Cytological, genetic, and proteomic analysis of a sesame (Sesamum indicum L.) mutant Siyl‑1 with yellow–green leaf color

Tong‑Mei Gao,Shuang‑Ling Wei,Jing Chen,Yin Wu,Feng Li,Li‑Bin Wei,Chun Li,Yan‑Juan Zeng,Yuan Tian,Dong‑Yong Wang,Hai‑Yang Zhang 한국유전학회 2020 Genes & Genomics Vol.42 No.1

Background Both photosynthetic pigments and chloroplasts in plant leaf cells play an important role in deciding on the photosynthetic capacity and efficiency in plants. Systematical investigating the regulatory mechanism of chloroplast development and chlorophyll (Chl) content variation is necessary for clarifying the photosynthesis mechanism for crops. Objective This study aims to explore the critical regulatory mechanism of leaf color mutation in a yellow–green leaf sesame mutant Siyl-1. Methods We performed the genetic analysis of the yellow-green leaf color mutation using the F2 population of the mutant Siyl-1. We compared the morphological structure of the chloroplasts, chlorophyll content of the three genotypes of the mutant F2 progeny. We performed the two-dimensional gel electrophoresis (2-DE) and compared the protein expression variation between the mutant progeny and the wild type. Results Genetic analysis indicated that there were 3 phenotypes of the F2 population of the mutant Siyl-1, i.e., YY type with light-yellow leaf color (lethal); Yy type with yellow-green leaf color, and yy type with normal green leaf color. The yellowgreen mutation was controlled by an incompletely dominant nuclear gene, Siyl-1. Compared with the wild genotype, the chloroplast number and the morphological structure in YY and Yy mutant lines varied evidently. The chlorophyll content also significantly decreased (P < 0.05). The 2-DE comparison showed that there were 98 differentially expressed proteins (DEPs) among YY, Yy, and yy lines. All the 98 DEPs were classified into 5 functional groups. Of which 82.7% DEPs proteins belonged to the photosynthesis and energy metabolism group. Conclusion The results revealed the genetic character of yellow-green leaf color mutant Siyl-1. 98 DEPs were found in YY and Yy mutant compared with the wild genotype. The regulation pathway related with the yellow leaf trait mutation in sesame was analyzed for the first time. The findings supplied the basic theoretical and gene basis for leaf color and chloroplast development mechanism in sesame.

Identification of candidate odorant‐degrading enzyme genes in the antennal transcriptome of Aphidius gifuensis

Kang Zhi‐Wei,Liu Fang‐Hua,Xu Yong‐Yu,Cheng Jia‐Hui,Lin Xiao‐Li,Jing Xiang‐Feng,Tian Hong‐Gang,Liu Tong‐Xian 한국곤충학회 2021 Entomological Research Vol.51 No.1

Odorant‐degrading enzymes (ODEs) have been found in insect antennae and play a critical role in signal chemical degradation once the message is conveyed. Significant progress has been made in characterizing ODEs in a variety of pests but very little is known in their natural enemies. We have carried out an antennae‐ and sex‐specific transcriptome of Aphidius gifuensis, a natural enemy of aphid, to identify the candidate ODEs. Based on the antennae‐ and sex‐specific transcriptome, a total of 100 putative ODEs were identified including one aldehyde oxidase (AOX), four alcohol dehydrogenases (ADs), eight UDP‐glucuronosyltransferases (UGTs), 45 cytochrome P450 (P450s), nine glutathione S‐transferases (GSTs) and 40 carboxylesterases (CCEs or CXEs). Additionally, we used RT‐qPCR to determine the expression profiles of these genes in tissues of both sexes. Based on the phylogenic analysis and tissue‐expression patterns, AgifEstE4, AgifCXE3, AgifCCE4, AgifCCE7, and AgifCCE18 were suggested as key ODEs in A. gifuensis. In addition, the female or male specifically enriched genes, such as AgifCCE17, AgifEstB1, AgifCYP18a1, AgifUGT2C2, were also considered to involve in the chemosensory processing in A. gifuensis. This study not only identified the candidate ODEs in A. gifuensis but also provided source for further exploration of the molecular mechanisms of chemical signal transductions in A. gifuensis, as well as other hymenopteran species.

