Data set for phylogenetic tree and RAMPAGE Ramachandran plot analysis of SODs in Gossypium raimondii and G. arboreum

AbstractThe data presented in this paper is supporting the research article “Genome-Wide Analysis of Superoxide Dismutase Gene Family in Gossypium raimondii and G. arboreum” [1]. In this data article, we present phylogenetic tree showing dichotomy with two different clusters of SODs inferred by the Bayesian method of MrBayes (version 3.2.4), “Bayesian phylogenetic inference under mixed models” [2], Ramachandran plots of G. raimondii and G. arboreum SODs, the protein sequence used to generate 3D sructure of proteins and the template accession via SWISS-MODEL server, “SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information.” [3] and motif sequences of SODs identified by InterProScan (version 4.8) with the Pfam database, “Pfam: the protein families database” [4]

Genome-Wide Profiling of miRNAs and Other Small Non-Coding RNAs in the <em>Verticillium dahliae</em>–Inoculated Cotton Roots

<div><p>MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) are short (19–25 nucleotides) non-coding RNA molecules that have large-scale regulatory effects on development and stress responses in plants. Verticillium wilt is a vascular disease in plants caused by the fungal pathogen <em>Verticillium dahliae</em>. The objective of this study is to investigate the transcriptional profile of miRNAs and other small non-coding RNAs in Verticillium–inoculated cotton roots. Four small RNA libraries were constructed from mocked and infected roots of two cotton cultured species which are with different Verticillium wilt tolerance (‘Hai-7124’, <em>Gossypium barbadense</em> L., a Verticillium-tolerant cultivar, and ‘Yi-11’, <em>Gossypium hirsutum</em> L. a Verticillium-sensitive cultivar). The length distribution of obtained small RNAs was significantly different between libraries. There were a total of 215 miRNA families identified in the two cotton species. Of them 14 were novel miRNAs. There were >65 families with different expression between libraries. We also identified two trans-acting siRNAs and thousands of endogenous siRNA candidates, and hundred of them exhibited altered expression after inoculation of Verticillium. Interesting, many siRNAs were found with a perfect match with retrotransposon sequences, suggested that retrotransposons maybe one of sources for the generation of plant endogenous siRNAs. The profiling of these miRNAs and other small non-coding RNAs lay the foundation for further understanding of small RNAs function in the regulation of Verticillium defence responses in cotton roots.</p> </div

Plant MicroRNAs in Cross-Kingdom Regulation of Gene Expression

MicroRNAs (miRNAs) are a class of noncoding small RNAs, which play a crucial role in post-transcriptional gene regulation. Recently, various reports revealed that miRNAs could be transmitted between species to mediate cross-kingdom regulation by integrating into a specific target gene-mediated regulatory pathway to exert relevant biological functions. Some scholars and researchers have observed this as an attractive hypothesis that may provide a foundation for novel approaches in the diagnosis, prognosis, and treatment of disease. Meanwhile, others deem the mentioned results were obtained from a &ldquo;false positive effect&rdquo; of performed experiments. Here, we focus on several current studies concerning plant miRNA-mediated cross-kingdom regulation (from both fronts) and discuss the existing issues that need further consideration. We also discuss possible miRNA horizontal transfer mechanisms from one species to another and analyze the relationship between miRNA-mediated cross-kingdom regulation and coevolution during a long-term specific host&ndash;pathogen interaction

Identification of miRNAs and Their Targets in Cotton Inoculated with Verticillium dahliae by High-Throughput Sequencing and Degradome Analysis

MicroRNAs (miRNAs) are a group of endogenous small non-coding RNAs that play important roles in plant growth, development, and stress response processes. Verticillium wilt is a vascular disease in plants mainly caused by Verticillium dahliae Kleb., the soil-borne fungal pathogen. However, the role of miRNAs in the regulation of Verticillium defense responses is mostly unknown. This study aimed to identify new miRNAs and their potential targets that are involved in the regulation of Verticillium defense responses. Four small RNA libraries and two degradome libraries from mock-infected and infected roots of cotton (both Gossypium hirsutum L. and Gossypium barbadense L.) were constructed for deep sequencing. A total of 140 known miRNAs and 58 novel miRNAs were identified. Among the identified miRNAs, many were differentially expressed between libraries. Degradome analysis showed that a total of 83 and 24 genes were the targets of 31 known and 14 novel miRNA families, respectively. Gene Ontology analysis indicated that many of the identified miRNA targets may function in controlling root development and the regulation of Verticillium defense responses in cotton. Our findings provide an overview of potential miRNAs involved in the regulation of Verticillium defense responses in cotton and the interactions between miRNAs and their corresponding targets. The profiling of these miRNAs lays the foundation for further understanding of the function of small RNAs in regulating plant response to fungal infection and Verticillium wilt in particular

Distribution of miRNA counts over different tag abundance categories from the four libraries.

<p>Distribution of miRNA counts over different tag abundance categories from the four libraries.</p

Differentially expressed miRNAs between libraries.

<p>Gh-mock: mock-infected <i>G. hirsutum</i> roots; Gh-inft: Verticillium-infected <i>G. hirsutum</i> roots; Gb-mock: mock-infected <i>G. barbadense</i> roots; Gb-inft: Verticillium-infected <i>G. barbadense</i> roots.</p

The length distribution of small RNAs in <i>G. hirsutum</i> roots (A) and <i>G. barbadense</i> roots (B).

<p>Gh-mock: mock-infected <i>G. hirsutum</i> roots; Gh-inft: Verticillium-infected <i>G. hirsutum</i> roots; Gb-mock: mock-infected <i>G. barbadense</i> roots; Gb-inft: Verticillium-infected <i>G. barbadense</i> roots.</p

Summary statistics of small RNAs sequenced from roots.

<p>Summary statistics of small RNAs sequenced from roots.</p

The small RNAs with a perfect match to U75227.1|GBU75227 <i>G. barbadense</i> strain Giza 75 <i>copia</i> retrotransposon.

<p>The color represents abundance of the sequences.</p

Abundance of two trans-acting siRNA genes (<i>TAS3</i>).

<p>Abundance of two trans-acting siRNA genes (<i>TAS3</i>).</p