The genome of the extremophile crucifer Thellungiella parvula

Dassanayake, Maheshi,Oh, Dong-Ha,Haas, Jeffrey S,Hernandez, Alvaro,Hong, Hyewon,Ali, Shahjahan,Yun, Dae-Jin,Bressan, Ray A,Zhu, Jian-Kang,Bohnert, Hans J,Cheeseman, John M Nature Publishing Group, a division of Macmillan P 2011 Nature genetics Vol.43 No.9

Thellungiella parvula is related to Arabidopsis thaliana and is endemic to saline, resource-poor habitats, making it a model for the evolution of plant adaptation to extreme environments. Here we present the draft genome for this extremophile species. Exclusively by next generation sequencing, we obtained the de novo assembled genome in 1,496 gap-free contigs, closely approximating the estimated genome size of 140 Mb. We anchored these contigs to seven pseudo chromosomes without the use of maps. We show that short reads can be assembled to a near-complete chromosome level for a eukaryotic species lacking prior genetic information. The sequence identifies a number of tandem duplications that, by the nature of the duplicated genes, suggest a possible basis for T. parvula's extremophile lifestyle. Our results provide essential background for developing genomically influenced testable hypotheses for the evolution of environmental stress tolerance.

Biotechnology for mechanisms that counteract salt stress in extremophile species: a genome-based view

레이브레산,박형철,Francesco Orsini,오동하,Maheshi Dassanayake,Gunsu Inan,윤대진,한스,Albino Maggio 한국식물생명공학회 2013 Plant biotechnology reports Vol.7 No.1

Molecular genetics has confirmed older research and generated new insights into the ways how plants deal with adverse conditions. This body of research is now being used to interpret stress behavior of plants in new ways, and to add results from most recent genomicsbased studies. The new knowledge now includes genome sequences of species that show extreme abiotic stress tolerances, which enables new strategies for applications through either molecular breeding or transgenic engineering. We will highlight some physiological features of the extremophile lifestyle, outline emerging features about halophytism based on genomics, and discuss conclusions about underlying mechanisms.

Gibberellin Signaling Requires Chromatin Remodeler PICKLE to Promote Vegetative Growth and Phase Transitions

Park, Jeongmoo,Oh, Dong-Ha,Dassanayake, Maheshi,Nguyen, Khoa Thi,Ogas, Joe,Choi, Giltsu,Sun, Tai-ping American Society of Plant Biologists 2017 Plant Physiology Vol.173 No.2

<P>PICKLE (PKL) is an ATP-dependent chromodomain-helicase-DNA-binding domain (CHD3) chromatin remodeling enzyme in Arabidopsis (Arabidopsis thaliana). Previous studies showed that PKL promotes embryonic-to-vegetative transition by inhibiting expression of seed-specific genes during seed germination. The pkl mutants display a low penetrance of the ' pickle root' phenotype, with a thick and green primary root that retains embryonic characteristics. The penetrance of this pickle root phenotype in pkl is dramatically increased in gibberellin (GA)-deficient conditions. At adult stages, the pkl mutants are semidwarfs with delayed flowering time, which resemble reduced GA-signaling mutants. These findings suggest that PKL may play a positive role in regulating GA signaling. A recent biochemical analysis further showed that PKL and GA signaling repressors DELLAs antagonistically regulate hypocotyl cell elongation genes by direct protein-protein interaction. To elucidate further the role of PKL in GA signaling and plant development, we studied the genetic interaction between PKL and DELLAs using the hextuple mutant containing pkl and della pentuple (dP) mutations. Here, we show that PKL is required for most of GA-promoted developmental processes, including vegetative growth such as hypocotyl, leaf, and inflorescence stem elongation, and phase transitions such as juvenile-to-adult leaf and vegetative-to-reproductive phase. The removal of all DELLA functions (in the dP background) cannot rescue these phenotypes in pkl. RNA-sequencing analysis using the ga1 (a GA-deficient mutant), pkl, and the ga1 pkl double mutant further shows that expression of 80% of GA-responsive genes in seedlings is PKL dependent, including genes that function in cell elongation, cell division, and phase transitions. These results indicate that the CHD3 chromatin remodeler PKL is required for regulating gene expression during most of GA-regulated developmental processes.</P>

Biotechnology for mechanisms that counteract salt stress in extremophile species: a genome-based view

Bressan, Ray A.,Park, Hyeong Cheol,Orsini, Francesco,Oh, Dong-Ha,Dassanayake, Maheshi,Inan, Gunsu,Yun, Dae-Jin,Bohnert, Hans J.,Maggio, Albino 한국식물생명공학회 2013 Plant biotechnology reports Vol.7 No.1

Molecular genetics has confirmed older research and generated new insights into the ways how plants deal with adverse conditions. This body of research is now being used to interpret stress behavior of plants in new ways, and to add results from most recent genomicsbased studies. The new knowledge now includes genome sequences of species that show extreme abiotic stress tolerances, which enables new strategies for applications through either molecular breeding or transgenic engineering. We will highlight some physiological features of the extremophile lifestyle, outline emerging features about halophytism based on genomics, and discuss conclusions about underlying mechanisms.

