Identification of Known and Novel microRNAs and Their Targets in Peach (<i>Prunus persica</i>) Fruit by High-Throughput Sequencing

<div><p>MicroRNAs (miRNAs) are a group of non-coding RNAs that have functions in post-transcriptional gene regulation in plants. Although the most important economic component of peach trees (<i>Prunus persica</i>) is the fruit, not much is known about miRNAs in this organ. In this study, miRNAs and their targets were identified and characterized from libraries of small RNAs of peach fruit through Solexa based-sequencing and bioinformatics approaches. A total of 557 known peach miRNAs belonging to 34 miRNA families were identified, and some of these miRNAs were found to be highly conserved in at least four other plant species. Using the most current criteria for miRNA annotation, 275 putative novel miRNAs were predicted, and the sequencing frequencies of these novel miRNAs were less than those of the conserved miRNAs. In total, 3959 and 1614 target genes for 349 known and 193 novel miRNAs, respectively, were predicted with the criteria that a single target gene can be targeted by different miRNAs and that a single miRNA can also have a large number of target genes. Three targets were even found to be targeted by 13 novel miRNAs that contained the same complete miRNA sequence at different locations and had different scaffolds. The proteins predicted to be targeted by the miRNAs identified in this study encompass a wide range of transcription factors and are involved in many biological processes and pathways, including development, metabolism, stress responses and signal transduction. A total of 115 and 101 target genes were identified to be cleaved by 60 known miRNAs and 27 novel miRNAs through degradome sequencing, respectively. These miRNAs induce cleavage of their targets precisely at the position between nucleotides 10 and 11 of the miRNA sequences from the 5’ to the 3’ end. Thirty conserved miRNAs and 19 novel miRNAs exhibited differential expression profiles in the peach, and the expression patterns of some miRNAs appeared to be tissue- or developmental stage-specific. The findings of this study provide an important basis for the analysis of miRNAs, their targets and the functions of these targets in peach fruit.</p></div

Statistical analysis of first nucleotide of 18- to 25-nt small RNAs in a library of the small RNAs of peach fruit.

<p>Statistical analysis of first nucleotide of 18- to 25-nt small RNAs in a library of the small RNAs of peach fruit.</p

Summary of small RNA reads obtained by Illumina sequencing from a library of the small RNAs of peach fruit.

<p>Summary of small RNA reads obtained by Illumina sequencing from a library of the small RNAs of peach fruit.</p

MXene-Based Electrode with Enhanced Pseudocapacitance and Volumetric Capacity for Power-Type and Ultra-Long Life Lithium Storage

Powerful yet thinner lithium-ion batteries (LIBs) are eagerly desired to meet the practical demands of electric vehicles and portable electronic devices. However, the use of soft carbon materials in current electrode design to improve the electrode conductivity and stability does not afford high volumetric capacity due to their low density and capacity for lithium storage. Herein, we report a strategy leveraging the MXene with superior conductivity and density to soft carbon as matrix and additive material for comprehensively enhancing the power capability, lifespan, and volumetric capacity of conversion-type anode. A kinetics favorable 2D nanohybrid with high conductivity, compact density, accumulated pseudocapacitance, and diffusion-controlled behavior is fabricated by coupling Ti₃C₂ MXene with high-density molybdenum carbide for fast lithium storage over 300 cycles with high capacities. By replacing the carbonaceous conductive agent with Ti₃C₂ MXene, the electrodes with better conductivity and dramatically reduced thickens could be further manufactured to achieve 37–40% improvement in capacity retention and ultra-long life of 5500 cycles with extremely slow capacity loss of 0.002% per cycle at high current rates. Ultrahigh volumetric capacity of 2460 mAh cm^–3 could be attained by such MXene-based electrodes, highlighting the great promise of MXene in the development of high-performance LIBs

Relative expression levels of some novel miRNAs in peach fruit.

