In silico comparative analysis of EST-SSRs in three cotton genomes

In this study, expressed sequence tags- simple sequence repeat (EST-SSRs) were surveyed in three cotton genomes (Gossypium arboreum, Ga; Gossypium raimondii, Gr and Gossypium hirsutum, Gh). The frequency of EST-SSRs was highest in Gr, and motif type for hexanucleotide was obviously abundant in Gr. Trinucleotide repeats were the most abundant motif; AT and AG, AAG and ATC were the most frequent motifs for dinucleotide and trinucleotide, respectively. The repeat number was greatly diverse between the three genomes with the highest variation in Gh. AG and AAG had a high frequency both in homologue groups (HGs) with and without repeat number change between genomes. The range of repeat number change in each HG was wider in Gr-Gh. The annotation of the SSR-ESTs showed that more Gene Ontology (GO) items targeted by SSR-ESTs of Ga and Gr than those of Gh. This study gave us new insights into the difference between the three cotton genomes, which will be more helpful to understand the differentiation and evolution of the three genomes.Key words: Cotton, simple sequence repeat, expressed sequence tags, motif, gene ontology

Glassy carbon electrode modified with 7,7,8,8-tetracyanoquinodimethane and graphene oxide triggered a synergistic effect: low-potential amperometric detection of reduced glutathione.

A sensitive electrochemical sensor based on the synergistic effect of 7,7,8,8-tetracyanoquinodimethane (TCNQ) and graphene oxide (GO) for low-potential amperometric detection of reduced glutathione (GSH) in pH 7.2 phosphate buffer solution (PBS) has been reported. This is the first time that the combination of GO and TCNQ have been successfully employed to construct an electrochemical sensor for the detection of glutathione. The surface of the glassy carbon electrode (GCE) was modified by a drop casting using TCNQ and GO. Cyclic voltammetric measurements showed that TCNQ and GO triggered a synergistic effect and exhibited an unexpected electrocatalytic activity towards GSH oxidation, compared to GCE modified with only GO, TCNQ or TCNQ/electrochemically reduced GO. Three oxidation waves for GSH were found at −0.05, 0.1 and 0.5 V, respectively. Amperometric techniques were employed to detect GSH sensitively using a GCE modified with TCNQ/GO at −0.05 V. The electrochemical sensor showed a wide linear range from 0.25 to 124.3 μM and 124.3 μM to 1.67 mM with a limit of detection of 0.15 μM. The electroanalytical sensor was successfully applied towards the detection of GSH in an eye drop solution

Electrografting of amino-TEMPO on graphene oxide and electrochemically reduced graphene oxide for electrocatalytic applications.

4-Amino-2,2,6,6-tetramethyl-1-piperridine N-oxyl (4-amino-TEMPO), an electroactive nitroxide radical, was attached to the surface of graphene oxide (GO) and electrochemically reduced graphene oxide (ERGO) modified glassy carbon electrode by a simple, rapid and green electrografting method. The electroactive interfaces were analyzed by X-ray photoelectron spectroscopy (XPS) and cyclic voltammetry (CV). The calculated surface coverage for 4-amino-TEMPO is up to 1.55 × 10− 9 mol·cm− 2. The modified electroactive interface exhibited excellent electrocatalytic activity towards the electro-oxidation of reduced glutathione (GSH) and hydrogen peroxide (H2O2)

Facile synthesis of a nickel sulfide (NiS) hierarchical flower for the electrochemical oxidation of H2O2 and the methanol oxidation reaction (MOR).

The synthesis of a novel hierarchical flower-like NiS via a solvothermal method for the electrochemcial oxidation of H2O2 on a carbon paste electrode with high catalytic activity for the (MOR) in an alkaline medium has been reported. Novel nickel sulfide (NiS) hierarchical flower-like structures were characterized by X-ray diffraction, scanning electron microscope, and transmission electron microscopy. A carbon paste electrode was modified with the as-prepared hierarchical flower-like NiS, resulting in a high electrocatalytic activity toward the oxidation of H2O2. The NiS-modified electrode was used for H2O2 sensing, which was achieved over a wide linear range from 0.5 μMto1.37mM(I/μA =-0.19025 + 0.06094 C/mM) with a low limit of detection (LOD) of 0.3 μM and a limit of quantitation (LOQ) of 0.8 μM. The hierarchical flower-like NiS also exhibited a high electrocatalytic activity for the methanol oxidation reaction (MOR) in an alkaline medium with a high tolerance toward the catalyst-poisoning species generated during the MOR. The MOR proceeded via the direct electrooxidation of methanol on the oxidized NiS surface layer because the oxidation peak potential of the MOR was more positive than that of the oxidation of NiS

Lignin metabolism has a central role in the resistance of cotton to the wilt fungus Verticillium dahliae as revealed by RNA-Seq-dependent transcriptional analysis and histochemistry