Global Awakening of Cryptic Biosynthetic Gene Clusters in <i>Burkholderia thailandensis</i>

Gupta, Ashish,Bedre, Renesh,Thapa, Sudarshan Singh,Sabrin, Afsana,Wang, Guannan,Dassanayake, Maheshi,Grove, Anne American Chemical Society 2017 ACS chemical biology Vol.12 No.12

<P>Many bacteria encode biosynthetic proteins that produce a vast array of natural products. These compounds are often synthesized during host invasion as they function as virulence factors. In addition, such secondary metabolites have yielded numerous molecular scaffolds with pharmaceutical and clinical importance. The gene clusters that encode proteins responsible for synthesis of these compounds are typically silenced or “cryptic” under laboratory growth conditions, hampering discovery of novel lead compounds. We report here that MftR is a global repressor of secondary metabolite synthesis in <I>Burkholderia thailandensis</I> and that urate functions as a physiologically relevant inducer of gene expression. Biosynthetic gene clusters under MftR control include those associated with production of the antimicrobial bactobolins, the iron siderophore malleobactin, and the virulence factor malleilactone. MftR also controls additional genes associated with survival in a host environment, such as genes encoding components of the type III secretion system (T3SS) and proteins linked to anaerobic respiration. This observation not only has implications for understanding activation of gene regulatory networks during host invasion, but it also paves the way for isolation of novel therapeutic leads.</P><P><B>Graphic Abstract</B> <IMG SRC='http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/acbcct/2017/acbcct.2017.12.issue-12/acschembio.7b00681/production/images/medium/cb-2017-00681f_0006.gif'></P><P><A href='http://pubs.acs.org/doi/suppl/10.1021/cb7b00681'>ACS Electronic Supporting Info</A></P>

Genome-wide analysis of brassinosteroid responsive small RNAs in Arabidopsis thaliana

박소영,Jae‑Han Choi,Dong‑Ha Oh,John C. Johnson,Maheshi Dassanayake,Dong‑Hoon Jeong,Man‑Ho Oh 한국유전학회 2020 Genes & Genomics Vol.42 No.8

Background Brassinosteroids (BRs) are a class of phytohormones with important roles in regulating physiological and developmental processes. Small RNAs, including small interfering RNAs and microRNAs (miRNAs), are non-protein coding RNAs that regulate gene expression at the transcriptional and post-transcriptional levels. However, the roles of small RNAs in BR response have not been studied well. Objective In this study, we aimed to identify BR-responsive small RNA clusters and miRNAs in Arabidopsis. In addition, the effect of BR-responsive small RNAs on their transcripts and target genes were examined. Methods Small RNA libraries were constructed from control and epibrassinolide-treated seedlings expressing wild-type BRI1-Flag protein under its native promoter in the bri1-5 mutant. After sequencing the small RNA libraries, differentially expressed small RNA clusters were identified by examining the expression levels of small RNAs in 100-nt bins of the Arabidopsis genome. To identify the BR-responsive miRNAs, the expression levels of all the annotated mature miRNAs, registered in miRBase, were analyzed. Previously published RNA-seq data were utilized to monitor the BR-responsive expression patterns of differentially expressed small RNA clusters and miRNA target genes. Results In results, 38 BR-responsive small RNA clusters, including 30 down-regulated and eight up-regulated clusters, were identified. These differentially expressed small RNA clusters were from miRNA loci, transposons, protein-coding genes, pseudogenes and others. Of these, a transgene, BRI1, accumulates small RNAs, which are not found in the wild type. Small RNAs in this transgene are up-regulated by BRs while BRI1 mRNA is down-regulated by BRs. By analyzing the expression patterns of mature miRNAs, we have identified BR-repressed miR398a-5p and BR-induced miR156g. Although miR398a5p is down-regulated by BRs, its predicted targets were not responsive to BRs. However, SPL3, a target of BR-inducible miR156g, is down-regulated by BRs. Conclusion BR-responsive small RNAs and miRNAs identified in this study will provide an insight into the role of small RNAs in BR responses in plants. Especially, we suggest that miR156g/SPL3 module might play a role in BR-mediated growth and development in Arabidopsis.

