Genetic diversity and population structure of core watermelon (Citrullus lanatus) genotypes using DArTseq-based SNPs

Watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai var. lanatus] is an economically important vegetable belonging to the Cucurbitaceae family. Genotypes that exhibit agronomically important traits are selected for the development of elite cultivars. Understanding the genetic diversity and the genotype population structure based on molecular markers at the genome level can speed up the utilization of diverse genetic resources for varietal improvement. In the present study, we carried out an analysis of genetic diversity based on 3882 SNP markers across 37 core watermelon genotypes, including the most widely used watermelon varieties and wild watermelon. Based on the SNP genotyping data of the 37 watermelon genotypes screened, gene diversity and polymorphism information content values across chromosomes varied between 0.03–0.5 and 0.02–0.38, with averages of 0.14 and 0.13, respectively. The two wild watermelon genotypes were distinct from cultivated varieties and the remaining 35 cultivated genotypes were differentiated into three major clusters: 20 genotypes were grouped in cluster I; 11 genotypes were grouped in cluster II; three advanced breeding lines of yellow fruit flesh and genotype SW043 were grouped in cluster III. The results from neighbour-joining dendrogram, principal coordinate analysis and STRUCTURE analysis approaches were consistent, and the grouping of genotypes was generally in agreement with their origins. Here we reveal the genetic relationships among the core watermelon genotypes maintained at the Jiangsu Academy of Agricultural Sciences, China. The molecular and phenotypic characterization of the existing core watermelon genotypes, together with specific agronomic characteristics, can be utilized by researchers and breeders for future watermelon improvement

Les découvertes récentes de statues de Sengqie et le culte de Sengqie

Sengqie was a monk of the Tang period from Heguo in Central Asia. After Sengqie died in AD 710, in a posture of meditation, his remains were buried in the Puguang wang si monastery in Sizhou. Following a series of evidential miracles, including the appearance of an image of the Eleven-faced Guanyin and repeated supernatural manifestations, Sengqie was canonized as the Grand Master of Universal Awakening Great Saint of Sizhou. By Song and Yuan times he had become the object of a popular cult. On the gilded wood-carved statue that was excavated in the crypt of the stūpa of Xianyan si monastery in Ruian (Zhejiang) is engraved the inscription "Grand Master of Universal Awakening Great Saint of Sizhou. " In Song and Yuan times many monasteries contained a Sengqie Hall in which Sengqie heshang, Monk Sengqie, was worshipped. In recent years, statues of Sengqie have been discovered in stūpa-foundations in many places. For example, the stūpa of Ruiguangsi monastery in Suzhou; the stūpa of Wanfo si monastery in Jinhua, the Baixiang ta pagoda in Wenzhou, the Tianfeng ta pagoda in Ningbo (Zhejiang), and the stūpa of Xingjiao si monastery in Shanghai all have statues of the Great Saint of Sizhou Sengqie sitting upright with his eyes closed, in an attitude of meditation. These images constitute material evidence of the popular cult of Sengqie in Tang and Song times.Pingfang Xu, Bujard Marianne. Les découvertes récentes de statues de Sengqie et le culte de Sengqie. In: Cahiers d'Extrême-Asie, vol. 10, 1998. Culte des sites et culte des saints en Chine. pp. 393-410

RNA-Seq Uncovers SNPs and Alternative Splicing Events in Asian Lotus (Nelumbo nucifera).

RNA-Seq is an efficient way to comprehensively identify single nucleotide polymorphisms (SNPs) and alternative splicing (AS) events from the expressed genes. In this study, we conducted transcriptome sequencing of four Asian lotus (Nelumbo nucifera) cultivars using Illumina HiSeq2000 platform to identify SNPs and AS events in lotus. A total of 505 million pair-end RNA-Seq reads were generated from four cultivars, of which 86% were mapped to the lotus reference genome. Using the four sets of data together, a total of 357,689 putative SNPs were identified with an average density of one SNP per 2.2 kb. These SNPs were located in 1,253 scaffolds and 15,016 expressed genes. A/G and C/T were the two major types of SNPs in the Asian lotus transcriptome. In parallel, a total of 177,540 AS events were detected in the four cultivars and were distributed in 64% of the expressed genes of lotus. The predominant type of AS events was alternative 5' first exon, which accounted for 41.2% of all the observed AS events, and exon skipping only accounted for 4.3% of all AS. Gene Ontology analysis was conducted to analyze the function of the genes containing SNPs and AS events. Validation of selected SNPs and AS events revealed that 74% of SNPs and 80% of AS events were reliable, which indicates that RNA-Seq is an efficient approach to uncover gene-associated SNPs and AS events. A large number of SNPs and AS events identified in our study will facilitate further genetic and functional genomics research in lotus

Engineering CRISPR interference system in Klebsiella pneumoniae for attenuating lactic acid synthesis

Abstract Background Klebsiella pneumoniae is a promising industrial species for bioproduction of bulk chemicals such as 1,3-propanediol, 2,3-butanediol and 3-hydroxypropionic acid (3-HP). However, lactic acid is a troublesome by-product when optimizing for 3-HP production. Therefore, it is highly desirable to minimize lactic acid. Results Here, we show that lactic acid synthesis can be largely blocked by an engineered CRISPR interference (CRISPRi) system in K. pneumoniae. EGFP was recruited as a reporter of this CRISPRi system. Fluorescence assay of this CRISPRi system showed that enhanced green fluorescent protein (EGFP) expression level was repressed by 85–90%. To further test this CRISPRi system, guide RNAs were designed to individually or simultaneously target four lactate-producing enzyme genes. Results showed that all lactate-producing enzyme genes were significantly repressed. Notably, d-lactate dehydrogenase (ldhA) was shown to be the most influential enzyme for lactic acid formation in micro-aerobic conditions, as inhibiting ldhA alone led to lactic acid level similar to simultaneously repressing four genes. In shake flask cultivation, the strain coexpressing puuC (an aldehyde dehydrogenase catalyzing 3-hydroxypropionaldehyde to 3-HP) and dCas9-sgRNA inhibiting ldhA produced 1.37-fold 3-HP relative to the reference strain. Furthermore, in bioreactor cultivation, this CRISPRi strain inhibiting ldhA produced 36.7 g/L 3-HP, but only generated 1 g/L lactic acid. Clearly, this engineered CRISPRi system largely simplified downstream separation of 3-HP from its isomer lactic acid, an extreme challenge for 3-HP bioprocess. Conclusions This study offers a deep understanding of lactic acid metabolism in diverse species, and we believe that this CRISPRi system will facilitate biomanufacturing and functional genome studies of K. pneumoniae or beyond

Number and type of SNPs identified from the Asian lotus transcriptome.

<p>(A) Venn diagram of SNPs discovered from the four cultivars. (B) Comparison of SNP number between our study (I) and the previous study of Zhang et al. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0125702#pone.0125702.ref016" target="_blank">16</a>] who discovered SNP by RAD-Seq technology (II). (C) Summary of SNP types identified from the Asian lotus transcriptome.</p

Classification of identified SNPs.

<p>Intergenic SNPs were identified from regions between genes, while Downstream and Upstream represents SNPs identified from regions of downstream and upstream of the genes.</p><p>Classification of identified SNPs.</p

Summary of gene number identified from the Asian lotus transcriptome.

<p>(A) Venn diagram of genes expressed in the four cultivars. (B) Correlations between detected genes number and reads number in the four cultivars.</p