1
|
Primo-Capella A, Forner-Giner MÁ, Martínez-Cuenca MR, Terol J. Comparative transcriptomic analyses of citrus cold-resistant vs. sensitive rootstocks might suggest a relevant role of ABA signaling in triggering cold scion adaption. BMC Plant Biol 2022; 22:209. [PMID: 35448939 PMCID: PMC9027863 DOI: 10.1186/s12870-022-03578-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 04/04/2022] [Indexed: 05/24/2023]
Abstract
BACKGROUND The citrus genus comprises a number of sensitive tropical and subtropical species to cold stress, which limits global citrus distribution to certain latitudes and causes major economic loss. We used RNA-Seq technology to analyze changes in the transcriptome of Valencia delta seedless orange in response to long-term cold stress grafted on two frequently used citrus rootstocks: Carrizo citrange (CAR), considered one of the most cold-tolerant accessions; C. macrophylla (MAC), a very sensitive one. Our objectives were to identify the genetic mechanism that produce the tolerant or sensitive phenotypes in citrus, as well as to gain insights of the rootstock-scion interactions that induce the cold tolerance or sensitivity in the scion. RESULTS Plants were kept at 1 ºC for 30 days. Samples were taken at 0, 15 and 30 days. The metabolomic analysis showed a significant increase in the concentration of free sugars and proline, which was higher for the CAR plants. Hormone quantification in roots showed a substantially increased ABA concentration during cold exposure in the CAR roots, which was not observed in MAC. Different approaches were followed to analyze gene expression. During the stress treatment, the 0-15-day comparison yielded the most DEGs. The functional characterization of DEGs showed enrichment in GO terms and KEGG pathways related to abiotic stress responses previously described in plant cold adaption. The DEGs analysis revealed that several key genes promoting cold adaption were up-regulated in the CAR plants, and those repressing it had higher expression levels in the MAC samples. CONCLUSIONS The metabolomic and transcriptomic study herein performed indicates that the mechanisms activated in plants shortly after cold exposure remain active in the long term. Both the hormone quantification and differential expression analysis suggest that ABA signaling might play a relevant role in promoting the cold hardiness or sensitiveness of Valencia sweet orange grafted onto Carrizo citrange or Macrophylla rootstocks, respectively. Our work provides new insights into the mechanisms by which rootstocks modulate resistance to abiotic stress in the production variety grafted onto them.
Collapse
Affiliation(s)
- Amparo Primo-Capella
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain.
| | - María Ángeles Forner-Giner
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain
| | - Mary-Rus Martínez-Cuenca
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain
| | - Javier Terol
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain
| |
Collapse
|
2
|
Borredá C, Perez-Roman E, Talon M, Terol J. Comparative transcriptomics of wild and commercial Citrus during early ripening reveals how domestication shaped fruit gene expression. BMC Plant Biol 2022; 22:123. [PMID: 35300613 PMCID: PMC8928680 DOI: 10.1186/s12870-022-03509-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 03/03/2022] [Indexed: 05/03/2023]
Abstract
BACKGROUND Interspecific hybridizations and admixtures were key in Citrus domestication, but very little is known about their impact at the transcriptomic level. To determine the effects of genome introgressions on gene expression, the transcriptomes of the pulp and flavedo of three pure species (citron, pure mandarin and pummelo) and four derived domesticated genetic admixtures (sour orange, sweet orange, lemon and domesticated mandarin) have been analyzed at color break. RESULTS Many genes involved in relevant physiological processes for domestication, such sugar/acid metabolism and carotenoid/flavonoid synthesis, were differentially expressed among samples. In the low-sugar, highly acidic species lemon and citron, many genes involved in sugar metabolism, the TCA cycle and GABA shunt displayed a reduced expression, while the P-type ATPase CitPH5 and most subunits of the vacuolar ATPase were overexpressed. The red-colored species and admixtures were generally characterized by the overexpression in the flavedo of specific pivotal genes involved in the carotenoid biosynthesis, including phytoene synthase, ζ-carotene desaturase, β-lycopene cyclase and CCD4b, a carotenoid cleavage dioxygenase. The expression patterns of many genes involved in flavonoid modifications, especially the flavonoid and phenylpropanoid O-methyltransferases showed extreme diversity. However, the most noticeable differential expression was shown by a chalcone synthase gene, which catalyzes a key step in the biosynthesis of flavonoids. This chalcone synthase was exclusively expressed in mandarins and their admixed species, which only expressed the mandarin allele. In addition, comparisons between wild and domesticated mandarins revealed that the major differences between their transcriptomes concentrate in the admixed regions. CONCLUSION In this work we present a first study providing broad evidence that the genome introgressions that took place during citrus domestication largely shaped gene expression in their fruits.
Collapse
Affiliation(s)
- Carles Borredá
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113, Moncada, Valencia, Spain
| | - Estela Perez-Roman
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113, Moncada, Valencia, Spain
| | - Manuel Talon
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113, Moncada, Valencia, Spain
| | - Javier Terol
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113, Moncada, Valencia, Spain.
| |
Collapse
|
3
|
Gonzalez-Ibeas D, Ibanez V, Perez-Roman E, Borredá C, Terol J, Talon M. Shaping the biology of citrus: I. Genomic determinants of evolution. Plant Genome 2021; 14:e20104. [PMID: 34275210 DOI: 10.1002/tpg2.20104] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 04/19/2021] [Indexed: 06/13/2023]
Abstract
We performed genomic analyses on wild species of the genus Citrus to identify major determinants of evolution. The most notable effect occurred on the pathogen-defense genes, as observed in many other plant genera. The gene space was also characterized by changes in gene families intimately related to relevant biochemical properties of citrus fruit, such as pectin modifying enzymes, HDR (4-hydroxy-3-methylbut-2-enyl diphosphate reductase) genes, and O-methyltransferases. Citrus fruits are highly abundant on pectins and secondary metabolites such as terpenoids and flavonoids, the targets of these families. Other gene types under positive selection, expanded through tandem duplications and retained as triplets from whole genome duplications, codified for purple acid phosphatases and MATE-efflux proteins. Although speciation has not been especially rapid in the genus, analyses of selective pressure at the codon level revealed that the extant species evolved from the ancestral citrus radiation show signatures of pervasive adaptive evolution and is therefore potentially responsible for the vast phenotypic differences observed among current species.
