De novo transcriptome sequencing in Bixa orellana to identify genes involved in methylerythritol phosphate, carotenoid and bixin biosynthesis.

Abstract:

BACKGROUND:Bixin or annatto is a commercially important natural orange-red pigment derived from lycopene that is produced and stored in seeds of Bixa orellana L. An enzymatic pathway for bixin biosynthesis was inferred from homology of putative proteins encoded by differentially expressed seed cDNAs. Some activities were later validated in a heterologous system. Nevertheless, much of the pathway remains to be clarified. For example, it is essential to identify the methylerythritol phosphate (MEP) and carotenoid pathways genes. RESULTS:In order to investigate the MEP, carotenoid, and bixin pathways genes, total RNA from young leaves and two different developmental stages of seeds from B. orellana were used for the construction of indexed mRNA libraries, sequenced on the Illumina HiSeq 2500 platform and assembled de novo using Velvet, CLC Genomics Workbench and CAP3 software. A total of 52,549 contigs were obtained with average length of 1,924 bp. Two phylogenetic analyses of inferred proteins, in one case encoded by thirteen general, single-copy cDNAs, in the other from carotenoid and MEP cDNAs, indicated that B. orellana is closely related to sister Malvales species cacao and cotton. Using homology, we identified 7 and 14 core gene products from the MEP and carotenoid pathways, respectively. Surprisingly, previously defined bixin pathway cDNAs were not present in our transcriptome. Here we propose a new set of gene products involved in bixin pathway. CONCLUSION:The identification and qRT-PCR quantification of cDNAs involved in annatto production suggest a hypothetical model for bixin biosynthesis that involve coordinated activation of some MEP, carotenoid and bixin pathway genes. These findings provide a better understanding of the mechanisms regulating these pathways and will facilitate the genetic improvement of B. orellana.

journal_name

BMC Genomics

journal_title

BMC genomics

authors

Cárdenas-Conejo Y,Carballo-Uicab V,Lieberman M,Aguilar-Espinosa M,Comai L,Rivera-Madrid R

doi

10.1186/s12864-015-2065-4

subject

Has Abstract

pub_date

2015-10-28 00:00:00

pages

877

issn

1471-2164

pii

10.1186/s12864-015-2065-4

journal_volume

16

pub_type

杂志文章
  • Delineation of condition specific Cis- and Trans-acting elements in plant promoters under various Endo- and exogenous stimuli.

    abstract:BACKGROUND:Transcription factors (TFs) play essential roles during plant development and response to environmental stresses. However, the relationships among transcription factors, cis-acting elements and target gene expression under endo- and exogenous stimuli have not been systematically characterized. RESULTS:Here,...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-018-4469-4

    authors: Chow CN,Chiang-Hsieh YF,Chien CH,Zheng HQ,Lee TY,Wu NY,Tseng KC,Hou PF,Chang WC

    更新日期:2018-05-09 00:00:00

  • Transcriptome profiling of developmental and xenobiotic responses in a keystone soil animal, the oligochaete annelid Lumbricus rubellus.

    abstract:BACKGROUND:Natural contamination and anthropogenic pollution of soils are likely to be major determinants of functioning and survival of keystone invertebrate taxa. Soil animals will have both evolutionary adaptation and genetically programmed responses to these toxic chemicals, but mechanistic understanding of such is...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-9-266

    authors: Owen J,Hedley BA,Svendsen C,Wren J,Jonker MJ,Hankard PK,Lister LJ,Stürzenbaum SR,Morgan AJ,Spurgeon DJ,Blaxter ML,Kille P

    更新日期:2008-06-03 00:00:00

  • Antimicrobial activity screening of rhizosphere soil bacteria from tomato and genome-based analysis of their antimicrobial biosynthetic potential.

    abstract:BACKGROUND:Tomato plant growth is frequently hampered by a high susceptibility to pests and diseases. Traditional chemical control causes a serious impact on both the environment and human health. Therefore, seeking environment-friendly and cost-effective green methods in agricultural production becomes crucial nowaday...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-020-07346-8

    authors: Zhou L,Song C,Li Z,Kuipers OP

    更新日期:2021-01-07 00:00:00

  • LPS-treatment of bovine endometrial epithelial cells causes differential DNA methylation of genes associated with inflammation and endometrial function.

    abstract:BACKGROUND:Lipopolysaccharide (LPS) endotoxin stimulates pro-inflammatory pathways and is a key player in the pathological mechanisms involved in the development of endometritis. This study aimed to investigate LPS-induced DNA methylation changes in bovine endometrial epithelial cells (bEECs), which may affect endometr...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-020-06777-7

    authors: Jhamat N,Niazi A,Guo Y,Chanrot M,Ivanova E,Kelsey G,Bongcam-Rudloff E,Andersson G,Humblot P