The incompatible pathosystem between resistant cotton (Gossypium barbadense cv. 7124) and Verticillium dahliae strain V991 was used to study the cotton transcriptome changes after pathogen inoculation by RNA-Seq. Of 32 774 genes detected by mapping the tags to assembly cotton contigs, 3442 defence-responsive genes were identified. Gene cluster analyses and functional assignments of differentially expressed genes indicated a significant transcriptional complexity. Quantitative real-time PCR (qPCR) was performed on selected genes with different expression levels and functional assignments to demonstrate the utility of RNA-Seq for gene expression profiles during the cotton defence response. Detailed elucidation of responses of leucine-rich repeat receptor-like kinases (LRR-RLKs), phytohormone signalling-related genes, and transcription factors described the interplay of signals that allowed the plant to fine-tune defence responses. On the basis of global gene regulation of phenylpropanoid metabolism-related genes, phenylpropanoid metabolism was deduced to be involved in the cotton defence response. A closer look at the expression of these genes, enzyme activity, and lignin levels revealed differences between resistant and susceptible cotton plants. Both types of plants showed an increased level of expression of lignin synthesis-related genes and increased phenylalanine-ammonia lyase (PAL) and peroxidase (POD) enzyme activity after inoculation with V. dahliae, but the increase was greater and faster in the resistant line. Histochemical analysis of lignin revealed that the resistant cotton not only retains its vascular structure, but also accumulates high levels of lignin. Furthermore, quantitative analysis demonstrated increased lignification and cross-linking of lignin in resistant cotton stems. Overall, a critical role for lignin was believed to contribute to the resistance of cotton to disease

Gene prioritization of resistant rice gene against Xanthomas oryzae pv. oryzae by using text mining technologies

To effectively assess the possibility of the unknown rice protein resistant to Xanthomonas oryzae pv. oryzae, a hybrid strategy is proposed to enhance gene prioritization by combining text mining technologies with a sequence-based approach. The text mining technique of term frequency inverse document frequency is used to measure the importance of distinguished terms which reflect biomedical activity in rice before candidate genes are screened and vital terms are produced. Afterwards, a built-in classifier under the chaos games representation algorithm is used to sieve the best possible candidate gene. Our experiment results show that the combination of these two methods achieves enhanced gene prioritization

Unraveling cis and trans regulatory evolution during cotton domestication

Cis and trans regulatory divergence underlies phenotypic and evolutionary diversification. Relatively little is understood about the complexity of regulatory evolution accompanying crop domestication, particularly for polyploid plants. Here, we compare the fiber transcriptomes between wild and domesticated cotton (Gossypium hirsutum) and their reciprocal F1 hybrids, revealing genome-wide (~15%) and often compensatory cis and trans regulatory changes under divergence and domestication. The high level of trans evolution (54%–64%) observed is likely enabled by genomic redundancy following polyploidy. Our results reveal that regulatory variation is significantly associated with sequence evolution, inheritance of parental expression patterns, co-expression gene network properties, and genomic loci responsible for domestication traits. With respect to regulatory evolution, the two subgenomes of allotetraploid cotton are often uncoupled. Overall, our work underscores the complexity of regulatory evolution during fiber domestication and may facilitate new approaches for improving cotton and other polyploid plants

The Gossypium longicalyx genome as a resource for cotton breeding and evolution

Cotton is an important crop that has made significant gains in production over the last century. Emerging pests such as the reniform nematode have threatened cotton production. The rare African diploid species Gossypium longicalyx is a wild species that has been used as an important source of reniform nematode immunity. While mapping and breeding efforts have made some strides in transferring this immunity to the cultivated polyploid species, the complexities of interploidal transfer combined with substantial linkage drag have inhibited progress in this area. Moreover, this species shares its most recent common ancestor with the cultivated A-genome diploid cottons, thereby providing insight into the evolution of long, spinnable fiber. Here we report a newly generated de novo genome assembly of G. longicalyx. This high-quality genome leveraged a combination of PacBio long-read technology, Hi-C chromatin conformation capture, and BioNano optical mapping to achieve a chromosome level assembly. The utility of the G. longicalyx genome for understanding reniform immunity and fiber evolution is discussed

Chloroplast Genomes in Populus (Salicaceae): Comparisons From an Intensively Sampled Genus Reveal Dynamic Patterns of Evolution

The chloroplast is one of two organelles containing a separate genome that codes for essential and distinct cellular functions such as photosynthesis. Given the importance of chloroplasts in plant metabolism, the genomic architecture and gene content have been strongly conserved through long periods of time and as such are useful molecular tools for evolutionary inferences. At present, complete chloroplast genomes from over 4000 species have been deposited into publicly accessible databases. Despite the large number of complete chloroplast genomes, comprehensive analyses regarding genome architecture and gene content have not been conducted for many lineages with complete species sampling. In this study, we employed the genus Populus to assess how more comprehensively sampled chloroplast genome analyses can be used in understanding chloroplast evolution in a broadly studied lineage of angiosperms. We conducted comparative analyses across Populus in order to elucidate variation in key genome features such as genome size, gene number, gene content, repeat type and number, SSR (Simple Sequence Repeat) abundance, and boundary positioning between the four main units of the genome. We found that some genome annotations were variable across the genus owing in part from errors in assembly or data checking and from this provided corrected annotations. We also employed complete chloroplast genomes for phylogenetic analyses including the dating of divergence times throughout the genus. Lastly, we utilized re-sequencing data to describe the variations of pan-chloroplast genomes at the population level for P. euphratica. The analyses used in this paper provide a blueprint for the types of analyses that can be conducted with publicly available chloroplast genomes as well as methods for building upon existing datasets to improve evolutionary inference

The Gossypium longicalyx genome as a resource for cotton breeding and evolution

Cotton is an important crop that has made significant gains in production over the last century. Emerging pests such as the reniform nematode have threatened cotton production. The rare African diploid specie