Orthologous based study to detect the fast evolutionary genes related to rice pre-harvest sprouting

Wei Tong,Tae-Sung Kim,Kyu-Won Kim,Yong-Jin Park 한국육종학회 2015 한국육종학회 심포지엄 Vol.2015 No.07

Pre-harvest sprouting (PHS) results in lower yields for rice and other crops, especially in rainy season before harvest. By using gene based functional studies to reveal the mechanism of PHS related pathways can be a good way in breeding for more PHS resistant accessions. Orthologous genes, which are homologous genes that diverged after a speciation event, generally maintain a similar function in different species to that of the ancestral gene in which they evolved from. Applied with a McDonald-Kreitman Test (MKT), we examined more than 10,000 orthologous genes between rice (Oryza sativa) and Brachypodium (outgroup) based on different phenotypic groups in order to find some fast evolutionary genes in rice PHS. Three groups which represented the PHS susceptible (group 1), PHS medium (group 2) and PHS resistant (group 3) were separated based on the phenotype and each group was examined with the outgroup for MKT. Total 60 fast evolutionary genes that have a positive selection with FDR ≤ 0.05 were found in the three groups, and 19, 5 and 8 genes were specific existed in group 1, 2 and 3, respectively. Annotation of these genes were conducted and the predicted functions were investigated, leading that one Ethylene receptor-like gene that may related to PHS based on the previous studies, which need to be validated later, however. In addition, network analysis of these characterized genes were also investigated, which could reveal the connection of genes between each other. Moreover, the association study between the candidate gene ethylene receptor and the PHS phenotype was performed and indicated that this gene is significantly correlated with PHS in rice. All these above indicated that with this orthologous based method, we can find some important candidate genes that may play an important role in some traits.

Rice Chloroplast Genome Variation Architecture and Phylogenetic Dissection in Diverse <i>Oryza</i> Species Assessed by Whole-Genome Resequencing

Tong, Wei,Kim, Tae-Sung,Park, Yong-Jin Springer US 2016 Rice Vol.9 No.-

<P><B>Background</B></P><P>Chloroplast genome variations have been detected, despite its overall conserved structure, which has been valuable for plant population genetics and evolutionary studies. Here, we described chloroplast variation architecture of 383 rice accessions from diverse regions and different ecotypes, in order to mine the rice chloroplast genome variation architecture and phylogenetic.</P><P><B>Results</B></P><P>A total of 3677 variations across the chloroplast genome were identified with an average density of 27.33 per kb, in which wild rice showing a higher variation density than cultivated groups. Chloroplast genome nucleotide diversity investigation indicated a high degree of diversity in wild rice than in cultivated rice. Genetic distance estimation revealed that African rice showed a low level of breeding and connectivity with the Asian rice, suggesting the big distinction of them. Population structure and principal component analysis revealed the existence of clear clustering of African and Asian rice, as well as the <I>indica</I> and <I>japonica</I> in Asian cultivated rice. Phylogenetic analysis based on maximum likelihood and Bayesian inference methods and the population splits test suggested and supported the independent origins of <I>indica</I> and <I>japonica</I> within Asian cultivated rice. In addition, the African cultivated rice was thought to be domesticated differently from Asian cultivated rice.</P><P><B>Conclusions</B></P><P>The chloroplast genome variation architecture in Asian and African rice are different, as well as within Asian or African rice. Wild rice and cultivated rice also have distinct nucleotide diversity or genetic distance. In chloroplast level, the independent origins of <I>indica</I> and <I>japonica</I> within Asian cultivated rice were suggested and the African cultivated rice was thought to be domesticated differently from Asian cultivated rice. These results will provide more candidate evidence for the further rice chloroplast genomic and evolution studies.</P><P><B>Electronic supplementary material</B></P><P>The online version of this article (doi:10.1186/s12284-016-0129-y) contains supplementary material, which is available to authorized users.</P>