<p>The relative expression levels of novel miRNAs in fruit tissue at five developmental stages were investigated by qRT-PCR and calculated using the 2^-ΔΔCT method. The x-axes show the fruit samples obtained 35, 55, 75, 90, and 105 days after full bloom. The vertical bars represent the ±SE of each mean value (n = 9).</p

Relative expression levels of some known miRNAs in peach.

<p>The relative expression levels of known miRNAs in different tissues at five developmental stages were investigated by qRT-PCR analysis and calculated using the 2^-ΔΔCT method. The x-axes show the leaf, fruit, and phloem samples obtained 35, 55, 75, 90, and 105 days after full bloom (DAFB). The vertical bars represent the ±SE of each mean value (n = 9).</p

Genome-wide identification and classification of <i>MYB</i> superfamily genes in peach

<div><p>The MYB transcription factor superfamily is one of the largest superfamilies modulating various biological processes in plants. Over the past few decades, many <i>MYB</i> superfamily genes have been identified and characterized in some plant species. However, genes belonging to the MYB superfamily in peach (<i>Prunus persica</i>) have not been comprehensively identified and characterized although the genome sequences of peach were released several years ago. In total, this study yielded a set of 256 <i>MYB</i> superfamily genes that was divided into five subfamilies: the R2R3-MYB (2R-MYB), R1R2R3-MYB (3R-MYB), MYB-related (1R-MYB), 4R-MYB, and Atypical-MYB subfamilies. These subfamilies contained 128, 4, 109, 1, and 14 members, respectively. The 128 R2R3-MYB subfamily genes in peach were further clustered into 35 groups, and the 109 MYB-related subfamily genes were further clustered into 6 groups: the CCA1-like, CPC-like, TBP-like, I-box-binding-like, R-R-type, and Peach-specific groups. The motif compositions and exon/intron structures within each group within the R2R3-MYB or MYB-related subfamily in peach were highly conserved. The logo sequences of the R2 and R3 repeats of R2R3-MYB subfamily members were highly conserved with those in these repeats of several other plant species. Except for 48 novel peach-specific <i>MYB</i> genes, the remaining 208 out of 256 <i>MYB</i> genes in peach were conserved with the corresponding 198 <i>MYB</i> genes in <i>A</i>. <i>thaliana</i>. Additionally, the 256 <i>MYB</i> genes unevenly distributed on chromosomes 1 to 8 of the peach genome. Eighty-one orthologous pairs of peach/<i>A</i>. <i>thaliana MYB</i> genes were identified among 256 <i>MYB</i> genes in peach and 198 <i>MYB</i> genes in <i>A</i>. <i>thaliana</i> in this study. In addition, 146 pairs of paralogous <i>MYB</i> genes were identified on the eight chromosomes of peach. The expression levels of some of the 51 <i>MYB</i> genes selected for qRT-PCR analysis decreased or increased with red-fleshed fruit development, while the expression patterns of some genes followed no clear rules over the five developmental stages of fruits. This study laid the foundation for further functional analysis of <i>MYB</i> superfamily genes in peach and enriched the knowledge of <i>MYB</i> superfamily genes in plant species.</p></div

Proportion of nucleotide bias at each position within novel miRNAs in a library of the small RNAs of peach fruit.

<p>Proportion of nucleotide bias at each position within novel miRNAs in a library of the small RNAs of peach fruit.</p

Proportion of first nucleotide bias within novel miRNAs of the same length in a library of the small RNAs of peach fruit.

<p>Proportion of first nucleotide bias within novel miRNAs of the same length in a library of the small RNAs of peach fruit.</p

Motif distribution of peach R2R3-MYB subfamily and R1R2R3-MYB (3R-MYB) subfamily proteins.

<p>Motifs of the R2R3-MYB and R1R2R3-MYB subfamily proteins were analyzed using the MEME web server. Fifteen kinds of colored blocks represent 15 kinds of motifs. The length of the gray line indicates the length of a sequence relative to that of all the other sequences. The position of each block indicates the location of a motif with a matching sequence. The red brace on the right marks the members of each group of the R2R3-MYB and R1R2R3-MYB subfamilies in peach.</p