Qixing Huang

Proteomics Profiling Reveals Carbohydrate Metabolic Enzymes and 14-3-3 Proteins Play Important Roles for Starch Accumulation during Cassava Root Tuberization.

Cassava is one of the most important root crops as a reliable source of food and carbohydrates. Carbohydrate metabolism and starch accumulation in cassava storage root is a cascade process that includes large amounts of proteins and cofactors. Here, comparative proteomics were conducted in cassava root at nine developmental stages. A total of 154 identified proteins were found to be differentially expressed during starch accumulation and root tuberization. Many enzymes involved in starch and sucrose metabolism were significantly up-regulated, and functional classification of the differentially expressed proteins demonstrated that the majority were binding-related enzymes. Many proteins were took part in carbohydrate metabolism to produce energy. Among them, three 14-3-3 isoforms were induced to be clearly phosphorylated during storage root enlargement. Overexpression of a cassava 14-3-3 gene in Arabidopsis thaliana confirmed that the older leaves of these transgenic plants contained higher sugar and starch contents than the wild-type leaves. The 14-3-3 proteins and their binding enzymes may play important roles in carbohydrate metabolism and starch accumulation during cassava root tuberization. These results not only deepened our understanding of the tuberous root proteome, but also uncovered new insights into carbohydrate metabolism and starch accumulation during cassava root enlargement.

Comparative Physiological and Transcriptomic Analyses Reveal the Actions of Melatonin in the Delay of Postharvest Physiological Deterioration of Cassava

Melatonin plays important roles in various aspects of biological processes. However, it is less known on the effects and mechanism of melatonin on the postharvest physiological deterioration (PPD) process of cassava, which largely restricts the potential of cassava as a food and industrial crop. In this study, we found that exogenous application of melatonin significantly delayed PPD of cassava tuberous roots by reducing H2O2 content and improving activities of catalase and peroxidase. Moreover, 3425 differentially expressed genes by melatonin during the PPD process were identified by transcriptomic analysis. Several pathways were markedly affected by melatonin treatments, including metabolic-, ion homeostasis-, and enzyme activity-related processes. Further detailed analysis revealed that melatonin acted through activation of ROS-scavenging and ROS signal transduction pathways, including antioxidant enzymes, calcium signaling, MAPK cascades, and transcription factors at early stages. Notably, the starch degradation pathway was also activated at early stages, whereas it was repressed by melatonin at middle and late stages, thereby indicating its regulatory role in starch metabolism during PPD. Taken together, this study yields new insights into the effect and underlying mechanism of melatonin on the delay of PPD and provides a good strategy for extending shelf life and improvement of cassava tuberous roots.

Analysis of key genes of jasmonic acid mediated signal pathway for defense against insect damages by comparative transcriptome sequencing.

Corn defense systems against insect herbivory involve activation of genes that lead to metabolic reconfigurations to produce toxic compounds, proteinase inhibitors, oxidative enzymes, and behavior-modifying volatiles. Similar responses occur when the plant is exposed to methyl jasmonate (MeJA). To compare the defense responses between stalk borer feeding and exogenous MeJA on a transcriptional level, we employed deep transcriptome sequencing methods following Ostrinia furnacalis leaf feeding and MeJA leaf treatment. 39,636 genes were found to be differentially expressed with O. furnacalis feeding, MeJA application, and O. furnacalis feeding and MeJA application. Following Gene Ontology enrichment analysis of the up- or down- regulated genes, many were implicated in metabolic processes, stimuli-responsive catalytic activity, and transfer activity. Fifteen genes that indicated significant changes in the O. furnacalis feeding group: LOX1, ASN1, eIF3, DXS, AOS, TIM, LOX5, BBTI2, BBTI11, BBTI12, BBTI13, Cl-1B, TPS10, DOX, and A20/AN1 were found to almost all be involved in jasmonate defense signaling pathways. All of the data demonstrate that the jasmonate defense signal pathway is a major defense signaling pathways of Asian corn borer’s defense against insect herbivory. The transcriptome data are publically available at NCBI SRA: SRS965087.