Collapse
Affiliation(s)
- Daniel Gonzalez-Ibeas
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Carretera Moncada CV-315, Km 10, Valencia, 46113, Spain
| | - Victoria Ibanez
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Carretera Moncada CV-315, Km 10, Valencia, 46113, Spain
| | - Estela Perez-Roman
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Carretera Moncada CV-315, Km 10, Valencia, 46113, Spain
| | - Carles Borredá
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Carretera Moncada CV-315, Km 10, Valencia, 46113, Spain
| | - Javier Terol
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Carretera Moncada CV-315, Km 10, Valencia, 46113, Spain
| | - Manuel Talon
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Carretera Moncada CV-315, Km 10, Valencia, 46113, Spain
| |
Collapse
|
4
|
Gonzalez-Ibeas D, Ibanez V, Perez-Roman E, Borredá C, Terol J, Talon M. Shaping the biology of citrus: II. Genomic determinants of domestication. Plant Genome 2021; 14:e20133. [PMID: 34464512 DOI: 10.1002/tpg2.20133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 04/19/2021] [Indexed: 06/13/2023]
Abstract
We performed genomic analyses on species and varieties of the genus Citrus to identify several determinants of domestication, based on the pattern of pummelo [Citrus maxima (Burr. f) Merr] and mandarin (Citrus reticulata Blanco) admixture into the ancestral genome, as well as population genetic tests at smaller scales. Domestication impacted gene families regulating pivotal components of citrus flavor (such as acidity) because in edible mandarin varieties, chromosome areas with negative Tajimas values were enriched with genes associated with the regulation of citric acid. Detection of sweeps in edible mandarins that diverged from wild relatives indicated that domestication reduced chemical defenses involving cyanogenesis and alkaloid synthesis, thus increasing palatability. Also, a cluster of SAUR genes in domesticated mandarins derived from the pummelo genome appears to contain candidate genes controlling fruit size. Similarly, conserved stretches of pure mandarin areas were likely important as well for domestication, as, for example, a fragment in chromosome 1 that is involved in the apomictic reproduction of most edible mandarins. Interestingly, our results also support the hypothesis that various genes subject to selective pressure during evolution or derived from whole genome duplication events later became potential targets of domestication.
Collapse
Affiliation(s)
- Daniel Gonzalez-Ibeas
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Carretera Moncada CV-315, Km 10, Valencia, 46113, Spain
| | - Victoria Ibanez
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Carretera Moncada CV-315, Km 10, Valencia, 46113, Spain
| | - Estela Perez-Roman
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Carretera Moncada CV-315, Km 10, Valencia, 46113, Spain
| | - Carles Borredá
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Carretera Moncada CV-315, Km 10, Valencia, 46113, Spain
| | - Javier Terol
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Carretera Moncada CV-315, Km 10, Valencia, 46113, Spain
| | - Manuel Talon
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Carretera Moncada CV-315, Km 10, Valencia, 46113, Spain
| |
Collapse
|
5
|
Ventimilla D, Velázquez K, Ruiz-Ruiz S, Terol J, Pérez-Amador MA, Vives MC, Guerri J, Talon M, Tadeo FR. IDA (INFLORESCENCE DEFICIENT IN ABSCISSION)-like peptides and HAE (HAESA)-like receptors regulate corolla abscission in Nicotiana benthamiana flowers. BMC Plant Biol 2021; 21:226. [PMID: 34020584 PMCID: PMC8139003 DOI: 10.1186/s12870-021-02994-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 04/22/2021] [Indexed: 05/10/2023]
Abstract
BACKGROUND Abscission is an active, organized, and highly coordinated cell separation process enabling the detachment of aerial organs through the modification of cell-to-cell adhesion and breakdown of cell walls at specific sites on the plant body known as abscission zones. In Arabidopsis thaliana, abscission of floral organs and cauline leaves is regulated by the interaction of the hormonal peptide INFLORESCENCE DEFICIENT IN ABSCISSION (IDA), a pair of redundant receptor-like protein kinases, HAESA (HAE) and HAESA-LIKE2 (HSL2), and SOMATIC EMBRYOGENESIS RECEPTOR-LIKE KINASE (SERK) co-receptors. However, the functionality of this abscission signaling module has not yet been demonstrated in other plant species. RESULTS The expression of the pair of NbenIDA1 homeologs and the receptor NbenHAE.1 was supressed at the base of the corolla tube by the inoculation of two virus-induced gene silencing (VIGS) constructs in Nicotiana benthamiana. These gene suppression events arrested corolla abscission but did not produce any obvious effect on plant growth. VIGS plants retained a higher number of corollas attached to the flowers than control plants, an observation related to a greater corolla breakstrength. The arrest of corolla abscission was associated with the preservation of the parenchyma tissue at the base of the corolla tube that, in contrast, was virtually collapsed in normal corollas. In contrast, the inoculation of a viral vector construct that increased the expression of NbenIDA1A at the base of the corolla tube negatively affected the growth of the inoculated plants accelerating the timing of both corolla senescence and abscission. However, the heterologous ectopic overexpression of citrus CitIDA3 and Arabidopsis AtIDA in N. benthamiana did not alter the standard plant phenotype suggesting that the proteolytic processing machinery was unable to yield active peptides. CONCLUSION Here, we demonstrate that the pair of NbenIDA1 homeologs encoding small peptides of the IDA-like family and the receptor NbenHAE.1 control cellular breakdown at the base of the corolla tube awhere an adventitious AZ should be formed and, therefore, corolla abscission in N. benthamiana flowers. Altogether, our results provide the first evidence supporting the notion that the IDA-HAE/HSL2 signaling module is conserved in angiosperms.
Collapse
Affiliation(s)
- Daniel Ventimilla
- Centro de Genómica - Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, 46113 Valencia, Spain
| | - Karelia Velázquez
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, 46113 Valencia, Spain
| | - Susana Ruiz-Ruiz
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, 46113 Valencia, Spain
| | - Javier Terol
- Centro de Genómica - Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, 46113 Valencia, Spain
| | - Miguel A. Pérez-Amador
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universidad Politécnica de Valencia. CPI Ed. 8E, Camino de Vera s/n, 46022 Valencia, Spain
| | - Mª. Carmen Vives
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, 46113 Valencia, Spain
| | - José Guerri
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, 46113 Valencia, Spain
| | - Manuel Talon
- Centro de Genómica - Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, 46113 Valencia, Spain
| | - Francisco R. Tadeo
- Centro de Genómica - Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, 46113 Valencia, Spain
| |
Collapse
|
6
|
Mendes S, Régis T, Terol J, Soares Filho WDS, Talon M, Pedrosa-Harand A. Integration of mandarin ( Citrus reticulata) cytogenetic map with its genome sequence. Genome 2020; 63:437-444. [PMID: 32758104 DOI: 10.1139/gen-2020-0046] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Citrus is an extremely important genus in terms of world fruit production. Despite its economic importance and the small genome sizes of its species (2n = 18, 1C = 430 ± 68 Mbp), entire genomic assemblies have only recently become available for some of its representatives. Together with the previous CMA/DAPI banding and fluorescence in situ hybridization (FISH) in the group, these data are important for understanding the complex relationships between its species and for assisting breeding programs. To anchor genomic data with the cytogenetic map of mandarin (Citrus reticulata), the parental species of several economically important hybrids such as sweet orange and clementine, 18 BAC (bacterial artificial chromosome) clones were used. Eleven clementine BACs were positioned by BAC-FISH, doubling the number of chromosome markers so far available for BAC-FISH in citrus. Additionally, six previously mapped BACs were end-sequenced, allowing, together with one BAC previously sequenced, their assignment to scaffolds and the subsequent integration of chromosomes and the genome assembly. This study therefore established correlations between mandarin scaffolds and chromosomes, allowing further structural genomic and comparative study with the sweet orange genome, as well as insights into the chromosomal evolution of the group.
