Comparative analysis of Cd-responsive maize and rice transcriptomes highlights Cd co-modulated orthologs.


BACKGROUND:Metal tolerance is often an integrative result of metal uptake and distribution, which are fine-tuned by a network of signaling cascades and metal transporters. Thus, with the goal of advancing the molecular understanding of such metal homeostatic mechanisms, comparative RNAseq-based transcriptome analysis was conducted to dissect differentially expressed genes (DEGs) in maize roots exposed to cadmium (Cd) stress. RESULTS:To unveil conserved Cd-responsive genes in cereal plants, the obtained 5166 maize DEGs were compared with 2567 Cd-regulated orthologs in rice roots, and this comparison generated 880 universal Cd-responsive orthologs groups composed of 1074 maize DEGs and 981 rice counterparts. More importantly, most of the orthologous DEGs showed coordinated expression pattern between Cd-treated maize and rice, and these include one large orthologs group of pleiotropic drug resistance (PDR)-type ABC transporters, two clusters of amino acid transporters, and 3 blocks of multidrug and toxic compound extrusion (MATE) efflux family transporters, and 3 clusters of heavy metal-associated domain (HMAD) isoprenylated plant proteins (HIPPs), as well as all 4 groups of zinc/iron regulated transporter protein (ZIPs). Additionally, several blocks of tandem maize paralogs, such as germin-like proteins (GLPs), phenylalanine ammonia-lyases (PALs) and several enzymes involved in JA biosynthesis, displayed consistent co-expression pattern under Cd stress. Out of the 1074 maize DEGs, approximately 30 maize Cd-responsive genes such as ZmHIPP27, stress-responsive NAC transcription factor (ZmSNAC1) and 9-cis-epoxycarotenoid dioxygenase (NCED, vp14) were also common stress-responsive genes reported to be uniformly regulated by multiple abiotic stresses. Moreover, the aforementioned three promising Cd-upregulated genes with rice counterparts were identified to be novel Cd-responsive genes in maize. Meanwhile, one maize glutamate decarboxylase (ZmGAD1) with Cd co-modulated rice ortholog was selected for further analysis of Cd tolerance via heterologous expression, and the results suggest that ZmGAD1 can confer Cd tolerance in yeast and tobacco leaves. CONCLUSIONS:These novel findings revealed the conserved function of Cd-responsive orthologs and paralogs, which would be valuable for elucidating the genetic basis of the plant response to Cd stress and unraveling Cd tolerance genes.


BMC Genomics


BMC genomics


Cheng D,Tan M,Yu H,Li L,Zhu D,Chen Y,Jiang M




Has Abstract


2018-09-26 00:00:00












  • Analysis of gene expression in soybean (Glycine max) roots in response to the root knot nematode Meloidogyne incognita using microarrays and KEGG pathways.

    abstract:BACKGROUND:Root-knot nematodes are sedentary endoparasites that can infect more than 3000 plant species. Root-knot nematodes cause an estimated $100 billion annual loss worldwide. For successful establishment of the root-knot nematode in its host plant, it causes dramatic morphological and physiological changes in plan...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Ibrahim HM,Hosseini P,Alkharouf NW,Hussein EH,Gamal El-Din Ael K,Aly MA,Matthews BF

    更新日期:2011-05-10 00:00:00

  • Diet, gonadal sex, and sex chromosome complement influence white adipose tissue miRNA expression.

    abstract:BACKGROUND:MicroRNAs (miRNAs) are small non-coding RNA molecules that regulate gene expression by targeting specific mRNA species for degradation or interfering with translation. Specific miRNAs are key regulators of adipogenesis, and are expressed at different levels in adipose tissue from lean and obese mice. The deg...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Link JC,Hasin-Brumshtein Y,Cantor RM,Chen X,Arnold AP,Lusis AJ,Reue K

    更新日期:2017-01-17 00:00:00

  • A genome-wide deletion mutant screen identifies pathways affected by nickel sulfate in Saccharomyces cerevisiae.