Use of RNAi technology to develop a PRSV-resistant transgenic papaya

Papaya ringspot virus (PRSV) seriously limits papaya (Carica papaya L.) production in tropical and subtropical areas throughout the world. Coat protein (CP)- transgenic papaya lines resistant to PRSV isolates in the sequence-homology-dependent manner have been developed in the U.S.A. and Taiwan. A previous investigation revealed that genetic divergence among Hainan isolates of PRSV has allowed the virus to overcome the CP-mediated transgenic resistance. In this study, we designed a comprehensive RNAi strategy targeting the conserved domain of the PRSV CP gene to develop a broader-spectrum transgenic resistance to the Hainan PRSV isolates. We used an optimized particle-bombardment transformation system to produce RNAi-CP-transgenic papaya lines. Southern blot analysis and Droplet Digital PCR revealed that line 474 contained a single transgene insert. Challenging this line with different viruses (PRSV I, II and III subgroup) under greenhouse conditions validated the transgenic resistance of line 474 to the Hainan isolates. Northern blot analysis detected the siRNAs products in virus-free transgenic papaya tissue culture seedlings. The siRNAs also accumulated in PRSV infected transgenic papaya lines. Our results indicated that this transgenic papaya line has a useful application against PRSV in the major growing area of Hainan, China.

Genome Sequencing and Analysis of the Filamentous Fungus Penicillium sclerotiorum 113, Isolated after Hurricane Sandy

ABSTRACT Penicillium sclerotiorum is a distinctive species within the genus Penicillium that usually produces vivid orange to red colonies, sometimes with colorful sclerotia. Here, we report the first draft genome sequence of P. sclerotiorum strain 113, isolated in 2013 in the aftermath of Hurricane Sandy from a flooded home in New Jersey.

Datasets for transcriptomic analyses of maize leaves in response to Asian corn borer feeding and/or jasmonic acid

Corn is one of the most widely grown crops throughout the world. However, many corn fields develop pest problems such as corn borers every year that seriously affect its yield and quality. Corn′s response to initial insect damage involves a variety of changes to the levels of defensive enzymes, toxins, and communicative volatiles. Such a dramatic change secondary metabolism necessitates the regulation of gene expression at the transcript level. In this paper, we summarized the datasets of the transcriptome of corn plants in response to corn stalk borers (Ostrinia furnacalis) and/or methyl jasmonate (MeJA). Altogether, 39, 636 genes were found to be differentially expressed. The sequencing data are available in the NCBI SRA database under accession number SRS965087. Our dataset will provide more scientific and valuable information for future work such as the study of the functions of important genes or proteins and develop new insect-resistant maize varieties.

Publisher Correction: Use of RNAi technology to develop a PRSV-resistant transgenic papaya

 A correction to this article has been published and is linked from the HTML version of this paper. The error has been fixed in the paper.

Genome Sequencing and Analysis of the Postharvest Fungus Penicillium expansum R21

ABSTRACT Blue mold is the vernacular name of a common postharvest disease of stored apples, pears, and quince that is caused by several common species of Penicillium. This study reports the draft genome sequence of Penicillium expansum strain R21, which was isolated from a red delicious apple in 2011 in Pennsylvania.

A Comprehensive Assessment of the Effects of Transgenic Cry1Ac/Cry1Ab Rice Huahui 1 on Adult Micraspis discolor (Fabricius) (Coleoptera: Coccinellidae)

Micraspis discolor (Fabricius) (Coleoptera: Coccinellidae) is a widely distributed coleoptera predator in southern Asia in rice ecosystem, and adult M. discolor feed on both rice pollen and soft-bodied arthropods. Bitrophic bioassay and tritrophic bioassay were conducted to evaluate the potential impact of Cry1Ac/Cry1Ab-expressing rice Huahui 1 and its non-transgenic counterpart Minghui 63 on fitness parameters of adult M. discolor. The results showed that the survival, and fecundity of this beetle’ adults were not different when they fed on Bt rice or non-Bt rice pollen or Nilaparvata lugens (Stål) reared on Bt rice or non-Bt rice. Toxicity assessment to ensure M. discolor adults were not sensitive to Cry1Ab or Cry1Ac protein independent from the pollen background, M. discolor adults were fed with an artificial diet containing Cry1Ac, Cry1Ab or both protein approximately 10 times higher concentration than in Huahui 1 rice pollen. No difference was detected for any of the life-table parameters tested between Cry protein-containing and pure diet. Artificial diet containing E-64 (N-(trans-Epoxysuccinyl)-L-leucine 4-guanidinobutylamide) was included as a positive control. In contrast, the pre-oviposition and fecundity of M. discolor were significantly adversely affected by feeding on E-64-containing diet. In both bioassays, the uptakes of Cry protein by adult M. discolor were tested by ELISA measurements. These results indicated that adults of M. discolor are not affected by Cry1Ab- or Cry1Ac-expressing rice pollen and are not sensitive to Cry protein at concentrations exceeding the levels in rice pollen in Huahui1. This suggests that M. discolor adults would not be harmed by Cry1Ac/Cry1Ab rice if Bt rice Huahui 1 were commercialized.