    更新日期:2020-06-03 00:00:00

  • A comparison of gene transcription profiles of domesticated and wild Atlantic salmon (Salmo salar L.) at early life stages, reared under controlled conditions.

    abstract:BACKGROUND:Atlantic salmon have been subject to domestication for approximately ten generations, beginning in the early 1970s. This process of artificial selection will have created various genetic differences between wild and farmed stocks. Each year, hundreds of thousands of farmed fish escape into the wild. These es...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-15-884

    authors: Bicskei B,Bron JE,Glover KA,Taggart JB

    更新日期:2014-10-09 00:00:00

  • A phenomics-based approach for the detection and interpretation of shared genetic influences on 29 biochemical indices in southern Chinese men.

    abstract:BACKGROUND:Phenomics provides new technologies and platforms as a systematic phenome-genome approach. However, few studies have reported on the systematic mining of shared genetics among clinical biochemical indices based on phenomics methods, especially in China. This study aimed to apply phenomics to systematically e...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-019-6363-0

    authors: Hu Y,Tan A,Yu L,Hou C,Kuang H,Wu Q,Su J,Zhou Q,Zhu Y,Zhang C,Wei W,Li L,Li W,Huang Y,Huang H,Xie X,Lu T,Zhang H,Yang X,Gao Y,Li T,Jiang Y,Mo Z

    更新日期:2019-12-16 00:00:00

  • Whole genome sequencing analysis of multiple Salmonella serovars provides insights into phylogenetic relatedness, antimicrobial resistance, and virulence markers across humans, food animals and agriculture environmental sources.

    abstract:BACKGROUND:Salmonella enterica is a significant foodborne pathogen, which can be transmitted via several distinct routes, and reports on acquisition of antimicrobial resistance (AMR) are increasing. To better understand the association between human Salmonella clinical isolates and the potential environmental/animal re...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-018-5137-4

    authors: Pornsukarom S,van Vliet AHM,Thakur S

    更新日期:2018-11-06 00:00:00

  • Differential gene expression and alternative splicing in insect immune specificity.

    abstract:BACKGROUND:Ecological studies routinely show genotype-genotype interactions between insects and their parasites. The mechanisms behind these interactions are not clearly understood. Using the bumblebee Bombus terrestris/trypanosome Crithidia bombi model system (two bumblebee colonies by two Crithidia strains), we have ...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-15-1031

    authors: Riddell CE,Lobaton Garces JD,Adams S,Barribeau SM,Twell D,Mallon EB

    更新日期:2014-11-27 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

    doi:10.1186/1471-2164-11-683

    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

  • High frequency of microsatellites in S. cerevisiae meiotic recombination hotspots.

    abstract:BACKGROUND:Microsatellites are highly abundant in eukaryotic genomes but their function and evolution are not yet well understood. Their elevated mutation rate makes them ideal markers of genetic difference, but high levels of unexplained heterogeneity in mutation rates among microsatellites at different genomic locati...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-9-49

    authors: Bagshaw AT,Pitt JP,Gemmell NJ

    更新日期:2008-01-28 00:00:00

  • Identification of Nicotiana benthamiana microRNAs and their targets using high throughput sequencing and degradome analysis.

    abstract:BACKGROUND:Nicotiana benthamiana is a widely used model plant species for research on plant-pathogen interactions as well as other areas of plant science. It can be easily transformed or agroinfiltrated, therefore it is commonly used in studies requiring protein localization, interaction, or plant-based systems for pro...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-015-2209-6

    authors: Baksa I,Nagy T,Barta E,Havelda Z,Várallyay É,Silhavy D,Burgyán J,Szittya G

    更新日期:2015-12-01 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

    doi:10.1186/1471-2164-13-203

    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

  • RNAseq expression analysis of resistant and susceptible mice after influenza A virus infection identifies novel genes associated with virus replication and important for host resistance to infection.

    abstract:BACKGROUND:The host response to influenza A infections is strongly influenced by host genetic factors. Animal models of genetically diverse mouse strains are well suited to identify host genes involved in severe pathology, viral replication and immune responses. Here, we have utilized a dual RNAseq approach that allowe...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-015-1867-8

    authors: Wilk E,Pandey AK,Leist SR,Hatesuer B,Preusse M,Pommerenke C,Wang J,Schughart K

    更新日期:2015-09-02 00:00:00

  • Sequencing and analysis of the gene-rich space of cowpea.

    abstract:BACKGROUND:Cowpea, Vigna unguiculata (L.) Walp., is one of the most important food and forage legumes in the semi-arid tropics because of its drought tolerance and ability to grow on poor quality soils. Approximately 80% of cowpea production takes place in the dry savannahs of tropical West and Central Africa, mostly b...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-9-103

    authors: Timko MP,Rushton PJ,Laudeman TW,Bokowiec MT,Chipumuro E,Cheung F,Town CD,Chen X

