ShortStack: Comprehensive annotation and quantification of small RNA genes

Axtell, Michael J.

doi:10.1261/rna.035279.112

Cited by 396 publications

(427 citation statements)

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“…Genome-wide prediction of miRNAs was performed combining Shortstack version 3.4 (ref. 37) and an adapted version of the pipeline described in ref. 38, post-processed with the stringent criteria proposed by MiRBase 39 .…”

Section: Letter Research Methodsmentioning

confidence: 99%

The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution

Badouin¹,

Gouzy²,

Grassa³

et al. 2017

Nature

581

705

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The domesticated sunflower, Helianthus annuus L., is a global oil crop that has promise for climate change adaptation, because it can maintain stable yields across a wide variety of environmental conditions, including drought 1 . Even greater resilience is achievable through the mining of resistance alleles from compatible wild sunflower relatives 2,3 , including numerous extremophile species 4 . Here we report a high-quality reference for the sunflower genome (3.6 gigabases), together with extensive transcriptomic data from vegetative and floral organs. The genome mostly consists of highly similar, related sequences 5 and required single-molecule realtime sequencing technologies for successful assembly. Genome analyses enabled the reconstruction of the evolutionary history of the Asterids, further establishing the existence of a whole-genome triplication at the base of the Asterids II clade 6 and a sunflowerspecific whole-genome duplication around 29 million years ago 7 . An integrative approach combining quantitative genetics, expression and diversity data permitted development of comprehensive gene networks for two major breeding traits, flowering time and oil metabolism, and revealed new candidate genes in these networks. We found that the genomic architecture of flowering time has been shaped by the most recent whole-genome duplication, which suggests that ancient paralogues can remain in the same regulatory networks for dozens of millions of years. This genome represents a cornerstone for future research programs aiming to exploit genetic diversity to improve biotic and abiotic stress resistance and oil production, while also considering agricultural constraints and human nutritional needs 8,9 .As the only major crop domesticated in North America, with its sunlike inflorescence that inspired artists, the sunflower is both a social icon and a major research focus for scientists. In evolutionary biology, the Helianthus genus is a long-time model for hybrid speciation and adaptive introgression 10 . In plant science, the sunflower is a model for understanding solar tracking 11 and inflorescence development 12 .Despite this large interest, assembling its genome has been extremely difficult as it mainly consists of long and highly similar repeats. This complexity has challenged leading-edge assembly protocols for close to a decade 13 .To finally overcome this challenge, we generated a 102× sequencing coverage of the genome of the inbred line XRQ using 407 singlemolecule real-time (SMRT) cells on the PacBio RS II platform. Production of 32 million very long reads allowed us to generate a genome assembly that captures 3 gigabases (Gb) (80% of the estimated genome size) in 13,957 sequence contigs. Four high-density genetic maps were combined with a sequence-based physical map to build the sequences of the 17 pseudo-chromosomes that anchor 97% of the gene content (Fig.

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Section: Letter Research Methodsmentioning

confidence: 99%

The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution

Badouin¹,

Gouzy²,

Grassa³

et al. 2017

Nature

581

705

View full text Add to dashboard Cite

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“…Small RNAs were profiled by sRNA-seq in triplicate for each time point of the time course (using the same RNA on which RNA-seq was conducted). De novo annotation and quantification of siRNAs was then performed using ShortStack (Axtell, 2013;Shahid and Axtell, 2014) to determine regulatory siRNA clusters and identify siRNA producing loci. In total, between 16,731 and 27,495 siRNA loci were identified per time point (Supplemental Data Set 8), consistent with previous reports of siRNA cluster number in Arabidopsis aerial tissue (Axtell 2013).…”

Section: Endogenous Transcripts Protected From Sirna Silencingmentioning

confidence: 99%

“…De novo annotation and quantification of siRNAs was then performed using ShortStack (Axtell, 2013;Shahid and Axtell, 2014) to determine regulatory siRNA clusters and identify siRNA producing loci. In total, between 16,731 and 27,495 siRNA loci were identified per time point (Supplemental Data Set 8), consistent with previous reports of siRNA cluster number in Arabidopsis aerial tissue (Axtell 2013). On average 76.5% of the siRNA clusters overlap with transposable elements (TEs), accounting for 14,160, or 45.4% of all TEs.…”

Section: Endogenous Transcripts Protected From Sirna Silencingmentioning

confidence: 99%

Rapid Recovery Gene Downregulation during Excess-Light Stress and Recovery in Arabidopsis

et al. 2017

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Stress recovery may prove to be a promising approach to increase plant performance and, theoretically, mRNA instability may facilitate faster recovery. Transcriptome (RNA-seq, qPCR, sRNA-seq, and PARE) and methylome profiling during repeated excess-light stress and recovery was performed at intervals as short as 3 min. We demonstrate that 87% of the stress-upregulated mRNAs analyzed exhibit very rapid recovery. For instance, HSP101 abundance declined 2-fold every 5.1 min. We term this phenomenon rapid recovery gene downregulation (RRGD), whereby mRNA abundance rapidly decreases promoting transcriptome resetting. Decay constants (k) were modeled using two strategies, linear and nonlinear least squares regressions, with the latter accounting for both transcription and degradation. This revealed extremely short half-lives ranging from 2.7 to 60.0 min for 222 genes. Ribosome footprinting using degradome data demonstrated RRGD loci undergo cotranslational decay and identified changes in the ribosome stalling index during stress and recovery. However, small RNAs and 5ʹ-3ʹ RNA decay were not essential for recovery of the transcripts examined, nor were any of the six excess light-associated methylome changes. We observed recovery-specific gene expression networks upon return to favorable conditions and six transcriptional memory types. In summary, rapid transcriptome resetting is reported in the context of active recovery and cellular memory.

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“…Small RNA-seq reads were mapped onto genomic inverted repeats predicted by EMBOSS einverted 44 . miRNA loci were identified from the mapping results using ShortStack v1.2.3 45 . For homology-based prediction, 7,385 mature miRNA sequences of Viridiplantae species were retrieved from miRbase release 20 46 .…”

Section: Gene Prediction For Gene Predictions We Used Homology-basementioning

confidence: 99%

Genome of the pitcher plant Cephalotus reveals genetic changes associated with carnivory

et al. 2017

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Carnivorous plants exploit animals as a nutritional source and have inspired long-standing questions about the origin and evolution of carnivory-related traits. To investigate the molecular bases of carnivory, we sequenced the genome of the heterophyllous pitcher plant Cephalotus follicularis, in which we succeeded in regulating the developmental switch between carnivorous and non-carnivorous leaves. Transcriptome comparison of the two leaf types and gene repertoire analysis identified genetic changes associated with prey attraction, capture, digestion and nutrient absorption. Analysis of digestive fluid proteins from C. follicularis and three other carnivorous plants with independent carnivorous origins revealed repeated co-options of stress-responsive protein lineages coupled with convergent amino acid substitutions to acquire digestive physiology. These results imply constraints on the available routes to evolve plant carnivory.

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ShortStack: Comprehensive annotation and quantification of small RNA genes

Cited by 396 publications

References 50 publications

The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution

The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution

Rapid Recovery Gene Downregulation during Excess-Light Stress and Recovery in Arabidopsis

Genome of the pitcher plant Cephalotus reveals genetic changes associated with carnivory

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