Collapse
Affiliation(s)
- Sandra Mendes
- Laboratório de Citogenética e Evolução Vegetal, Departamento de Botânica, Universidade Federal de Pernambuco - UFPE, Recife, PE, Brazil
| | - Thallita Régis
- Laboratório de Citogenética e Evolução Vegetal, Departamento de Botânica, Universidade Federal de Pernambuco - UFPE, Recife, PE, Brazil
| | - Javier Terol
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia, Spain
| | | | - Manuel Talon
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia, Spain
| | - Andrea Pedrosa-Harand
- Laboratório de Citogenética e Evolução Vegetal, Departamento de Botânica, Universidade Federal de Pernambuco - UFPE, Recife, PE, Brazil
| |
Collapse
|
7
|
Borredá C, Pérez-Román E, Ibanez V, Terol J, Talon M. Reprogramming of Retrotransposon Activity during Speciation of the Genus Citrus. Genome Biol Evol 2020; 11:3478-3495. [PMID: 31710678 PMCID: PMC7145672 DOI: 10.1093/gbe/evz246] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/04/2019] [Indexed: 12/13/2022] Open
Abstract
Speciation of the genus Citrus from a common ancestor has recently been established to begin ∼8 Ma during the late Miocene, a period of major climatic alterations. Here, we report the changes in activity of Citrus LTR retrotransposons during the process of diversification that gave rise to the current Citrus species. To reach this goal, we analyzed four pure species that diverged early during Citrus speciation, three recent admixtures derived from those species and an outgroup of the Citrus clade. More than 30,000 retrotransposons were grouped in ten linages. Estimations of LTR insertion times revealed that retrotransposon activity followed a species-specific pattern of change that could be ascribed to one of three different models. In some genomes, the expected pattern of gradual transposon accumulation was suddenly arrested during the radiation of the ancestor that gave birth to the current Citrus species. The individualized analyses of retrotransposon lineages showed that in each and every species studied, not all lineages follow the general pattern of the species itself. For instance, in most of the genomes, the retrotransposon activity of elements from the SIRE lineage reached its highest level just before Citrus speciation, while for Retrofit elements, it has been steadily growing. Based on these observations, we propose that Citrus retrotransposons may respond to stressful conditions driving speciation as a part of the genetic response involved in adaptation. This proposal implies that the evolving conditions of each species interact with the internal regulatory mechanisms of the genome controlling the proliferation of mobile elements.
Collapse
Affiliation(s)
- Carles Borredá
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain
| | - Estela Pérez-Román
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain
| | - Victoria Ibanez
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain
| | - Javier Terol
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain
| | - Manuel Talon
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain
| |
Collapse
|
8
|
Terol J, Nueda MJ, Ventimilla D, Tadeo F, Talon M. Transcriptomic analysis of Citrus clementina mandarin fruits maturation reveals a MADS-box transcription factor that might be involved in the regulation of earliness. BMC Plant Biol 2019; 19:47. [PMID: 30704398 PMCID: PMC6357379 DOI: 10.1186/s12870-019-1651-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 01/14/2019] [Indexed: 05/20/2023]
Abstract
BACKGROUND Harvest time is a relevant economic trait in citrus, and selection of cultivars with different fruit maturity periods has a remarkable impact in the market share. Generation of early- and late-maturing cultivars is an important target for citrus breeders, therefore, generation of knowledge regarding the genetic mechanisms controlling the ripening process and causing the early and late phenotypes is crucial. In this work we analyze the evolution of the transcriptome during fruit ripening in 3 sport mutations derived from the Fina clementine (Citrus clementina) mandarin: Clemenules (CLE), Arrufatina (ARR) and Hernandina (HER) that differ in their harvesting periods. CLE is considered a mid-season cultivar while ARR and HER are early- and late-ripening mutants, respectively. RESULTS We used RNA-Seq technology to carry out a time course analysis of the transcriptome of the 3 mutations along the ripening period. The results indicated that in these mutants, earliness and lateness during fruit ripening correlated with the advancement or delay in the expression of a set of genes that may be implicated in the maturation process. A detailed analysis of the transcription factors known to be involved in the regulation of fruit ripening identified a member of the MADS box family whose expression was lower in ARR, the early-ripening mutant, and higher in HER, the late-ripening mutant. The pattern of expression of this gene during the maturation period was basically contrary to those of the ethylene biosynthetic genes, SAM and ACC synthases and ACC oxidase. The gene was present in hemizygous dose in the early-ripening mutant. CONCLUSIONS Our analysis provides new clues about the genetic control of fruit ripening in citrus and allowed the identification of a transcription factor that could be involved in the early phenotype.
Collapse
Affiliation(s)
- Javier Terol
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Moncada, Valencia Spain
| | - M. José Nueda
- Facultad de Ciencias, Universidad de Alicante, Alicante, Spain
| | - Daniel Ventimilla
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Moncada, Valencia Spain
| | - Francisco Tadeo
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Moncada, Valencia Spain
| | - Manuel Talon
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Moncada, Valencia Spain
| |
Collapse
|
9
|
Chen Y, Grimplet J, David K, Castellarin SD, Terol J, Wong DCJ, Luo Z, Schaffer R, Celton JM, Talon M, Gambetta GA, Chervin C. Ethylene receptors and related proteins in climacteric and non-climacteric fruits. Plant Sci 2018; 276:63-72. [PMID: 30348329 DOI: 10.1023/a:1011357320259] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 07/23/2018] [Accepted: 07/27/2018] [Indexed: 05/22/2023]
Abstract
Fruits have been traditionally classified into two categories based on their capacity to produce and respond to ethylene during ripening. Fruits whose ripening is associated to a peak of ethylene production and a respiration burst are referred to as climacteric, while those that are not are referred to as non-climacteric. However, an increasing body of literature supports an important role for ethylene in the ripening of both climacteric and non-climacteric fruits. Genome and transcriptomic data have become available across a variety of fruits and we leverage these data to compare the structure and transcriptional regulation of the ethylene receptors and related proteins. Through the analysis of four economically important fruits, two climacteric (tomato and apple), and two non-climacteric (grape and citrus), this review compares the structure and transcriptional regulation of the ethylene receptors and related proteins in both types of fruit, establishing a basis for the annotation of ethylene-related genes. This analysis reveals two interesting differences between climacteric and non-climacteric fruit: i) a higher number of ETR genes are found in climacteric fruits, and ii) non-climacteric fruits are characterized by an earlier ETR expression peak relative to sugar accumulation.