    更新日期:2008-02-27 00:00:00

  • The serine/threonine kinase 33 is present and expressed in palaeognath birds but has become a unitary pseudogene in neognaths about 100 million years ago.

    abstract:BACKGROUND:Serine/threonine kinase 33 (STK33) has been shown to be conserved across all major vertebrate classes including reptiles, mammals, amphibians and fish, suggesting its importance within vertebrates. It has been shown to phosphorylate vimentin and might play a role in spermatogenesis and organ ontogenesis. In ...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-015-1769-9

    authors: Lautwein T,Lerch S,Schäfer D,Schmidt ER

    更新日期:2015-07-22 00:00:00

  • MLTreeMap--accurate Maximum Likelihood placement of environmental DNA sequences into taxonomic and functional reference phylogenies.

    abstract:BACKGROUND:Shotgun sequencing of environmental DNA is an essential technique for characterizing uncultivated microbes in situ. However, the taxonomic and functional assignment of the obtained sequence fragments remains a pressing problem. RESULTS:Existing algorithms are largely optimized for speed and coverage; in con...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-11-461

    authors: Stark M,Berger SA,Stamatakis A,von Mering C

    更新日期:2010-08-05 00:00:00

  • Treatment-independent miRNA signature in blood of Wilms tumor patients.

    abstract:BACKGROUND:Blood-born miRNA signatures have recently been reported for various tumor diseases. Here, we compared the miRNA signature in Wilms tumor patients prior and after preoperative chemotherapy according to SIOP protocol 2001. RESULTS:We did not find a significant difference between miRNA signature of both groups...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-13-379

    authors: Schmitt J,Backes C,Nourkami-Tutdibi N,Leidinger P,Deutscher S,Beier M,Gessler M,Graf N,Lenhof HP,Keller A,Meese E

    更新日期:2012-08-07 00:00:00

  • In silico identification and comparative analysis of differentially expressed genes in human and mouse tissues.

    abstract:BACKGROUND:Screening for differentially expressed genes on the genomic scale and comparative analysis of the expression profiles of orthologous genes between species to study gene function and regulation are becoming increasingly feasible. Expressed sequence tags (ESTs) are an excellent source of data for such studies ...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-7-86

    authors: Pao SY,Lin WL,Hwang MJ

    更新日期:2006-04-21 00:00:00

  • Effect of paleopolyploidy and allopolyploidy on gene expression in banana.

    abstract:BACKGROUND:Bananas (Musa spp.) are an important crop worldwide. Most modern cultivars resulted from a complex polyploidization history that comprised three whole genome duplications (WGDs) shaping the haploid Musa genome, followed by inter- and intra-specific crosses between Musa acuminata and M. balbisiana (A and B ge...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-019-5618-0

    authors: Cenci A,Hueber Y,Zorrilla-Fontanesi Y,van Wesemael J,Kissel E,Gislard M,Sardos J,Swennen R,Roux N,Carpentier SC,Rouard M

    更新日期:2019-03-27 00:00:00

  • Comparative analysis of surface-exposed virulence factors of Acinetobacter baumannii.

    abstract:BACKGROUND:Acinetobacter baumannii is a significant hospital pathogen, particularly due to the dissemination of highly multidrug resistant isolates. Genome data have revealed that A. baumannii is highly genetically diverse, which correlates with major variations seen at the phenotypic level. Thus far, comparative genom...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-15-1020

    authors: Eijkelkamp BA,Stroeher UH,Hassan KA,Paulsen IT,Brown MH

    更新日期:2014-11-25 00:00:00

  • The transcriptome of the invasive eel swimbladder nematode parasite Anguillicola crassus.

    abstract:BACKGROUND:Anguillicola crassus is an economically and ecologically important parasitic nematode of eels. The native range of A. crassus is in East Asia, where it infects Anguilla japonica, the Japanese eel. A. crassus was introduced into European eels, Anguilla anguilla, 30 years ago. The parasite is more pathogenic i...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-14-87

    authors: Heitlinger E,Bridgett S,Montazam A,Taraschewski H,Blaxter M

    更新日期:2013-02-08 00:00:00

  • In silico analysis of the core signaling proteome from the barley powdery mildew pathogen (Blumeria graminis f.sp. hordei).

    abstract:BACKGROUND:Compared to other ascomycetes, the barley powdery mildew pathogen Blumeria graminis f.sp. hordei (Bgh) has a large genome (ca. 120 Mbp) that harbors a relatively small number of protein-coding genes (ca. 6500). This genomic assemblage is thought to be the result of numerous gene losses, which likely represen...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-15-843

    authors: Kusch S,Ahmadinejad N,Panstruga R,Kuhn H

    更新日期:2014-10-02 00:00:00

  • Deep sequencing of the uterine immune response to bacteria during the equine oestrous cycle.