A chloroplast variation map generated using whole genome re-sequencing of Korean landrace rice reveals phylogenetic relationships among Oryza sativa subspecies

Wei Tong,Qiang He,Xiao-Qiang Wang,Min-Young Yoon,Won-Hee Ra,Feng Peng Li,Jie Yu,Win Htet Oo,Sun-Kyung Min,Buung Choi,Eun-Beom Heo,Byoung-Kook Yun,Kyu-Won Kim,Tae-Sung Kim,Chang-Yong Lee,Yong-Jin Park 한국육종학회 2015 한국육종학회 심포지엄 Vol.2015 No.07

Although the overall structure of the chloroplast genome is generally conserved, a number of sequence variations have been identified, which are valuable for plant population and evolutionary studies. Here, we constructed a chloroplast variation map of 30 landrace rice strains of Korean origin, using the Oryza rufipogon chloroplast genome (Genbank: NC_017835) as a reference. Differential distribution of single nucleotide polymorphisms (SNPs) and indels across the rice chloroplast genome is suggestive of a region-specific variation. Population structure clustering revealed the existence of two clear subgroups (indica and japonica) and an admixture group (aus). Phylogenetic analysis of the 30 landrace rice strains and six rice chloroplast references suggested and supported independent evolution of O. sativa indica and japonica. Interestingly, two “aus” type accessions, which were thought to be indica type, shared a closer relationship with the japonica type. One hypothesis is that “Korean aus” was intentionally introduced and may have obtained japonica chloroplasts during cultivation. We also calculated the nucleotide diversity of 30 accessions and compared to six rice chloroplast references, which shown a higher diversity in the indica and aus groups than in the japonica group in lower level substitution diversity.

Insights from 295 diverse origin rice to elucidate chloroplast variation and evolution based on whole genome re-sequencing

Wei Tong,Tae-Sung Kim,Yong-Jin Park 한국육종학회 2014 한국육종학회 심포지엄 Vol.2014 No.07

Chloroplast (cp) DNA sequence data are a versatile tool for plant identification, barcoding and establishing genetic relationships among plant species. Different chloroplast loci have been utilized to infer evolutionary relationship of plant species. Although the overall structure of the chloroplast genome is generally well conserved, a number of mutations have been observed. Thus, documentation of chloroplast sequence variation has also been an valuable asset in plant population and evolutionary studies for over two decades. Recently, advance in chloroplast genome assembly from whole genome NGS data has become available. In the present study, chloroplast variations among 295 diverse origin accessions were detected based on Oryza rufipogon, which thought to be the progenitor of cultivated rice.. Variation calling was carried out using the whole genome re-sequencing data of those accessions along with the five rice reference cp genomes. Phylogenetic and evolution analysis of the six references and 295 accessions were performed using the whole reference genome sequence and the variation data, respectively. Also, nucleotide polymorphisms of 295 rice accessions were validated by using previously characterized 50 ecotypes. Differential SNP frequency across the rice cp genome suggests a regional dependent preferential high variation occurrence during the evolution of chloroplast

Adaptive Differentiated Integrated Routing Scheme for GMPLS-based Optical Internet

Wei, Wei,Zeng, Qingji,Ye, Tong,Lomone, David The Korea Institute of Information and Commucation 2004 Journal of communications and networks Vol.6 No.3

A new online multi-layer integrated routing (MLIR) scheme that combines IP (electrical) layer routing with WDM (optical) layer routing is investigated. It is a highly efficient and cost-effective routing scheme viable for the next generation integrated optical Internet. A new simplified weighted graph model for the integrated optical Internet consisted of optical routers with multi-granularity optical-electrical hybrid switching capability is firstly proposed. Then, based on the proposed graph model, we develop an online integrated routing scheme called differentiated weighted fair algorithm (DWFA) employing adaptive admission control (routing) strategies with the motivation of service/bandwidth differentiation, which can jointly solve multi-layer routing problem by simply applying the minimal weighted path computation algorithm. The major objective of DWFA is fourfold: 1) Quality of service (QoS) routing for traffic requests with various priorities; 2) blocking fairness for traffic requests with various bandwidth granularities; 3) adaptive routing according to the policy parameters from service provider; 4) lower computational complexity. Simulation results show that DWFA performs better than traditional overlay routing schemes such as optical-first-routing (OFR) and electrical-first-routing (EFR), in terms of traffic blocking ratio, traffic blocking fairness, average traffic logical hop counts, and global network resource utilization. It has been proved that the DWFA is a simple, comprehensive, and practical scheme of integrated routing in optical Internet for service providers.

