Transcriptome assembly and annotation of johnsongrass (<i>Sorghum halepense</i>) rhizomes identify candidate rhizome‐specific genes

Ryder, Nathan; Dorn, Kevin M.; Huitsing, Mark; Adams, Micah; Ploegstra, Jeff; DeHaan, Lee; Larson, Steve; Tintle, Nathan L.

doi:10.1002/pld3.65

Cited by 8 publications

(8 citation statements)

References 21 publications

(28 reference statements)

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“…We found that only a small proportion of lowly expressed transcripts assembled from Bridger (11.1%), BinPacker (12.5%), SOAP denovo (6.7%), Trans-ABySS (10.3%), and Trinity (13.3%) supported by evidence of: 1) read depth > 2; 2) genome mapping rate > 50%; 3) CDS mapping rate > 60%; and 4) NR annotations (Additional file 1: Figure S3). This finding suggests the limitations of the current de novo transcriptome assemblers on the lowly expressed transcripts of tea plants, which is similar to those found in other plant species [53–55]. Nevertheless, the assembly accuracy of BinPacker, Bridger and Trinity are comparable and much higher than that of SOAP denovo and Trans-ABySS regarding the construction of lowly expressed transcripts.…”

Section: Resultssupporting

confidence: 77%

Optimized sequencing depth and de novo assembler for deeply reconstructing the transcriptome of the tea plant, an economically important plant species

Tong

Xia

et al. 2019

BMC Bioinformatics

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BackgroundTea is the oldest and among the world’s most popular non-alcoholic beverages, which has important economic, health and cultural values. Tea is commonly produced from the leaves of tea plants (Camellia sinensis), which belong to the genus Camellia of family Theaceae. In the last decade, many studies have generated the transcriptomes of tea plants at different developmental stages or under abiotic and/or biotic stresses to investigate the genetic basis of secondary metabolites that determine tea quality. However, these results exhibited large differences, particularly in the total number of reconstructed transcripts and the quality of the assembled transcriptomes. These differences largely result from limited knowledge regarding the optimized sequencing depth and assembler for transcriptome assembly of structurally complex plant species genomes.ResultsWe employed different amounts of RNA-sequencing data, ranging from 4 to 84 Gb, to assemble the tea plant transcriptome using five well-known and representative transcript assemblers. Although the total number of assembled transcripts increased with increasing sequencing data, the proportion of unassembled transcripts became saturated as revealed by plant BUSCO datasets. Among the five representative assemblers, the Bridger package shows the best performance in both assembly completeness and accuracy as evaluated by the BUSCO datasets and genome alignment. In addition, we showed that Bridger and BinPacker harbored the shortest runtimes followed by SOAPdenovo and Trans-ABySS.ConclusionsThe present study compares the performance of five representative transcript assemblers and investigates the key factors that affect the assembly quality of the transcriptome of the tea plants. This study will be of significance in helping the tea research community obtain better sequencing and assembly of tea plant transcriptomes under conditions of interest and may thus help to answer major biological questions currently facing the tea industry.

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Section: Resultssupporting

confidence: 77%

Optimized sequencing depth and de novo assembler for deeply reconstructing the transcriptome of the tea plant, an economically important plant species

Tong

Xia

et al. 2019

BMC Bioinformatics

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“…Therefore, no further research has been reported about these perennialism-related loci/genes. Recently, Ryder et al (2018) reported a set of 98 expressed contigs in Johnsongrass ( Sorghum halepense ) that are likely associated with rhizome development.…”

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confidence: 99%

The Genetics and Genome-Wide Screening of Regrowth Loci, a Key Component of Perennialism in Zea diploperennis