Collapse
Affiliation(s)
- Yi Chen
- Université de Toulouse, Genomics & Biotechnology of Fruits, INRA, Toulouse INP, ENSAT, BP 32607, F-31326 Castanet-Tolosan, France.
| | - Jérôme Grimplet
- Departamento de Viticultura, Instituto de Ciencias de la Vid y del Vino, CSIC, Universidad de La Rioja, Gobierno de la Rioja, Logroño, Spain.
| | - Karine David
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland Mail Centre, Auckland 1142, New Zealand.
| | - Simone Diego Castellarin
- University of British Columbia, Wine Research Centre, 2205 East Mall, Vancouver, BC, V6T1Z4, Canada.
| | - Javier Terol
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias, Carretera CV-315, km 10,7, Moncada, Valencia, Spain.
| | - Darren C J Wong
- Ecology and Evolution, Research School of Biology, Australian National University, Acton, ACT 2601, Australia.
| | - Zhiwei Luo
- Plant & Food Research, Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand.
| | - Robert Schaffer
- Plant & Food Research, Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand.
| | - Jean-Marc Celton
- Institut de Recherche en Horticulture et Semences, INRA, BP 60057, 49071 Beaucouze Cedex, France.
| | - Manuel Talon
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias, Carretera CV-315, km 10,7, Moncada, Valencia, Spain.
| | - Gregory Alan Gambetta
- Bordeaux Science Agro, Institut des Sciences de la Vigne et du Vin, Ecophysiologie et Génomique Fonctionnelle de la Vigne, UMR 1287, 33140 Villenave d'Ornon, France.
| | - Christian Chervin
- Université de Toulouse, Genomics & Biotechnology of Fruits, INRA, Toulouse INP, ENSAT, BP 32607, F-31326 Castanet-Tolosan, France.
| |
Collapse
|
10
|
Chen Y, Grimplet J, David K, Castellarin SD, Terol J, Wong DCJ, Luo Z, Schaffer R, Celton JM, Talon M, Gambetta GA, Chervin C. Ethylene receptors and related proteins in climacteric and non-climacteric fruits. Plant Sci 2018; 276:63-72. [PMID: 30348329 DOI: 10.1016/j.plantsci.2018.07.012] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 07/23/2018] [Accepted: 07/27/2018] [Indexed: 05/10/2023]
Abstract
Fruits have been traditionally classified into two categories based on their capacity to produce and respond to ethylene during ripening. Fruits whose ripening is associated to a peak of ethylene production and a respiration burst are referred to as climacteric, while those that are not are referred to as non-climacteric. However, an increasing body of literature supports an important role for ethylene in the ripening of both climacteric and non-climacteric fruits. Genome and transcriptomic data have become available across a variety of fruits and we leverage these data to compare the structure and transcriptional regulation of the ethylene receptors and related proteins. Through the analysis of four economically important fruits, two climacteric (tomato and apple), and two non-climacteric (grape and citrus), this review compares the structure and transcriptional regulation of the ethylene receptors and related proteins in both types of fruit, establishing a basis for the annotation of ethylene-related genes. This analysis reveals two interesting differences between climacteric and non-climacteric fruit: i) a higher number of ETR genes are found in climacteric fruits, and ii) non-climacteric fruits are characterized by an earlier ETR expression peak relative to sugar accumulation.
Collapse
Affiliation(s)
- Yi Chen
- Université de Toulouse, Genomics & Biotechnology of Fruits, INRA, Toulouse INP, ENSAT, BP 32607, F-31326 Castanet-Tolosan, France.
| | - Jérôme Grimplet
- Departamento de Viticultura, Instituto de Ciencias de la Vid y del Vino, CSIC, Universidad de La Rioja, Gobierno de la Rioja, Logroño, Spain.
| | - Karine David
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland Mail Centre, Auckland 1142, New Zealand.
| | - Simone Diego Castellarin
- University of British Columbia, Wine Research Centre, 2205 East Mall, Vancouver, BC, V6T1Z4, Canada.
| | - Javier Terol
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias, Carretera CV-315, km 10,7, Moncada, Valencia, Spain.
| | - Darren C J Wong
- Ecology and Evolution, Research School of Biology, Australian National University, Acton, ACT 2601, Australia.
| | - Zhiwei Luo
- Plant & Food Research, Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand.
| | - Robert Schaffer
- Plant & Food Research, Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand.
| | - Jean-Marc Celton
- Institut de Recherche en Horticulture et Semences, INRA, BP 60057, 49071 Beaucouze Cedex, France.
| | - Manuel Talon
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias, Carretera CV-315, km 10,7, Moncada, Valencia, Spain.
| | - Gregory Alan Gambetta
- Bordeaux Science Agro, Institut des Sciences de la Vigne et du Vin, Ecophysiologie et Génomique Fonctionnelle de la Vigne, UMR 1287, 33140 Villenave d'Ornon, France.
| | - Christian Chervin
- Université de Toulouse, Genomics & Biotechnology of Fruits, INRA, Toulouse INP, ENSAT, BP 32607, F-31326 Castanet-Tolosan, France.
| |
Collapse
|
11
|
Wu GA, Terol J, Ibanez V, López-García A, Pérez-Román E, Borredá C, Domingo C, Tadeo FR, Carbonell-Caballero J, Alonso R, Curk F, Du D, Ollitrault P, Roose ML, Dopazo J, Gmitter FG, Rokhsar DS, Talon M. Genomics of the origin and evolution of Citrus. Nature 2018; 554:311-316. [PMID: 29414943 DOI: 10.1038/nature25447] [Citation(s) in RCA: 279] [Impact Index Per Article: 46.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 12/10/2017] [Indexed: 01/01/2023]
Abstract
The genus Citrus, comprising some of the most widely cultivated fruit crops worldwide, includes an uncertain number of species. Here we describe ten natural citrus species, using genomic, phylogenetic and biogeographic analyses of 60 accessions representing diverse citrus germ plasms, and propose that citrus diversified during the late Miocene epoch through a rapid southeast Asian radiation that correlates with a marked weakening of the monsoons. A second radiation enabled by migration across the Wallace line gave rise to the Australian limes in the early Pliocene epoch. Further identification and analyses of hybrids and admixed genomes provides insights into the genealogy of major commercial cultivars of citrus. Among mandarins and sweet orange, we find an extensive network of relatedness that illuminates the domestication of these groups. Widespread pummelo admixture among these mandarins and its correlation with fruit size and acidity suggests a plausible role of pummelo introgression in the selection of palatable mandarins. This work provides a new evolutionary framework for the genus Citrus.
