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












  • Gut microbiota dysbiosis and bacterial community assembly associated with cholesterol gallstones in large-scale study.

    abstract:BACKGROUND:Elucidating gut microbiota among gallstone patients as well as the complex bacterial colonization of cholesterol gallstones may help in both the prediction and subsequent lowered risk of cholelithiasis. To this end, we studied the composition of bacterial communities of gut, bile, and gallstones from 29 gall...

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    pub_type: 杂志文章


    authors: Wu T,Zhang Z,Liu B,Hou D,Liang Y,Zhang J,Shi P

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  • Comparative analysis of the kinomes of three pathogenic trypanosomatids: Leishmania major, Trypanosoma brucei and Trypanosoma cruzi.

    abstract:BACKGROUND:The trypanosomatids Leishmania major, Trypanosoma brucei and Trypanosoma cruzi cause some of the most debilitating diseases of humankind: cutaneous leishmaniasis, African sleeping sickness, and Chagas disease. These protozoa possess complex life cycles that involve development in mammalian and insect hosts, ...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Parsons M,Worthey EA,Ward PN,Mottram JC

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  • Comparative analysis of Mycobacterium and related Actinomycetes yields insight into the evolution of Mycobacterium tuberculosis pathogenesis.

    abstract:BACKGROUND:The sequence of the pathogen Mycobacterium tuberculosis (Mtb) strain H37Rv has been available for over a decade, but the biology of the pathogen remains poorly understood. Genome sequences from other Mtb strains and closely related bacteria present an opportunity to apply the power of comparative genomics to...

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    pub_type: 杂志文章


    authors: McGuire AM,Weiner B,Park ST,Wapinski I,Raman S,Dolganov G,Peterson M,Riley R,Zucker J,Abeel T,White J,Sisk P,Stolte C,Koehrsen M,Yamamoto RT,Iacobelli-Martinez M,Kidd MJ,Maer AM,Schoolnik GK,Regev A,Galagan J

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  • Whole genome resequencing of the Iranian native dogs and wolves to unravel variome during dog domestication.

    abstract:BACKGROUND:Advances in genome technology have simplified a new comprehension of the genetic and historical processes crucial to rapid phenotypic evolution under domestication. To get new insight into the genetic basis of the dog domestication process, we conducted whole-genome sequence analysis of three wolves and thre...

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    pub_type: 杂志文章


    authors: Amiri Ghanatsaman Z,Wang GD,Asadollahpour Nanaei H,Asadi Fozi M,Peng MS,Esmailizadeh A,Zhang YP

    更新日期:2020-03-04 00:00:00

  • Fungal genomes mining to discover novel sterol esterases and lipases as catalysts.

    abstract:BACKGROUND:Sterol esterases and lipases are enzymes able to efficiently catalyze synthesis and hydrolysis reactions of both sterol esters and triglycerides and due to their versatility could be widely used in different industrial applications. Lipases with this ability have been reported in the yeast Candida rugosa tha...

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    authors: Barriuso J,Prieto A,Martínez MJ

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

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    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

  • Construction of gene clusters resembling genetic causal mechanisms for common complex disease with an application to young-onset hypertension.

    abstract:BACKGROUND:Lack of power and reproducibility are caveats of genetic association studies of common complex diseases. Indeed, the heterogeneity of disease etiology demands that causal models consider the simultaneous involvement of multiple genes. Rothman's sufficient-cause model, which is well known in epidemiology, pro...

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    authors: Lynn KS,Lu CH,Yang HY,Hsu WL,Pan WH

    更新日期:2013-07-23 00:00:00

  • Molecular and phylogenetic characterization of the homoeologous EPSP Synthase genes of allohexaploid wheat, Triticum aestivum (L.).