    abstract:BACKGROUND:The understanding of the biological function, regulation, and cellular interactions of the yeast genome and proteome, along with the high conservation in gene function found between yeast genes and their human homologues, has allowed for Saccharomyces cerevisiae to be used as a model organism to deduce biolo...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Arita A,Zhou X,Ellen TP,Liu X,Bai J,Rooney JP,Kurtz A,Klein CB,Dai W,Begley TJ,Costa M

    更新日期:2009-11-15 00:00:00

  • Recurrence-associated pathways in hepatitis B virus-positive hepatocellular carcinoma.

    abstract:BACKGROUND:Despite the recent identification of several prognostic gene signatures, the lack of common genes among experimental cohorts has posed a considerable challenge in uncovering the molecular basis underlying hepatocellular carcinoma (HCC) recurrence for application in clinical purposes. To overcome the limitati...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Kim BY,Choi DW,Woo SR,Park ER,Lee JG,Kim SH,Koo I,Park SH,Han CJ,Kim SB,Yeom YI,Yang SJ,Yu A,Lee JW,Jang JJ,Cho MH,Jeon WK,Park YN,Suh KS,Lee KH

    更新日期:2015-04-10 00:00:00

  • Analysis of the genome sequence of Phomopsis longicolla: a fungal pathogen causing Phomopsis seed decay in soybean.

    abstract:BACKGROUND:Phomopsis longicolla T. W. Hobbs (syn. Diaporthe longicolla) is a seed-borne fungus causing Phomopsis seed decay in soybean. This disease is one of the most devastating diseases reducing soybean seed quality worldwide. To facilitate investigation of the genomic basis of pathogenicity and to understand the me...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Li S,Darwish O,Alkharouf NW,Musungu B,Matthews BF

    更新日期:2017-09-05 00:00:00

  • Changes in activity of metabolic and regulatory pathways during germination of S. coelicolor.

    abstract:BACKGROUND:Bacterial spore germination is a developmental process during which all required metabolic pathways are restored to transfer cells from their dormant state into vegetative growth. Streptomyces are soil dwelling filamentous bacteria with complex life cycle, studied mostly for they ability to synthesize second...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Bobek J,Strakova E,Zikova A,Vohradsky J

    更新日期:2014-12-23 00:00:00

  • RNA-seq analysis provides insights into cold stress responses of Xanthomonas citri pv. citri.

    abstract:BACKGROUND:Xanthomonas citri pv. citri (Xcc) is a citrus canker causing Gram-negative bacteria. Currently, little is known about the biological and molecular responses of Xcc to low temperatures. RESULTS:Results depicted that low temperature significantly reduced growth and increased biofilm formation and unsaturated ...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Liao JX,Li KH,Wang JP,Deng JR,Liu QG,Chang CQ

    更新日期:2019-11-06 00:00:00

  • Genetic variation and population structure of maize inbred lines adapted to the mid-altitude sub-humid maize agro-ecology of Ethiopia using single nucleotide polymorphic (SNP) markers.

    abstract:BACKGROUND:Molecular characterization is important for efficient utilization of germplasm and development of improved varieties. In the present study, we investigated the genetic purity, relatedness and population structure of 265 maize inbred lines from the Ethiopian Institute of Agricultural Research (EIAR), the Inte...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Ertiro BT,Semagn K,Das B,Olsen M,Labuschagne M,Worku M,Wegary D,Azmach G,Ogugo V,Keno T,Abebe B,Chibsa T,Menkir A

    更新日期:2017-10-12 00:00:00

  • Comparative transcriptome analysis of the interaction between Actinidia chinensis var. chinensis and Pseudomonas syringae pv. actinidiae in absence and presence of acibenzolar-S-methyl.

    abstract:BACKGROUND:Since 2007, bacterial canker caused by Pseudomonas syringae pv. actinidiae (Psa) has become a pandemic disease leading to important economic losses in every country where kiwifruit is widely cultivated. Options for controlling this disease are very limited and rely primarily on the use of bactericidal compou...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Michelotti V,Lamontanara A,Buriani G,Orrù L,Cellini A,Donati I,Vanneste JL,Cattivelli L,Tacconi G,Spinelli F