Making Epidermal Bladder Cells Bigger: Developmental- and Salinity-Induced Endopolyploidy in a Model Halophyte

Barkla, Bronwyn J.,Rhodes, Timothy,Tran, Kieu-Nga T.,Wijesinghege, Chathura,Larkin, John C.,Dassanayake, Maheshi American Society of Plant Biologists 2018 PLANT PHYSIOLOGY - Vol.177 No.2

<P>Salinity-induced endopolyploidy in Mesembryanthemum crystallinum plays a role in leaf development and the enlargement of epidermal bladder cells to increase their sodium storage capacity.</P><P>Endopolyploidy occurs when DNA replication takes place without subsequent mitotic nuclear division, resulting in cell-specific ploidy levels within tissues. In plants, endopolyploidy plays an important role in sustaining growth and development, but only a few studies have demonstrated a role in abiotic stress response. In this study, we investigated the function of ploidy level and nuclear and cell size in leaf expansion throughout development and tracked cell type-specific ploidy in the halophyte <I>Mesembryanthemum crystallinum</I>. In addition to developmental endopolyploidy, we examined the effects of salinity stress on ploidy level. We focused specifically on epidermal bladder cells (EBC), which are modified balloon-like trichomes, due to their large size and role in salt accumulation. Our results demonstrate that ploidy increases as the leaves expand in a similar manner for each leaf type, and ploidy levels up to 512C were recorded for nuclei in EBC of leaves of adult plants. Salt treatment led to a significant increase in ploidy levels in the EBC, and these cells showed spatially related differences in their ploidy and nuclear and cell size depending on the positions on the leaf and stem surface. Transcriptome analysis highlighted salinity-induced changes in genes involved in DNA replication, cell cycle, endoreduplication, and trichome development in EBC. The increase in cell size and ploidy observed in <I>M. crystallinum</I> under salinity stress may contribute to salt tolerance by increasing the storage capacity for sodium sequestration brought about by higher metabolic activity driving rapid cell enlargement in the leaf tissue and EBC.</P>

Transcriptomic view of survival during early seedling growth of the extremophyte <i>Haloxylon ammodendron</i>

Fan, Ligang,Wang, Guannan,Hu, Wei,Pantha, Pramod,Tran, Kieu-Nga,Zhang, Hua,An, Lizhe,Dassanayake, Maheshi,Qiu, Quan-Sheng Elsevier 2018 Vol. No.

<P><B>Abstract</B></P> <P>Seedling establishment in an extreme environment requires an integrated genomic and physiological response to survive multiple abiotic stresses. The extremophyte, <I>Haloxylon ammodendron</I> is a pioneer species capable of colonizing temperate desert sand dunes. We investigated the induced and basal transcriptomes in <I>H. ammodendron</I> under water-deficit stress during early seedling establishment. We find that not only drought-responsive genes, but multiple genes in pathways associated with salt, osmotic, cold, UV, and high-light stresses were induced, suggesting an altered regulatory stress response system. Additionally, <I>H. ammodendron</I> exhibited enhanced biotic stress tolerance by down-regulation of genes that were generally up-regulated during pathogen entry in susceptible plants. By comparing the <I>H. ammodendron</I> basal transcriptome to six closely related transcriptomes in Amaranthaceae, we detected enriched basal level transcripts in <I>H. ammodendron</I> that shows preadaptation to abiotic stress and pathogens. We found transcripts that were generally maintained at low levels and some induced only under abiotic stress in the stress-sensitive model, <I>Arabidopsis thaliana</I> to be highly expressed under basal conditions in the Amaranthaceae transcriptomes including <I>H. ammodendron</I>. <I>H. ammodendron</I> shows coordinated expression of genes that regulate stress tolerance and seedling development resource allocation to support survival against multiple stresses in a sand dune dominated temperate desert environment.</P> <P><B>Highlights</B></P> <P> <UL> <LI> We report the transcriptomic signals of <I>H. ammodendron</I> in response to drought that contribute to plant survival. </LI> <LI> We highlight the transcriptional and biological processes for the survival of <I>H. ammodendron</I> at early developmental stage. </LI> <LI> We find abundant orthologs in extremophytes that are rare in Arabidopsis. </LI> <LI> These orthologs provide novel candidates to discover networks naturally selected as adaptations to environmental stresses. </LI> </UL> </P>