Collapse
Affiliation(s)
- Guohong Albert Wu
- US Department of Energy Joint Genome Institute, Walnut Creek, California, USA
| | - Javier Terol
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia, Spain
| | - Victoria Ibanez
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia, Spain
| | - Antonio López-García
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia, Spain
| | - Estela Pérez-Román
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia, Spain
| | - Carles Borredá
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia, Spain
| | - Concha Domingo
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia, Spain
| | - Francisco R Tadeo
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia, Spain
| | - Jose Carbonell-Caballero
- Computational Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
| | - Roberto Alonso
- Computational Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
| | - Franck Curk
- AGAP Research Unit, Institut National de la Recherche Agronomique (INRA), San Giuliano, France
| | - Dongliang Du
- Citrus Research and Education Center (CREC), Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, Florida, USA
| | - Patrick Ollitrault
- AGAP Research Unit, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Petit-Bourg, Guadeloupe, France
| | - Mikeal L Roose
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, California, USA
| | - Joaquin Dopazo
- Computational Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain.,Functional Genomics Node, Spanish National Institute of Bioinformatics (ELIXIR-es) at CIPF, Valencia, Spain
| | - Frederick G Gmitter
- Citrus Research and Education Center (CREC), Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, Florida, USA
| | - Daniel S Rokhsar
- US Department of Energy Joint Genome Institute, Walnut Creek, California, USA.,Department of Molecular and Cell Biology and Center for Integrative Genomics, University of California, Berkeley, Berkeley, California, USA.,Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Manuel Talon
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia, Spain
| |
Collapse
|
12
|
Reig-Valiente JL, Viruel J, Sales E, Marqués L, Terol J, Gut M, Derdak S, Talón M, Domingo C. Genetic Diversity and Population Structure of Rice Varieties Cultivated in Temperate Regions. Rice (N Y) 2016; 9:58. [PMID: 27766601 PMCID: PMC5073090 DOI: 10.1186/s12284-016-0130-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 10/13/2016] [Indexed: 05/29/2023]
Abstract
BACKGROUND After its domestication, rice cultivation expanded from tropical regions towards northern latitudes with temperate climate in a progressive process to overcome limiting photoperiod and temperature conditions. This process has originated a wide range of diversity that can be regarded as a valuable resource for crop improvement. In general, current rice breeding programs have to deal with a lack of both germplasm accessions specifically adapted to local agro-environmental conditions and adapted donors carrying desired agronomical traits. Comprehensive maps of genome variability and population structure would facilitate genome-wide association studies of complex traits, functional gene investigations and the selection of appropriate donors for breeding purposes. RESULTS A collection of 217 rice varieties mainly cultivated in temperate regions was generated. The collection encompasses modern elite and old cultivars, as well as traditional landraces covering a wide genetic diversity available for rice breeders. Whole Genome Sequencing was performed on 14 cultivars representative of the collection and the genomic profiles of all cultivars were constructed using a panel of 2697 SNPs with wide coverage throughout the rice genome, obtained from the sequencing data. The population structure and genetic relationship analyses showed a strong substructure in the temperate rice population, predominantly based on grain type and the origin of the cultivars. Dendrogram also agrees population structure results. CONCLUSIONS Based on SNP markers, we have elucidated the genetic relationship and the degree of genetic diversity among a collection of 217 temperate rice varieties possessing an enormous variety of agromorphological and physiological characters. Taken together, the data indicated the occurrence of relatively high gene flow and elevated rates of admixture between cultivars grown in remote regions, probably favoured by local breeding activities. The results of this study significantly expand the current genetic resources available for temperate varieties of rice, providing a valuable tool for future association mapping studies.
Collapse
Affiliation(s)
- Juan L. Reig-Valiente
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias, Carretera CV 315 Km 10,7 (Carretera Moncada – Náquera Km 4.5), 46113 Moncada, Spain
| | - Juan Viruel
- Dpto. Biología Vegetal y Ecología, SGI Herbario – Universidad de Sevilla, Edif. Celestino Mutis, Av. Reina Mercedes s/n, 41012 Sevilla, Spain
- Institut Méditerranéen de Biodiversité et d’Ecologie Marine et Continentale (IMBE), Aix Marseille Université, Chemin de la Batterie des Lions, 13007 Marseille, France
| | - Ester Sales
- Dpto. Ciencias Agrarias y del Medio Natural, Escuela Politécnica Superior, Universidad de Zaragoza, Ctra. Cuarte s/n, 22071 Huesca, Spain
| | - Luis Marqués
- Cooperativa de Productores de Semillas de Arroz, Avenida del Mar 1, 46410 Sueca, Spain
| | - Javier Terol
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias, Carretera CV 315 Km 10,7 (Carretera Moncada – Náquera Km 4.5), 46113 Moncada, Spain
| | - Marta Gut
- Centre Nacional d’Anàlisi Genòmica - Centre for Genomic Regulation (CNAG-CRG), Barcelona Institute of Science and Technology (BIST), Baldiri Reixac, 4, 08028 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Sophia Derdak
- Centre Nacional d’Anàlisi Genòmica - Centre for Genomic Regulation (CNAG-CRG), Barcelona Institute of Science and Technology (BIST), Baldiri Reixac, 4, 08028 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Manuel Talón
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias, Carretera CV 315 Km 10,7 (Carretera Moncada – Náquera Km 4.5), 46113 Moncada, Spain
| | - Concha Domingo
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias, Carretera CV 315 Km 10,7 (Carretera Moncada – Náquera Km 4.5), 46113 Moncada, Spain
| |
Collapse
|
13
|
Terol J, Tadeo F, Ventimilla D, Talon M. An RNA-Seq-based reference transcriptome for Citrus. Plant Biotechnol J 2016; 14:938-50. [PMID: 26261026 DOI: 10.1111/pbi.12447] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 06/04/2015] [Accepted: 07/01/2015] [Indexed: 05/20/2023]
Abstract
Previous RNA-Seq studies in citrus have been focused on physiological processes relevant to fruit quality and productivity of the major species, especially sweet orange. Less attention has been paid to vegetative or reproductive tissues, while most Citrus species have never been analysed. In this work, we characterized the transcriptome of vegetative and reproductive tissues from 12 Citrus species from all main phylogenetic groups. Our aims were to acquire a complete view of the citrus transcriptome landscape, to improve previous functional annotations and to obtain genetic markers associated with genes of agronomic interest. 28 samples were used for RNA-Seq analysis, obtained from 12 Citrus species: C. medica, C. aurantifolia, C. limon, C. bergamia, C. clementina, C. deliciosa, C. reshni, C. maxima, C. paradisi, C. aurantium, C. sinensis and Poncirus trifoliata. Four different organs were analysed: root, phloem, leaf and flower. A total of 3421 million Illumina reads were produced and mapped against the reference C. clementina genome sequence. Transcript discovery pipeline revealed 3326 new genes, the number of genes with alternative splicing was increased to 19,739, and a total of 73,797 transcripts were identified. Differential expression studies between the four tissues showed that gene expression is overall related to the physiological function of the specific organs above any other variable. Variants discovery analysis revealed the presence of indels and SNPs in genes associated with fruit quality and productivity. Pivotal pathways in citrus such as those of flavonoids, flavonols, ethylene and auxin were also analysed in detail.
Collapse
Affiliation(s)
- Javier Terol
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia, Spain
| | - Francisco Tadeo
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia, Spain
| | - Daniel Ventimilla
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia, Spain
| | - Manuel Talon
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia, Spain
| |
Collapse
|
14
|
Carbonell-Caballero J, Alonso R, Ibañez V, Terol J, Talon M, Dopazo J. A Phylogenetic Analysis of 34 Chloroplast Genomes Elucidates the Relationships between Wild and Domestic Species within the Genus Citrus. Mol Biol Evol 2015; 32:2015-35. [PMID: 25873589 PMCID: PMC4833069 DOI: 10.1093/molbev/msv082] [Citation(s) in RCA: 198] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Citrus genus includes some of the most important cultivated fruit trees worldwide. Despite being extensively studied because of its commercial relevance, the origin of cultivated citrus species and the history of its domestication still remain an open question. Here, we present a phylogenetic analysis of the chloroplast genomes of 34 citrus genotypes which constitutes the most comprehensive and detailed study to date on the evolution and variability of the genus Citrus. A statistical model was used to estimate divergence times between the major citrus groups. Additionally, a complete map of the variability across the genome of different citrus species was produced, including single nucleotide variants, heteroplasmic positions, indels (insertions and deletions), and large structural variants. The distribution of all these variants provided further independent support to the phylogeny obtained. An unexpected finding was the high level of heteroplasmy found in several of the analyzed genomes. The use of the complete chloroplast DNA not only paves the way for a better understanding of the phylogenetic relationships within the Citrus genus but also provides original insights into other elusive evolutionary processes, such as chloroplast inheritance, heteroplasmy, and gene selection.