    abstract:BACKGROUND:The steroid hormone environment in healthy horses seems to have a significant impact on the efficiency of their uterine immune response. The objective of this study was to characterize the changes in gene expression in the equine endometrium in response to the introduction of bacterial pathogens and the infl...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-015-2139-3

    authors: Marth CD,Young ND,Glenton LY,Noden DM,Browning GF,Krekeler N

    更新日期:2015-11-14 00:00:00

  • Distribution of segmental duplications in the context of higher order chromatin organisation of human chromosome 7.

    abstract:BACKGROUND:Segmental duplications (SDs) are not evenly distributed along chromosomes. The reasons for this biased susceptibility to SD insertion are poorly understood. Accumulation of SDs is associated with increased genomic instability, which can lead to structural variants and genomic disorders such as the Williams-B...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-15-537

    authors: Ebert G,Steininger A,Weißmann R,Boldt V,Lind-Thomsen A,Grune J,Badelt S,Heßler M,Peiser M,Hitzler M,Jensen LR,Müller I,Hu H,Arndt PF,Kuss AW,Tebel K,Ullmann R

    更新日期:2014-06-29 00:00:00

  • Inferring linkage disequilibrium from non-random samples.

    abstract:BACKGROUND:Linkage disequilibrium (LD) plays a fundamental role in population genetics and in the current surge of studies to screen for subtle genetic variants affecting complex traits. Methods widely implemented in LD analyses require samples to be randomly collected, which, however, are usually ignored and thus rais...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-11-328

    authors: Wang M,Jia T,Jiang N,Wang L,Hu X,Luo Z

    更新日期:2010-05-26 00:00:00

  • Classification and phylogenetic analyses of the Arabidopsis and tomato G-type lectin receptor kinases.

    abstract:BACKGROUND:Pathogen perception by plants is mediated by plasma membrane-localized immune receptors that have varied extracellular domains. Lectin receptor kinases (LecRKs) are among these receptors and are subdivided into 3 classes, C-type LecRKs (C-LecRKs), L-type LecRKs (L-LecRKs) and G-type LecRKs (G-LecRKs). While ...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-018-4606-0

    authors: Teixeira MA,Rajewski A,He J,Castaneda OG,Litt A,Kaloshian I

    更新日期:2018-04-06 00:00:00

  • Comparative transcriptomics between high and low rubber producing Taraxacum kok-saghyz R. plants.

    abstract:BACKGROUND:Taraxacum kok-saghyz R. (Tks) is a promising alternative species to Hevea brasiliensis for production of high quality natural rubber (NR). A comparative transcriptome analysis of plants with differential production of NR will contribute to elucidate which genes are involved in the synthesis, regulation and a...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-018-5287-4

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

    更新日期:2018-12-04 00:00:00

  • Identification of novel and differentially expressed MicroRNAs in goat enzootic nasal adenocarcinoma.

    abstract:BACKGROUND:MicroRNAs (miRNAs) post-transcriptionally regulate a variety of genes involved in eukaryotic cell growth, development, metabolism and other biological processes, and numerous miRNAs are implicated in the initiation and progression of cancer. Enzootic nasal adenocarcinoma (ENA), an epithelial tumor induced in...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-016-3238-5

    authors: Wang B,Ye N,Cao SJ,Wen XT,Huang Y,Yan QG

    更新日期:2016-11-08 00:00:00

  • Involvement of potential pathways in malignant transformation from oral leukoplakia to oral squamous cell carcinoma revealed by proteomic analysis.

    abstract:BACKGROUND:Oral squamous cell carcinoma (OSCC) is one of the most common forms of cancer associated with the presence of precancerous oral leukoplakia. Given the poor prognosis associated with oral leukoplakia, and the difficulties in distinguishing it from cancer lesions, there is an urgent need to elucidate the molec...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-10-383

    authors: Wang Z,Feng X,Liu X,Jiang L,Zeng X,Ji N,Li J,Li L,Chen Q

    更新日期:2009-08-19 00:00:00

  • DNA and RNA-sequence based GWAS highlights membrane-transport genes as key modulators of milk lactose content.

    abstract:BACKGROUND:Lactose provides an easily-digested energy source for neonates, and is the primary carbohydrate in milk in most species. Bovine lactose is also a key component of many human food products. However, compared to analyses of other milk components, the genetic control of lactose has been little studied. Here we ...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-017-4320-3

    authors: Lopdell TJ,Tiplady K,Struchalin M,Johnson TJJ,Keehan M,Sherlock R,Couldrey C,Davis SR,Snell RG,Spelman RJ,Littlejohn MD

    更新日期:2017-12-15 00:00:00