Characteristics of assembled transcripts and unigenes.

<p>Characteristics of assembled transcripts and unigenes.</p

Ploidy level estimation of the reference <i>M. anguillicaudatus</i> using the five diagnostic ESR-SSR markers^a.

<p>Ploidy level estimation of the reference <i>M. anguillicaudatus</i> using the five diagnostic ESR-SSR markers<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0195829#t004fn001" target="_blank">^a</a>.</p

Results of ploidy identification for randomly collected individuals from Liangzi Lake, China, using two separate methods: EST-SSR loci analysis and flow cytometry^a.

<p>Results of ploidy identification for randomly collected individuals from Liangzi Lake, China, using two separate methods: EST-SSR loci analysis and flow cytometry<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0195829#t005fn001" target="_blank">^a</a>.</p

Development of novel EST-SSR markers for ploidy identification based on <i>de novo</i> transcriptome assembly for <i>Misgurnus anguillicaudatus</i>

<div><p>The co-existence of several ploidy types in natural populations makes the cyprinid loach <i>Misgurnus anguillicaudatus</i> an exciting model system to study the genetic and phenotypic consequences of ploidy variations. A first step in such effort is to identify the specific ploidy of an individual. Currently popular methods of karyotyping via cytological preparation or flow cytometry require a large amount of tissue (such as blood) samples, which can be damaging or fatal to the fishes. Here, we developed novel microsatellite markers (SSR markers) from <i>M</i>. <i>anguillicaudatus</i> and show that they can effectively discriminate ploidy using samples collected in a minimally invasive way. Specifically, we generated whole genome transcriptomes from multiple <i>M</i>. <i>anguillicaudatus</i> using the Illumina paired-end sequencing. Approximately 150 million raw reads were assembled into 76,544 non-redundant unigenes. A total of 8,194 potential SSR markers were identified. We selected 98 pairs with more than five tandem repeats for further assays. Out of 45 putative EST-SSR markers that successfully amplified and harbored polymorphism in diploids, 11 markers displayed high variability in tetraploids. We further demonstrate that a set of five EST-SSR markers selected from these are sufficient to distinguish ploidy levels, by first validating them on 69 reference specimens with known ploidy levels and then subsequently using fresh-collected 96 ploidy-unknown specimens. The results from EST-SSR markers are highly concordant with those from independent flow cytometry analysis. The novel EST-SSR markers developed here should facilitate genetic studies of polyploidy in the emerging model system <i>M</i>. <i>anguillicaudatus</i>.</p></div

Development of novel EST-SSR markers for ploidy identification based on <i>de novo</i> transcriptome assembly for <i>Misgurnus anguillicaudatus</i> - Fig 2

<p><b>Examples of microsatellite banding patterns of the reference diploid, triploid and tetraploid <i>M</i>. <i>anguillicaudatus</i> at loci MATS2-33, MATS2-48, MATS2-55, MATS2-65 and MATS2-74, respectively (a) and the quantitative values corresponding to each allele (from the bottom up) (b)</b>. Coordinates on <i>X</i>-axis (b) refer to the tested samples corresponding to electrophoretic profiles (a), whereas coordinates on the <i>Y</i>-axis refers to the allelic quantitative values at each locus provided by the Bio-Rad Quantity One^® Bands software.</p

Additional file 1: of Synthesis and Supercapacitor Performance of Polyaniline/Nitrogen-Doped Ordered Mesoporous Carbon Composites

Figure S1. FT-IR spectra of PANI/NOMC-x materials. Figure S2. CV curves of PANI/NOMC-0.2 (a), PANI/NOMC-1 (c), PANI/NOMC-2 (e), and PANI/NOMC-4 (g) at different scan rates; galvanostatic charge/discharge curves of PANI/NOMC-0.2 (b), PANI/NOMC-1 (d), PANI/NOMC-2 (f), and PANI/NOMC-4 (h) at different current densities. Figure S3. N2 adsorption–desorption isotherms of NOMC, PANI/NOMC-0.2, PANI/NOMC-0.5, PANI/NOMC-1, PANI/NOMC-2, and PANI/NOMC-4 (a); pore size distribution of PANI/NOMC-0.2, PANI/NOMC-1, and PANI/NOMC-2. (DOCX 3025 kb

Image_2_Mining key genes related to root morphogenesis through genome-wide identification and expression analysis of RR gene family in citrus.pdf