    更新日期:2018-08-06 00:00:00

  • Massive parallel sequencing of mRNA in identification of unannotated salinity stress-inducible transcripts in rice (Oryza sativa L.).

    abstract:BACKGROUND:Microarray technology is limited to monitoring the expression of previously annotated genes that have corresponding probes on the array. Computationally annotated genes have not fully been validated, because ESTs and full-length cDNAs cannot cover entire transcribed regions. Here, mRNA-Seq (an Illumina cDNA ...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Mizuno H,Kawahara Y,Sakai H,Kanamori H,Wakimoto H,Yamagata H,Oono Y,Wu J,Ikawa H,Itoh T,Matsumoto T

    更新日期:2010-12-02 00:00:00

  • Mining microsatellite markers from public expressed sequence tags databases for the study of threatened plants.

    abstract:BACKGROUND:Simple Sequence Repeats (SSRs) are widely used in population genetic studies but their classical development is costly and time-consuming. The ever-increasing available DNA datasets generated by high-throughput techniques offer an inexpensive alternative for SSRs discovery. Expressed Sequence Tags (ESTs) hav...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Lopez L,Barreiro R,Fischer M,Koch MA

    更新日期:2015-10-13 00:00:00

  • Mitochondrial dysregulation and oxidative stress in patients with chronic kidney disease.

    abstract:BACKGROUND:Chronic renal disease (CKD) is characterized by complex changes in cell metabolism leading to an increased production of oxygen radicals, that, in turn has been suggested to play a key role in numerous clinical complications of this pathological condition. Several reports have focused on the identification o...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Granata S,Zaza G,Simone S,Villani G,Latorre D,Pontrelli P,Carella M,Schena FP,Grandaliano G,Pertosa G

    更新日期:2009-08-21 00:00:00

  • Fast multiclonal clusterization of V(D)J recombinations from high-throughput sequencing.

    abstract:BACKGROUND:V(D)J recombinations in lymphocytes are essential for immunological diversity. They are also useful markers of pathologies. In leukemia, they are used to quantify the minimal residual disease during patient follow-up. However, the full breadth of lymphocyte diversity is not fully understood. RESULTS:We prop...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Giraud M,Salson M,Duez M,Villenet C,Quief S,Caillault A,Grardel N,Roumier C,Preudhomme C,Figeac M

    更新日期:2014-05-28 00:00:00

  • Identification of soybean seed developmental stage-specific and tissue-specific miRNA targets by degradome sequencing.

    abstract:BACKGROUND:MicroRNAs (miRNAs) regulate the expression of target genes by mediating gene silencing in both plants and animals. The miRNA targets have been extensively investigated in Arabidopsis and rice using computational prediction, experimental validation by overexpression in transgenic plants, and by degradome or P...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Shamimuzzaman M,Vodkin L

    更新日期:2012-07-16 00:00:00

  • Overlap between eQTL and QTL associated with production traits and fertility in dairy cattle.

    abstract:BACKGROUND:Identifying causative mutations or genes through which quantitative trait loci (QTL) act has proven very difficult. Using information such as gene expression may help to identify genes and mutations underlying QTL. Our objective was to identify regions associated both with production traits or fertility and ...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: van den Berg I,Hayes BJ,Chamberlain AJ,Goddard ME

    更新日期:2019-04-15 00:00:00

  • Simple models of genomic variation in human SNP density.

    abstract:BACKGROUND:Descriptive hierarchical Poisson models and population-genetic coalescent mixture models are used to describe the observed variation in single-nucleotide polymorphism (SNP) density from samples of size two across the human genome. RESULTS:Using empirical estimates of recombination rate across the human geno...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Sainudiin R,Clark AG,Durrett RT

    更新日期:2007-06-06 00:00:00

  • Analysis of whole genome sequencing for the Escherichia coli O157:H7 typing phages.