Collapse
Affiliation(s)
- Jose Carbonell-Caballero
- Computational Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
| | - Roberto Alonso
- Computational Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
| | - Victoria Ibañez
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias, Moncada, Valencia, Spain
| | - Javier Terol
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias, Moncada, Valencia, Spain
| | - Manuel Talon
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias, Moncada, Valencia, Spain
| | - Joaquin Dopazo
- Computational Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain Functional Genomics Node, Spanish National Institute of Bioinformatics at CIPF, Valencia, Spain
| |
Collapse
|
15
|
Terol J, Ibañez V, Carbonell J, Alonso R, Estornell LH, Licciardello C, Gut IG, Dopazo J, Talon M. Involvement of a citrus meiotic recombination TTC-repeat motif in the formation of gross deletions generated by ionizing radiation and MULE activation. BMC Genomics 2015; 16:69. [PMID: 25758634 PMCID: PMC4334395 DOI: 10.1186/s12864-015-1280-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Accepted: 01/26/2015] [Indexed: 02/07/2023] Open
Abstract
Background Transposable-element mediated chromosomal rearrangements require the involvement of two transposons and two double-strand breaks (DSB) located in close proximity. In radiobiology, DSB proximity is also a major factor contributing to rearrangements. However, the whole issue of DSB proximity remains virtually unexplored. Results Based on DNA sequencing analysis we show that the genomes of 2 derived mutations, Arrufatina (sport) and Nero (irradiation), share a similar 2 Mb deletion of chromosome 3. A 7 kb Mutator-like element found in Clemenules was present in Arrufatina in inverted orientation flanking the 5′ end of the deletion. The Arrufatina Mule displayed “dissimilar” 9-bp target site duplications separated by 2 Mb. Fine-scale single nucleotide variant analyses of the deleted fragments identified a TTC-repeat sequence motif located in the center of the deletion responsible of a meiotic crossover detected in the citrus reference genome. Conclusions Taken together, this information is compatible with the proposal that in both mutants, the TTC-repeat motif formed a triplex DNA structure generating a loop that brought in close proximity the originally distinct reactive ends. In Arrufatina, the loop brought the Mule ends nearby the 2 distinct insertion target sites and the inverted insertion of the transposable element between these target sites provoked the release of the in-between fragment. This proposal requires the involvement of a unique transposon and sheds light on the unresolved question of how two distinct sites become located in close proximity. These observations confer a crucial role to the TTC-repeats in fundamental plant processes as meiotic recombination and chromosomal rearrangements. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1280-3) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Javier Terol
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, 46113, Valencia, Spain.
| | - Victoria Ibañez
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, 46113, Valencia, Spain.
| | - José Carbonell
- Centro de Investigación Principe Felipe (CIPF), Avda, Autopista del Saler, 16-3, 46012, Valencia, Spain.
| | - Roberto Alonso
- Centro de Investigación Principe Felipe (CIPF), Avda, Autopista del Saler, 16-3, 46012, Valencia, Spain.
| | - Leandro H Estornell
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, 46113, Valencia, Spain.
| | - Concetta Licciardello
- CRA-ACM, Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Corso Savoia 190, 95024, Acireale, Catania, Italy.
| | - Ivo G Gut
- Centro Nacional de Análisis Genómico, Parc Científic de Barcelona, 08028, Barcelona, Spain.
| | - Joaquín Dopazo
- Centro de Investigación Principe Felipe (CIPF), Avda, Autopista del Saler, 16-3, 46012, Valencia, Spain.
| | - Manuel Talon
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, 46113, Valencia, Spain.
| |
Collapse
|
16
|
Wu GA, Prochnik S, Jenkins J, Salse J, Hellsten U, Murat F, Perrier X, Ruiz M, Scalabrin S, Terol J, Takita MA, Labadie K, Poulain J, Couloux A, Jabbari K, Cattonaro F, Del Fabbro C, Pinosio S, Zuccolo A, Chapman J, Grimwood J, Tadeo FR, Estornell LH, Muñoz-Sanz JV, Ibanez V, Herrero-Ortega A, Aleza P, Pérez-Pérez J, Ramón D, Brunel D, Luro F, Chen C, Farmerie WG, Desany B, Kodira C, Mohiuddin M, Harkins T, Fredrikson K, Burns P, Lomsadze A, Borodovsky M, Reforgiato G, Freitas-Astúa J, Quetier F, Navarro L, Roose M, Wincker P, Schmutz J, Morgante M, Machado MA, Talon M, Jaillon O, Ollitrault P, Gmitter F, Rokhsar D. Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication. Nat Biotechnol 2014; 32:656-62. [PMID: 24908277 PMCID: PMC4113729 DOI: 10.1038/nbt.2906] [Citation(s) in RCA: 320] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Accepted: 04/14/2014] [Indexed: 01/21/2023]
Abstract
Cultivated citrus are selections from, or hybrids of, wild progenitor species whose identities and contributions to citrus domestication remain controversial. Here we sequence and compare citrus genomes--a high-quality reference haploid clementine genome and mandarin, pummelo, sweet-orange and sour-orange genomes--and show that cultivated types derive from two progenitor species. Although cultivated pummelos represent selections from one progenitor species, Citrus maxima, cultivated mandarins are introgressions of C. maxima into the ancestral mandarin species Citrus reticulata. The most widely cultivated citrus, sweet orange, is the offspring of previously admixed individuals, but sour orange is an F1 hybrid of pure C. maxima and C. reticulata parents, thus implying that wild mandarins were part of the early breeding germplasm. A Chinese wild 'mandarin' diverges substantially from C. reticulata, thus suggesting the possibility of other unrecognized wild citrus species. Understanding citrus phylogeny through genome analysis clarifies taxonomic relationships and facilitates sequence-directed genetic improvement.