Arabidopsis thaliana Metallothionein, AtMT2a, Mediates ROS Balance during Oxidative Stress

Wei Zhu,Dong-Xiao Zhao,Qing Miao,Tong-Tong Xue,Xin-Zheng Li,Cheng-Chao Zheng 한국식물학회 2009 Journal of Plant Biology Vol.52 No.6

Cold stress has been shown to induce the production of reactive oxygen species (ROS), which can elicit a potentially damaging oxidative burden on cellular metabolism. Here, the expression of a metallothionein gene (AtMT2a) was upregulated under low temperature and hydrogen peroxide (H2O2) stresses. The Arabidopsis T-DNA insertion mutant, mt2a, exhibited more sensitivity to cold stress compared to WT plants during the seed germination, and H2O2 levels in mt2a mutant were higher than that in WT plants during the cold stress. Synthetic GFP fused to AtMT2a was observed to be localized in cytosol. These results indicated that AtMT2a functions in tolerance against cold stress by mediating the ROS balance in the cytosol. Interestingly, mRNA level of AtMT2a was increased in seedlings of Arabidopsis cat2 mutant after cold treatment compared to WT seedlings, and overexpression of AtMT2a in cat2 could improve CAT activity under chilling stress. Moreover, the enzymatic activity of CAT in mt2a was higher than that in WT plants after cold treatment, suggesting that AtMT2a and CAT might complement each other in antioxidative process potentially in Arabidopsis. Taken together, our results provided a novel insight into the relationship between MTs and antioxidative enzymes in the ROS-scavenging system in plants.

Bioprospecting of Endophytic Fungi as Promising Anti-MRSA Agents

Wei, Yee-Min,Tan, Joo-Shun,Tang, Hock-Wei,Tong, Woei-Yenn,Leong, Chean-Ring,Tan, Wen-Nee The Korean Society of Pharmacognosy 2022 Natural Product Sciences Vol.28 No.3

Methicillin-resistant Staphylococcus aureus (MRSA) is a serious threat to the global healthcare system. Ineffective and resistance to antibiotic treatments have increased morbidity and mortality rates worldwide. New and effective antibiotics are needed to combat against bacterial resistance. Endophytic fungi are crucial reservoirs of novel bioactive metabolites. In particular, the secondary metabolites show promising therapeutic potential, notably, antibacterial. This review discussed the emerging potential of endophytic fungi as anti-MRSA agents. The ecological sources of endophytic fungi were discussed with the synthesis of bioactive metabolites. The mode of antibacterial actions was elucidated to give a better understanding of the mechanisms involved. This review may serve as an important reference for future discovery and developments of anti-MRSA agents from endophytic fungi.

Regulating the monomer of polyhydroxyalkanoate from mixed microbial culture: with particular emphasis on substrate composition: A review

Tong Wei,Qian Fang 대한환경공학회 2022 Environmental Engineering Research Vol.27 No.5

Polyhydroxyalkanoate (PHA), produced by mixed microbial cultures (MMCs), is a biodegradable biopolyester that alleviates the global plastic crisis in the nearest future. Even PHA has become a research hotspot, reviews on PHA composition determining thermodynamic and processing properties of PHA products are rare. The primary focus of the evaluation relies on the factors affecting the PHA monomer composition of MMC-PHA production. Besides, since the volatile fatty acids (VFAs) composition of the substrates strongly influences the PHA monomer composition, regulating the ratio of even-carbon to odd-carbon VFAs, PHA, vary properties could be obtained predictably. So oriented acid production process, the first stage process in three-stage MMC-PHA production that can regulate the VFAs composition, is also comprehensively introduced to help understand PHA monomer regulation.