    abstract:BACKGROUND:Shiga toxin producing Escherichia coli O157 can cause severe bloody diarrhea and haemolytic uraemic syndrome. Phage typing of E. coli O157 facilitates public health surveillance and outbreak investigations, certain phage types are more likely to occupy specific niches and are associated with specific age gro...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Cowley LA,Beckett SJ,Chase-Topping M,Perry N,Dallman TJ,Gally DL,Jenkins C

    更新日期:2015-04-08 00:00:00

  • Genome and epigenome analysis of monozygotic twins discordant for congenital heart disease.

    abstract:BACKGROUND:Congenital heart disease (CHD) is the leading non-infectious cause of death in infants. Monozygotic (MZ) twins share nearly all of their genetic variants before and after birth. Nevertheless, MZ twins are sometimes discordant for common complex diseases. The goal of this study is to identify genomic and epig...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Lyu G,Zhang C,Ling T,Liu R,Zong L,Guan Y,Huang X,Sun L,Zhang L,Li C,Nie Y,Tao W

    更新日期:2018-06-04 00:00:00

  • Major aging-associated RNA expressions change at two distinct age-positions.

    abstract:BACKGROUND:Genome-wide expression profiles are altered during biological aging and can describe molecular regulation of tissue degeneration. Age-regulated mRNA expression trends from cross-sectional studies could describe how aging progresses. We developed a novel statistical methodology to identify age-regulated expre...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Gheorghe M,Snoeck M,Emmerich M,Bäck T,Goeman JJ,Raz V

    更新日期:2014-02-14 00:00:00

  • Identification of genomic aberrations in hemangioblastoma by droplet digital PCR and SNP microarray highlights novel candidate genes and pathways for pathogenesis.

    abstract:BACKGROUND:The genetic mechanisms underlying hemangioblastoma development are still largely unknown. We used high-resolution single nucleotide polymorphism microarrays and droplet digital PCR analysis to detect copy number variations (CNVs) in total of 45 hemangioblastoma tumors. RESULTS:We identified 94 CNVs with a m...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Mehrian-Shai R,Yalon M,Moshe I,Barshack I,Nass D,Jacob J,Dor C,Reichardt JK,Constantini S,Toren A

    更新日期:2016-01-14 00:00:00

  • Overlapping genes in the human and mouse genomes.

    abstract:BACKGROUND:Increasing evidence suggests that overlapping genes are much more common in eukaryotic genomes than previously thought. In this study we identified and characterized the overlapping genes in a set of 13,484 pairs of human-mouse orthologous genes. RESULTS:About 10% of the genes under study are overlapping ge...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Sanna CR,Li WH,Zhang L

    更新日期:2008-04-14 00:00:00

  • Single nucleotide polymorphisms (SNPs) distinguish Indian-origin and Chinese-origin rhesus macaques (Macaca mulatta).

    abstract:BACKGROUND:Rhesus macaques serve a critical role in the study of human biomedical research. While both Indian and Chinese rhesus macaques are commonly used, genetic differences between these two subspecies affect aspects of their behavior and physiology, including response to simian immunodeficiency virus (SIV) infecti...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Ferguson B,Street SL,Wright H,Pearson C,Jia Y,Thompson SL,Allibone P,Dubay CJ,Spindel E,Norgren RB Jr

    更新日期:2007-02-07 00:00:00

  • Identification of a radiosensitivity signature using integrative metaanalysis of published microarray data for NCI-60 cancer cells.

    abstract:BACKGROUND:In the postgenome era, a prediction of response to treatment could lead to better dose selection for patients in radiotherapy. To identify a radiosensitive gene signature and elucidate related signaling pathways, four different microarray experiments were reanalyzed before radiotherapy. RESULTS:Radiosensiti...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Kim HS,Kim SC,Kim SJ,Park CH,Jeung HC,Kim YB,Ahn JB,Chung HC,Rha SY

    更新日期:2012-07-30 00:00:00

  • Leaps and lulls in the developmental transcriptome of Dictyostelium discoideum.

