in tissues between males and females. We characterized a single DELLA family transcription factor gene (GIBBERELLIC ACID INSENSITIVE (SpGAI)) and observed inflorescence expression in females two-fold higher than in males. Reduction of SpGAI expression in females to male levels phenocopied exogenous GA application with respect to flower development. These results implicate SpGAI as the feminizing factor in spinach, and suggest that the feminizing pathway is epistatic to the masculinizing pathway. We present a unified model for alternative sexual development and discuss the implications for established theory.

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“…Beta vulgaris (sugar beet, Dohm et al, 2014), Spinacia oleracea (spinach, Xu et al, 2017), and Amaranthus hypochondriacus (amaranth, Clouse et al, 2016). Quinoa belongs to the subfamily Chenopodioideae, which has recently been revised and split into multiple smaller genera such as Chenopodiastrum, Oxybasis, Lipandra, and Dysphania, in addition to the previously recognised genera Chenopodium, Atriplex, Blitum, andSpinacia (Fuentes-Bazan et al, 2012a, Fuentes-Bazan et al, 2012b).…”

Section: Introductionmentioning

confidence: 99%

Satellite DNA landscapes after allotetraploidisation of quinoa (Chenopodium quinoa) reveal unique A and B subgenomes

Heitkam

Weber

Walter

et al. 2019

Preprint

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Key words: Chenopodium quinoa, polyploidy, tandem repeat, satellite DNA, 5S rDNA, fluorescent in situ hybridisation (FISH), single molecule real-time (SMRT) reads Word count: 7,901 (total without abstract, references and figure legends), divided into 754 (introduction), 3,578 (results), 2,181 (discussion), 1,164 (experimental procedures) SUMMARY If two related plant species hybridise, their genomes are combined within a single nucleus, thereby forming an allotetraploid. How the emerging plant balances two co-evolved genomes is still a matter of ongoing research. Here, we focus on satellite DNA (satDNA), the fastest turn-over sequence class in eukaryotes, aiming to trace its emergence, amplification and loss during plant speciation and allopolyploidisation. As a model, we used Chenopodium quinoa Willd. (quinoa), an allopolyploid crop with 2n=4x=36 chromosomes. Quinoa originated by hybridisation of an unknown female American Chenopodium diploid (AA genome) with an unknown male Old World diploid species (BB genome), dating back 3.3 to 6.3 million years.Applying short read clustering to quinoa (AABB), C. pallidicaule (AA), and C. suecicum (BB) whole genome shotgun sequences, we classified their repetitive fractions, and identified and characterised seven satDNA families, together with the 5S rDNA model repeat. We show unequal satDNA amplification (two families) and exclusive occurrence (four families) in the AA and BB diploids by read mapping as well as Southern, genomic and fluorescent in situ hybridisation. As C. pallidicaule harbours a unique satDNA profile, we are able to exclude it as quinoa's parental species. Using quinoa long reads and scaffolds, we detected only limited evidence of interlocus homogenisation of satDNA after allopolyploidisation, but were able to exclude dispersal of 5S rRNA genes between subgenomes. Our results exemplify the complex route of tandem repeat evolution through Chenopodium speciation and allopolyploidisation, and may provide sequence targets for the identification of quinoa's progenitors.

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Draft genome of spinach and transcriptome diversity of 120 Spinacia accessions

Cited by 151 publications

References 68 publications

Integrated annotations and analyses of small RNA-producing loci from 47 diverse plants

Integrated annotations and analyses of small RNA-producing loci from 47 diverse plants

Gender‐specific expression of GIBBERELLIC ACID INSENSITIVE is critical for unisexual organ initiation in dioecious Spinacia oleracea

Satellite DNA landscapes after allotetraploidisation of quinoa (Chenopodium quinoa) reveal unique A and B subgenomes

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