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    authors: Aramrak A,Kidwell KK,Steber CM,Burke IC

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    authors: Guo L,Luo C,Zhu S

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    pub_type: 杂志文章


    authors: Erickson T,Nicolson T

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    authors: Wang Z,Tang J,Hu R,Wu P,Hou XL,Song XM,Xiong AS

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    authors: Tan TW,Xie C,De Silva M,Lim KS,Patro CP,Lim SJ,Govindarajan KR,Tong JC,Choo KH,Ranganathan S,Khan AM

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    authors: Gong P,Nan X,Barker ND,Boyd RE,Chen Y,Wilkins DE,Johnson DR,Suedel BC,Perkins EJ

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    pub_type: 杂志文章


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    authors: Panara F,Lopez L,Daddiego L,Fantini E,Facella P,Perrotta G

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  • Enhanced sugar accumulation and regulated plant hormone signalling genes contribute to cold tolerance in hypoploid Saccharum spontaneum.

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    authors: Yang H,Wang T,Yu X,Yang Y,Wang C,Yang Q,Wang X

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    journal_title:BMC genomics

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    authors: Vihinen M

    更新日期:2012-06-18 00:00:00

  • Novel Moraxella catarrhalis prophages display hyperconserved non-structural genes despite their genomic diversity.

    abstract:BACKGROUND:Moraxella catarrhalis is an important pathogen that often causes otitis media in children, a disease that is not currently vaccine preventable. Asymptomatic colonisation of the human upper respiratory tract is common and lack of clearance by the immune system is likely due to the emergence of seroresistant g...

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    authors: Ariff A,Wise MJ,Kahler CM,Tay CY,Peters F,Perkins TT,Chang BJ

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    authors: Zhang J,Sharma A,Yu Q,Wang J,Li L,Zhu L,Zhang X,Chen Y,Ming R

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    abstract:BACKGROUND:Sequencing data from The Cancer Genome Atlas (TGCA), the International Cancer Genome Consortium and other research institutes have revealed the presence of genetic alterations in several tumor types, including gastric cancer. These data have been combined into a catalog of significantly mutated genes for eac...

    journal_title:BMC genomics

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    authors: Hirotsu Y,Kojima Y,Okimoto K,Amemiya K,Mochizuki H,Omata M

    更新日期:2016-10-26 00:00:00

  • The genomic architecture and association genetics of adaptive characters using a candidate SNP approach in boreal black spruce.

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    journal_title:BMC genomics

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    authors: Prunier J,Pelgas B,Gagnon F,Desponts M,Isabel N,Beaulieu J,Bousquet J

    更新日期:2013-06-01 00:00:00

  • Mapping a quantitative trait locus (QTL) conferring pyrethroid resistance in the African malaria vector Anopheles funestus.

    abstract:BACKGROUND:Pyrethroid resistance in Anopheles funestus populations has led to an increase in malaria transmission in southern Africa. Resistance has been attributed to elevated activities of cytochrome P450s but the molecular basis underlying this metabolic resistance is unknown. Microsatellite and SNP markers were use...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Wondji CS,Morgan J,Coetzee M,Hunt RH,Steen K,Black WC 4th,Hemingway J,Ranson H

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    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Chen V,Paisley J,Lu X

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  • An advanced bioinformatics approach for analyzing RNA-seq data reveals sigma H-dependent regulation of competence genes in Listeria monocytogenes.

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    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Liu Y,Orsi RH,Boor KJ,Wiedmann M,Guariglia-Oropeza V

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  • Investigation of regions impacting inbreeding depression and their association with the additive genetic effect for United States and Australia Jersey dairy cattle.

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    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Howard JT,Haile-Mariam M,Pryce JE,Maltecca C

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  • GWAS and fine-mapping of livability and six disease traits in Holstein cattle.

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    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Freebern E,Santos DJA,Fang L,Jiang J,Parker Gaddis KL,Liu GE,VanRaden PM,Maltecca C,Cole JB,Ma L

    更新日期:2020-01-13 00:00:00

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    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Kleinman-Ruiz D,Martínez-Cruz B,Soriano L,Lucena-Perez M,Cruz F,Villanueva B,Fernández J,Godoy JA

    更新日期:2017-07-21 00:00:00

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    journal_title:BMC genomics

    pub_type: 杂志文章


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    pub_type: 杂志文章


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    更新日期:2017-08-22 00:00:00