    abstract:BACKGROUND:Development of the soil amoeba Dictyostelium discoideum is triggered by starvation. When placed on a solid substrate, the starving solitary amoebae cease growth, communicate via extracellular cAMP, aggregate by tens of thousands and develop into multicellular organisms. Early phases of the developmental prog...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Rosengarten RD,Santhanam B,Fuller D,Katoh-Kurasawa M,Loomis WF,Zupan B,Shaulsky G

    更新日期:2015-04-13 00:00:00

  • Integrative analysis of multi-omics data for identifying multi-markers for diagnosing pancreatic cancer.

    abstract:BACKGROUND:microRNA (miRNA) expression plays an influential role in cancer classification and malignancy, and miRNAs are feasible as alternative diagnostic markers for pancreatic cancer, a highly aggressive neoplasm with silent early symptoms, high metastatic potential, and resistance to conventional therapies. METHOD...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Kwon MS,Kim Y,Lee S,Namkung J,Yun T,Yi SG,Han S,Kang M,Kim SW,Jang JY,Park T

    更新日期:2015-01-01 00:00:00

  • Transcriptome analysis of human brain tissue identifies reduced expression of complement complex C1Q Genes in Rett syndrome.

    abstract:BACKGROUND:MECP2, the gene mutated in the majority of Rett syndrome cases, is a transcriptional regulator that can activate or repress transcription. Although the transcription regulatory function of MECP2 has been known for over a decade, it remains unclear how transcriptional dysregulation leads to the neurodevelopme...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Lin P,Nicholls L,Assareh H,Fang Z,Amos TG,Edwards RJ,Assareh AA,Voineagu I

    更新日期:2016-06-06 00:00:00

  • Identification of three extra-chromosomal replicons in Leptospira pathogenic strain and development of new shuttle vectors.

    abstract:BACKGROUND:The genome of pathogenic Leptospira interrogans contains two chromosomes. Plasmids and prophages are known to play specific roles in gene transfer in bacteria and can potentially serve as efficient genetic tools in these organisms. Although plasmids and prophage remnants have recently been reported in Leptos...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Zhu W,Wang J,Zhu Y,Tang B,Zhang Y,He P,Zhang Y,Liu B,Guo X,Zhao G,Qin J

    更新日期:2015-02-15 00:00:00

  • Effect of sample stratification on dairy GWAS results.

    abstract:BACKGROUND:Artificial insemination and genetic selection are major factors contributing to population stratification in dairy cattle. In this study, we analyzed the effect of sample stratification and the effect of stratification correction on results of a dairy genome-wide association study (GWAS). Three methods for s...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Ma L,Wiggans GR,Wang S,Sonstegard TS,Yang J,Crooker BA,Cole JB,Van Tassell CP,Lawlor TJ,Da Y

    更新日期:2012-10-06 00:00:00

  • A genome-wide survey of Major Histocompatibility Complex (MHC) genes and their paralogues in zebrafish.

    abstract:BACKGROUND:The genomic organisation of the Major Histocompatibility Complex (MHC) varies greatly between different vertebrates. In mammals, the classical MHC consists of a large number of linked genes (e.g. greater than 200 in humans) with predominantly immune function. In some birds, it consists of only a small number...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Sambrook JG,Figueroa F,Beck S

    更新日期:2005-11-04 00:00:00

  • Development of a dense SNP-based linkage map of an apple rootstock progeny using the Malus Infinium whole genome genotyping array.

    abstract:BACKGROUND:A whole-genome genotyping array has previously been developed for Malus using SNP data from 28 Malus genotypes. This array offers the prospect of high throughput genotyping and linkage map development for any given Malus progeny. To test the applicability of the array for mapping in diverse Malus genotypes, ...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Antanaviciute L,Fernández-Fernández F,Jansen J,Banchi E,Evans KM,Viola R,Velasco R,Dunwell JM,Troggio M,Sargent DJ

    更新日期:2012-05-25 00:00:00