Collapse
Affiliation(s)
- G. Albert Wu
- US-Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Simon Prochnik
- US-Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Jerry Jenkins
- HudsonAlpha Biotechnology Institute, Huntsville, AL, USA
| | - Jerome Salse
- INRA/UBP UMR 1095 GDEC, Clermont Ferrand, France
| | - Uffe Hellsten
- US-Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | | | | | | | | | - Javier Terol
- Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain
| | | | - Karine Labadie
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France
| | - Julie Poulain
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France
| | - Arnaud Couloux
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France
| | - Kamel Jabbari
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France
| | | | | | | | - Andrea Zuccolo
- Istituto di Genomica Applicata, Udine, Italy
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
| | - Jarrod Chapman
- US-Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Jane Grimwood
- HudsonAlpha Biotechnology Institute, Huntsville, AL, USA
| | - Francisco R. Tadeo
- Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain
| | - Leandro H. Estornell
- Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain
| | - Juan V. Muñoz-Sanz
- Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain
| | - Victoria Ibanez
- Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain
| | - Amparo Herrero-Ortega
- Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain
| | - Pablo Aleza
- Centro de Protección Vegetal y Biotecnología-IVIA, Moncada, Valencia, Spain
| | | | | | - Dominique Brunel
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France
- INRA, US EPGV_1279, Evry, France
| | | | - Chunxian Chen
- Citrus Research and Education Center (CREC), Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, FL, USA
| | - William G. Farmerie
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, USA
| | - Brian Desany
- 454 Life Sciences, A Roche Company, 15 Commercial Street, Branford CT, USA
| | - Chinnappa Kodira
- 454 Life Sciences, A Roche Company, 15 Commercial Street, Branford CT, USA
| | - Mohammed Mohiuddin
- 454 Life Sciences, A Roche Company, 15 Commercial Street, Branford CT, USA
| | - Tim Harkins
- 454 Life Sciences, A Roche Company, 15 Commercial Street, Branford CT, USA
| | - Karin Fredrikson
- 454 Life Sciences, A Roche Company, 15 Commercial Street, Branford CT, USA
| | - Paul Burns
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
- School of Computational Science & Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Alexandre Lomsadze
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
- School of Computational Science & Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Mark Borodovsky
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
- School of Computational Science & Engineering, Georgia Institute of Technology, Atlanta, GA, USA
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Giuseppe Reforgiato
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura (CRA-ACM), Acireale, Italy
| | - Juliana Freitas-Astúa
- Centro de Citricultura Sylvio Moreira, IAC, Cordeirópolis, SP, Brazil
- Embrapa Cassava and Fruits, Cruz das Almas, BA, Brazil
| | - Francis Quetier
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France
- Département de Biologie, Université d’Evry, Evry, France
| | - Luis Navarro
- Centro de Protección Vegetal y Biotecnología-IVIA, Moncada, Valencia, Spain
| | - Mikeal Roose
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Patrick Wincker
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France
- Département de Biologie, Université d’Evry, Evry, France
- Centre National de Recherche Scientifique (CNRS), Evry, France
| | - Jeremy Schmutz
- HudsonAlpha Biotechnology Institute, Huntsville, AL, USA
| | - Michele Morgante
- Istituto di Genomica Applicata, Udine, Italy
- Department of Agriculture and Environmental Sciences, University of Udine, Udine, Italy
| | | | - Manuel Talon
- Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain
| | - Olivier Jaillon
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France
- Département de Biologie, Université d’Evry, Evry, France
- Centre National de Recherche Scientifique (CNRS), Evry, France
| | | | - Frederick Gmitter
- Citrus Research and Education Center (CREC), Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, FL, USA
| | - Daniel Rokhsar
- US-Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
- Division of Genetics, Genomics, and Development, University of California, Berkeley, CA, USA
| |
Collapse
|
17
|
Ollitrault P, Terol J, Chen C, Federici CT, Lotfy S, Hippolyte I, Ollitrault F, Bérard A, Chauveau A, Cuenca J, Costantino G, Kacar Y, Mu L, Garcia-Lor A, Froelicher Y, Aleza P, Boland A, Billot C, Navarro L, Luro F, Roose ML, Gmitter FG, Talon M, Brunel D. A reference genetic map of C. clementina hort. ex Tan.; citrus evolution inferences from comparative mapping. BMC Genomics 2012; 13:593. [PMID: 23126659 PMCID: PMC3546309 DOI: 10.1186/1471-2164-13-593] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2012] [Accepted: 10/29/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Most modern citrus cultivars have an interspecific origin. As a foundational step towards deciphering the interspecific genome structures, a reference whole genome sequence was produced by the International Citrus Genome Consortium from a haploid derived from Clementine mandarin. The availability of a saturated genetic map of Clementine was identified as an essential prerequisite to assist the whole genome sequence assembly. Clementine is believed to be a 'Mediterranean' mandarin × sweet orange hybrid, and sweet orange likely arose from interspecific hybridizations between mandarin and pummelo gene pools. The primary goals of the present study were to establish a Clementine reference map using codominant markers, and to perform comparative mapping of pummelo, sweet orange, and Clementine. RESULTS Five parental genetic maps were established from three segregating populations, which were genotyped with Single Nucleotide Polymorphism (SNP), Simple Sequence Repeats (SSR) and Insertion-Deletion (Indel) markers. An initial medium density reference map (961 markers for 1084.1 cM) of the Clementine was established by combining male and female Clementine segregation data. This Clementine map was compared with two pummelo maps and a sweet orange map. The linear order of markers was highly conserved in the different species. However, significant differences in map size were observed, which suggests a variation in the recombination rates. Skewed segregations were much higher in the male than female Clementine mapping data. The mapping data confirmed that Clementine arose from hybridization between 'Mediterranean' mandarin and sweet orange. The results identified nine recombination break points for the sweet orange gamete that contributed to the Clementine genome. CONCLUSIONS A reference genetic map of citrus, used to facilitate the chromosome assembly of the first citrus reference genome sequence, was established. The high conservation of marker order observed at the interspecific level should allow reasonable inferences of most citrus genome sequences by mapping next-generation sequencing (NGS) data in the reference genome sequence. The genome of the haploid Clementine used to establish the citrus reference genome sequence appears to have been inherited primarily from the 'Mediterranean' mandarin. The high frequency of skewed allelic segregations in the male Clementine data underline the probable extent of deviation from Mendelian segregation for characters controlled by heterozygous loci in male parents.
Collapse
|
18
|
Ollitrault F, Terol J, Martin AA, Pina JA, Navarro L, Talon M, Ollitrault P. Development of indel markers from Citrus clementina (Rutaceae) BAC-end sequences and interspecific transferability in Citrus. Am J Bot 2012; 99:e268-73. [PMID: 22733984 DOI: 10.3732/ajb.1100569] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
PREMISE OF THE STUDY Indel markers were developed from BAC-end sequences of Citrus clementina cv. Nules. Transferability and polymorphism were tested in the Citrus genus to estimate the potential of indel markers mined from a single genotype for use in genetic studies. METHODS AND RESULTS Using polyacrylamide gel electrophoresis and DNA silver staining, 89 indel markers were tested for their transferability and polymorphism. Thirty-eight markers were selected. Heterozygosity in C. clementina cv. Nules was confirmed for 33 of these indel pairs. A preliminary diversity study using a capillary electrophoresis fragment analyzer was conducted with 21 indels using 45 accessions representing Citrus genus diversity. Intraspecific and interspecific polymorphisms were observed. CONCLUSIONS These results indicate the utility of indel markers developed from sequence data of a single genotype of interspecific origin. In Citrus, these markers will be useful for genetic mapping, germplasm characterization, and phylogenetic assignment of DNA fragments.
