High-Throughput Sequencing Reveals Diverse Sets of Conserved, Nonconserved, and Species-Specific miRNAs in Jute

Peng

et al. 2019

Heliyon

Panax ginseng C. A. Meyer is a precious traditional Chinese medicine that has been clinically used for over thousands of years. In general, ginseng needs to be prepared to ginseng decoction before taking it. MicroRNAs are a class of small (18–24 nt), single-stranded molecules that regulate gene expression at the post-transcriptional level. Considering that ginseng miRNAs may be bioactive compounds, we used Illumina high-throughput sequencing and quantitative real-time PCR (qRT-PCR) to validate the existence of miRNAs in fresh ginseng decoction which have been boiled at high temperature. Our previous studies have demonstrated that there are several miRNAs in fresh ginseng. The roots of fresh Panax ginseng were prepared according to routine methods, from which miRNAs were extracted and sequenced. A total of 43 miRNAs were identified from water decoction by Illumina high-throughput sequencing, belonging to 71 miRNA families. The target genes of these miRNAs were predicted by sequencing, and were annotated by GO, KEGG and Nr databases. The functions of these target genes mainly included plant hormone signal transduction, transcription regulation, macromolecular metabolism and auxin signaling. Nine highly expressed miRNAs (miR159, miR167, miR396, miR166, miR168, miR156, miR165, miR162 and miR394) were verified by qRT-PCR, and the results of Illumina high-throughput sequencing and qRT-PCR were consistent. Results from this study indicate that miRNAs remained stable in P. ginseng after high-temperature boiling. Additionally, Illumina high-throughput sequencing was superior in the acquisition of higher amount of small RNAs.

Section: Methodsmentioning

confidence: 99%

Verification of miRNAs in ginseng decoction by high-throughput sequencing and quantitative real-time PCR

Peng

et al. 2019

Heliyon

“…In terms of the global requirements for natural fiber crops, jute is second only to cotton ( Gossypium sp.) and provides ∼80% of the global bast fiber production (Islam et al., 2015; Islam et al., 2017). At present, although there are more than 100 species of jute (Islam et al., 2015), only two reproductively isolated jute species, Corchorus capsularis and Corchorus olitorius , are distributed in the tropical, subtropical and warm temperate regions of Asia and Africa (Saleem et al., 2020).…”

Section: Introductionmentioning

confidence: 99%

“…and provides ∼80% of the global bast fiber production (Islam et al., 2015; Islam et al., 2017). At present, although there are more than 100 species of jute (Islam et al., 2015), only two reproductively isolated jute species, Corchorus capsularis and Corchorus olitorius , are distributed in the tropical, subtropical and warm temperate regions of Asia and Africa (Saleem et al., 2020). Interestingly, C. olitorius has been domesticated in Africa as a leafy vegetable crop species and in India as a fiber crop species through the development of a preferred type from an African wild‐type (Kundu et al., 2013; Sarkar et al., 2019).…”

Section: Introductionmentioning

confidence: 99%

“…The increasing demand for jute worldwide can be attributed to its broad‐spectrum of applications (Kumari et al., 2019). For example, it grows easily and rapidly, has a high fiber and biomass yield per acre, and is resistant to insects, disease and low soil fertility (Islam et al., 2015). Moreover, jute can enrich the soil and clean the air by assimilating three times more CO 2 than an average tree.…”

Section: Introductionmentioning

confidence: 99%

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Multi‐omics provides new insights into the domestication and improvement of dark jute (Corchorus olitorius)

Yang

Tian

et al. 2022

The Plant Journal

SUMMARY Jute (Corchorus sp.) is the most important bast fiber crop worldwide; however, the mechanisms underlying domestication and improvement remain largely unknown. We performed multi‐omics analysis by integrating de novo sequencing, resequencing, and transcriptomic and epigenetic sequencing to clarify the domestication and improvement of dark jute Corchorus olitorius. We demonstrated that dark jute underwent early domestication and a relatively moderate genetic bottleneck during improvement breeding. A genome‐wide association study of 11 important agronomic traits identified abundant candidate loci. We characterized the selective sweeps in the two breeding stages of jute, prominently, soil salinity differences played an important role in environmental adaptation during domestication, and the strongly selected genes for improvement had an increased frequency of favorable haplotypes. Furthermore, we speculated that an encoding auxin/indole‐3‐acetic acid protein COS07g_00652 could enhance the flexibility and strength of the stem to improve fiber yield. Our study not only provides valuable genetic resources for future fiber breeding in jute, but also is of great significance for reviewing the genetic basis of early crop breeding.

“…Moreover, the availability of complete genome sequence for a number of these miRNAs encoding genes from diverse plant species has allowed a better understanding of miRNA evolution in plants (Zhu et al, 2011b). However, an analysis of high throughput sequencing data is a challenge, especially in the absence of native genome sequence (Islam et al, 2015). Finger millet a closely related species to Foxtail millet has its genome sequenced (Bennetzen et al, 2012) and the miRNAs have been identified using high throughput sequencing (Yi et al, 2013).…”

Section: Introductionmentioning

confidence: 99%

Identification of microRNAs and their targets in Finger millet by high throughput sequencing

Usha

Jyothi

Sharadamma

et al. 2015

Gene

a b s t r a c t a r t i c l e i n f oMicroRNAs are short non-coding RNAs which play an important role in regulating gene expression by mRNA cleavage or by translational repression. The majority of identified miRNAs were evolutionarily conserved; however, others expressed in a species-specific manner. Finger millet is an important cereal crop; nonetheless, no practical information is available on microRNAs to date. In this study, we have identified 95 conserved microRNAs belonging to 39 families and 3 novel microRNAs by high throughput sequencing. For the identified conserved and novel miRNAs a total of 507 targets were predicted. 11 miRNAs were validated and tissue specificity was determined by stem loop RT-qPCR, Northern blot. GO analyses revealed targets of miRNA were involved in wide range of regulatory functions. This study implies large number of known and novel miRNAs found in Finger millet which may play important role in growth and development.