Ma¹,

Qiu²,

Raihan

et al. 2019

G3 Genes|Genomes|Genetics

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Perennialism is common among the higher plants, yet little is known about its inheritance. Previous genetic studies of the perennialism in Zea have yielded contradictory results. In this study, we take a reductionist approach by specifically focusing on one trait: regrowth (the plant’s ability to restart a new life cycle after senescence on the same body). To address this, six hybrids were made by reciprocally crossing perennial Zea diploperennis Iltis, Doebley & R. Guzman with inbred lines B73 and Mo17 and Rhee Flint, a heirloom variety, of Z . mays L. ssp. mays . All the F 1 plants demonstrated several cycles of growth, flowering, senescence and regrowth into normal flowering plants, indicating a dominant effect of the Z. diploperennis alleles. The regrowability ( i.e. , the plants’ ability to regrow after senescence) was stably transmitted to progeny of the hybrids. Segregation ratios of regrowth in the F 2 generations are consistent with the trait controlled by two dominant, complementary loci, but do not exclude the influence of other modifiers or environment. Genome-wide screening with genotyping-by-sequencing technology indicated two major regrowth loci, regrowth 1 ( reg1 ) and regrowth 2 ( reg2 ), were on chromosomes 2 and 7, respectively. These findings lay the foundation for further exploration of the molecular mechanism of regrowth in Z. diploperennis . Importantly, our data indicate that there is no major barrier to transferring this trait into maize or other grass crops for perennial crop development with proper technology, which enhances sustainability of grain crop production in an environmentally friendly way.

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“…One of the remarkable prosperity factors of Johnsongrass is selfpollination (Dweikat 2005). It blooms 46 days after emergence and produces up to 80000 seed per plant in a single season which remain viable for up to 10 years in the soil (McWhorter 1961;Ryder et al 2018). Johnsongrass has a broad seed depth germination rate ranging from 64% at 1 cm to 30% at 20 cm depth.…”

Section: Johnsongrass As Invasive Plant Speciesmentioning

confidence: 99%

“…Its bioinformatic coding sequence analysis between Thinopyrum intermedium, a rhizomatous and perennial grass, and the seasonal nonrhizomatous S. bicolor resulted in the identification of 98 candidate sequences involved in Johnsongrass rhizome development. Among these, the most expressed protein families belong to ZIM (zinc finger inflorescence meristem) family, DNA binding proteins, transcription factors and the Armadillo (ARM)repeat superfamily which have been shown to play crucial roles in hormone signaling, development by exhibiting a differential expression pattern during environmental stress responses (Ryder et al 2018). Similarly, the analysis of Johnsongrass ancestor S. propinquum promoter regions shows an enrichment of cisregulatory elements involved in abscisic acid (ABA) and gibberellic acid (GA) responses, suggesting a cross-talk between those hormones in rhizomes.…”

Section: Johnsongrass As Invasive Plant Speciesmentioning

confidence: 99%

“…The earliest introduction occurred around 1830 through contaminated cotton seeds from Egypt successfully invading agricultural pastures and natural plains in South Carolina (McWhorter 1971). Johnsongrass is classifies as weed in over 53 countries occurring in 30 different crops (Masood et al 2017;Ryder et al 2018). Dense Johnsongrass populations in crop fields have been shown to impact the yield quantity causing substantial damage to agriculture.…”

Section: Introductionmentioning

confidence: 99%

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Invasive Johnsongrass, a threat to native grasslands and agriculture

Klein

Smith

2020

Biologia

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Among the weedy plant species, Johnsongrass (Sorghum halepense) is one of the most destructive. Johnsongrass has invaded new habitats beyond its native Eurasian origin by outcompeting native flora and cultivated crops. The Johnsongrass habitat is expanding continuously due to clonal and self-pollinating reproduction strategy, accelerated growth and the progressing climate change. As a result, Johnsongrass has reduced native plant diversity in grasslands and inflicted economic damage to agriculture on every continent. Johnsongrass is a growing threat to crop production, as it serves as a refuge for a variety of agricultural pests and plant viral diseases. Over the past decades, herbicides extensively applied to control Johnsongrass have boosted selection pressure, resulting in the independent evolution of herbicide-resistant ecotypes across multiple locations. The apparent threat to native flora and agriculture caused by the invasive Johnsongrass is a subject to a long and ongoing research. This review provides a historical and research overview on Johnsongrass expansion, its current as well future impact particularly on North American and European grasslands and agriculture.

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Transcriptome assembly and annotation of johnsongrass (Sorghum halepense) rhizomes identify candidate rhizome‐specific genes

Cited by 8 publications

References 21 publications

Optimized sequencing depth and de novo assembler for deeply reconstructing the transcriptome of the tea plant, an economically important plant species

Optimized sequencing depth and de novo assembler for deeply reconstructing the transcriptome of the tea plant, an economically important plant species

The Genetics and Genome-Wide Screening of Regrowth Loci, a Key Component of Perennialism in Zea diploperennis

Invasive Johnsongrass, a threat to native grasslands and agriculture

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