Morphogenesis of root is a vital factor to determine the root system architecture. Cytokinin response regulators (RRs) are the key transcription factors in cytokinin signaling, which play important roles in regulating the root morphogenesis. In this study, 29 RR proteins, including 21 RRs and 8 pseudo RRs, were identified from the genome of citrus, and termed as CcRR1-21 and CcPRR1-8, respectively. Phylogenetic analysis revealed that the 29 CcRRs could be classified into four types according to their representative domains. Analysis of cis-elements of CcRRs indicated that they were possibly involved in the regulation of growth and abiotic stress resistance in citrus. Within the type A and type B CcRRs, CcRR4, CcRR5, CcRR6 and CcRR16 highly expressed in roots and leaves, and dramatically responded to the treatments of hormones and abiotic stresses. CcRR2, CcRR10, CcRR14 and CcRR19 also highly expressed in roots under different treatments. Characteristic analysis revealed that the above 8 CcRRs significantly and differentially expressed in the three zones of root, suggesting their functional differences in regulating root growth and development. Further investigation of the 3 highly and differentially expressed CcRRs, CcRR5, CcRR10 and CcRR14, in 9 citrus rootstocks showed that the expression of CcRR5, CcRR10 and CcRR14 was significantly correlated to the length of primary root, the number of lateral roots, and both primary root and the number of lateral roots, respectively. Results of this study indicated that CcRRs were involved in regulating the growth and development of the root in citrus with different functions among the members.</p

Blue Light Simultaneously Induces Peel Anthocyanin Biosynthesis and Flesh Carotenoid/Sucrose Biosynthesis in Mango Fruit

Previous studies focused on the effects of light on fruit appearance, especially the peel color. However, the effect of light on fruit internal quality and the underlying mechanisms are unclear. In this study, we analyzed the effects of blue light on the appearance and internal quality of mango fruit (Mangifera indica L.). Blue light simultaneously induced peel anthocyanin and flesh sucrose/carotenoid biosynthesis in mango fruit. Analyses of co-expression networks and gene expression trends in mango fruit peel and flesh identified candidate genes, including transcription factor genes, involved in blue light-regulated anthocyanin, carotenoid, and sucrose biosynthesis pathways. Key blue light signaling-related genes (MiCRY and MiHY5) and blue light-triggered phytohormones were involved in these pathways. Additionally, there were common and tissue-specific pathways for the blue light-promoted accumulation of anthocyanins, carotenoids, and sucrose. Our results provide new insights into the regulatory effects of light on the appearance and internal quality of mango fruit

Image_1_Mining key genes related to root morphogenesis through genome-wide identification and expression analysis of RR gene family in citrus.pdf

Morphogenesis of root is a vital factor to determine the root system architecture. Cytokinin response regulators (RRs) are the key transcription factors in cytokinin signaling, which play important roles in regulating the root morphogenesis. In this study, 29 RR proteins, including 21 RRs and 8 pseudo RRs, were identified from the genome of citrus, and termed as CcRR1-21 and CcPRR1-8, respectively. Phylogenetic analysis revealed that the 29 CcRRs could be classified into four types according to their representative domains. Analysis of cis-elements of CcRRs indicated that they were possibly involved in the regulation of growth and abiotic stress resistance in citrus. Within the type A and type B CcRRs, CcRR4, CcRR5, CcRR6 and CcRR16 highly expressed in roots and leaves, and dramatically responded to the treatments of hormones and abiotic stresses. CcRR2, CcRR10, CcRR14 and CcRR19 also highly expressed in roots under different treatments. Characteristic analysis revealed that the above 8 CcRRs significantly and differentially expressed in the three zones of root, suggesting their functional differences in regulating root growth and development. Further investigation of the 3 highly and differentially expressed CcRRs, CcRR5, CcRR10 and CcRR14, in 9 citrus rootstocks showed that the expression of CcRR5, CcRR10 and CcRR14 was significantly correlated to the length of primary root, the number of lateral roots, and both primary root and the number of lateral roots, respectively. Results of this study indicated that CcRRs were involved in regulating the growth and development of the root in citrus with different functions among the members.</p

Blue Light Simultaneously Induces Peel Anthocyanin Biosynthesis and Flesh Carotenoid/Sucrose Biosynthesis in Mango Fruit

Previous studies focused on the effects of light on fruit appearance, especially the peel color. However, the effect of light on fruit internal quality and the underlying mechanisms are unclear. In this study, we analyzed the effects of blue light on the appearance and internal quality of mango fruit (Mangifera indica L.). Blue light simultaneously induced peel anthocyanin and flesh sucrose/carotenoid biosynthesis in mango fruit. Analyses of co-expression networks and gene expression trends in mango fruit peel and flesh identified candidate genes, including transcription factor genes, involved in blue light-regulated anthocyanin, carotenoid, and sucrose biosynthesis pathways. Key blue light signaling-related genes (MiCRY and MiHY5) and blue light-triggered phytohormones were involved in these pathways. Additionally, there were common and tissue-specific pathways for the blue light-promoted accumulation of anthocyanins, carotenoids, and sucrose. Our results provide new insights into the regulatory effects of light on the appearance and internal quality of mango fruit