Collapse
Affiliation(s)
- Frédérique Ollitrault
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Apartado Oficial, Moncada, Valencia, Spain.
| | | | | | | | | | | | | |
Collapse
|
19
|
Ollitrault P, Terol J, Garcia-Lor A, Bérard A, Chauveau A, Froelicher Y, Belzile C, Morillon R, Navarro L, Brunel D, Talon M. SNP mining in C. clementina BAC end sequences; transferability in the Citrus genus (Rutaceae), phylogenetic inferences and perspectives for genetic mapping. BMC Genomics 2012; 13:13. [PMID: 22233093 PMCID: PMC3320530 DOI: 10.1186/1471-2164-13-13] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Accepted: 01/10/2012] [Indexed: 01/18/2024] Open
Abstract
Background With the increasing availability of EST databases and whole genome sequences, SNPs have become the most abundant and powerful polymorphic markers. However, SNP chip data generally suffers from ascertainment biases caused by the SNP discovery and selection process in which a small number of individuals are used as discovery panels. The ongoing International Citrus Genome Consortium sequencing project of the highly heterozygous Clementine and sweet orange genomes will soon result in the release of several hundred thousand SNPs. The primary goals of this study were: (i) to estimate the transferability within the genus Citrus of SNPs discovered from Clementine BACend sequencing (BES), (ii) to estimate bias associated with the very narrow discovery panel, and (iii) to evaluate the usefulness of the Clementine-derived SNP markers for diversity analysis and comparative mapping studies between the different cultivated Citrus species. Results Fifty-four accessions covering the main Citrus species and 52 interspecific hybrids between pummelo and Clementine were genotyped on a GoldenGate array platform using 1,457 SNPs mined from Clementine BES and 37 SNPs identified between and within C. maxima, C. medica, C. reticulata and C. micrantha. Consistent results were obtained from 622 SNP loci. Of these markers, 116 displayed incomplete transferability primarily in C. medica, C. maxima and wild Citrus species. The two primary biases associated with the SNP mining in Clementine were an overestimation of the C. reticulata diversity and an underestimation of the interspecific differentiation. However, the genetic stratification of the gene pool was high, with very frequent significant linkage disequilibrium. Furthermore, the shared intraspecific polymorphism and accession heterozygosity were generally enough to perform interspecific comparative genetic mapping. Conclusions A set of 622 SNP markers providing consistent results was selected. Of the markers mined from Clementine, 80.5% were successfully transferred to the whole Citrus gene pool. Despite the ascertainment biases in relation to the Clementine origin, the SNP data confirm the important stratification of the gene pools around C. maxima, C. medica and C. reticulata as well as previous hypothesis on the origin of secondary species. The implemented SNP marker set will be very useful for comparative genetic mapping in Citrus and genetic association in C. reticulata.
Collapse
Affiliation(s)
- Patrick Ollitrault
- CIRAD, UMR AGAP, Avenue Agropolis, TA A-108/02, 34398 Montpellier, Cedex 5, France.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
20
|
Vera Ruiz EM, Soriano JM, Romero C, Zhebentyayeva T, Terol J, Zuriaga E, Llácer G, Abbott AG, Badenes ML. Narrowing down the apricot Plum pox virus resistance locus and comparative analysis with the peach genome syntenic region. Mol Plant Pathol 2011; 12:535-47. [PMID: 21722293 PMCID: PMC6640391 DOI: 10.1111/j.1364-3703.2010.00691.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Sharka disease, caused by the Plum pox virus (PPV), is one of the main limiting factors for stone fruit crops worldwide. Only a few resistance sources have been found in apricot (Prunus armeniaca L.), and most studies have located a major PPV resistance locus (PPVres) on linkage group 1 (LG1). However, the mapping accuracy was not sufficiently reliable and PPVres was predicted within a low confidence interval. In this study, we have constructed two high-density simple sequence repeat (SSR) improved maps with 0.70 and 0.68 markers/cm, corresponding to LG1 of 'Lito' and 'Goldrich' PPV-resistant cultivars, respectively. Using these maps, and excluding genotype-phenotype incongruent individuals, a new binary trait locus (BTL) analysis for PPV resistance was performed, narrowing down the PPVres support intervals to 7.3 and 5.9 cm in 'Lito' and 'Goldrich', respectively. Subsequently, 71 overlapping oligonucleotides (overgo) probes were hybridized against an apricot bacterial artificial chromosome (BAC) library, identifying 870 single BACs from which 340 were anchored onto a map region of approximately 30-40 cm encompassing PPVres. Partial BAC contigs assigned to the two allelic haplotypes (resistant/susceptible) of the PPVres locus were built by high-information content fingerprinting (HICF). In addition, a total of 300 BAC-derived sequences were obtained, and 257 showed significant homology with the peach genome scaffold_1 corresponding to LG1. According to the peach syntenic genome sequence, PPVres was predicted within a region of 2.16 Mb in which a few candidate resistance genes were identified.
Collapse
Affiliation(s)
- Elsa María Vera Ruiz
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Apartado Oficial, Moncada, Valencia, Spain
| | | | | | | | | | | | | | | | | |
Collapse
|
21
|
Ollitrault F, Terol J, Pina JA, Navarro L, Talon M, Ollitrault P. Development of SSR markers from Citrus clementina (Rutaceae) BAC end sequences and interspecific transferability in Citrus. Am J Bot 2010; 97:e124-9. [PMID: 21616814 DOI: 10.3732/ajb.1000280] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
PREMISE OF THE STUDY Microsatellite primers were developed from bacterial artificial chromosome (BAC) end sequences of Citrus clementina and their transferability and polymorphism tested in the genus Citrus for future anchorage of physical and genetic maps and comparative interspecific genetic mapping. • METHODS AND RESULTS Using PAGE and DNA silver staining, 79 primer pairs were selected for their transferability and polymorphism among 526 microsatellites mined in BES. A preliminary diversity study in Citrus was conducted with 18 of them, in C. reticulata, C. maxima, C. medica, C. sinensis, C. aurantium, C. paradisi, C. lemon, C. aurantifolia, and some papedas (wild citrus), using a capillary electrophoresis fragment analyzer. Intra- and interspecific polymorphism was observed, and heterozygous markers were identified for the different genotypes to be used for genetic mapping. • CONCLUSIONS These results indicate the utility of the developed primers for comparative mapping studies and the integration of physical and genetic maps.
Collapse
Affiliation(s)
- Frédérique Ollitrault
- Centro de Protección Vegetal y Biotecnología, IVIA, Apartado Oficial 46113 Moncada (Valencia), Spain
| | | | | | | | | | | |
Collapse
|
22
|
Abstract
BACKGROUND Research on citrus fruit ripening has received considerable attention because of the importance of citrus fruits for the human diet. Organic acids are among the main determinants of taste and organoleptic quality of fruits and hence the control of fruit acidity loss has a strong economical relevance. In citrus, organic acids accumulate in the juice sac cells of developing fruits and are catabolized thereafter during ripening. Aconitase, that transforms citrate to isocitrate, is the first step of citric acid catabolism and a major component of the citrate utilization machinery. In this work, the citrus aconitase gene family was first characterized and a phylogenetic analysis was then carried out in order to understand the evolutionary history of this family in plants. Gene expression analyses of the citrus aconitase family were subsequently performed in several acidic and acidless genotypes to elucidate their involvement in acid homeostasis. RESULTS Analysis of 460,000 citrus ESTs, followed by sequencing of complete cDNA clones, identified in citrus 3 transcription units coding for putatively active aconitate hydratase proteins, named as CcAco1, CcAco2 and CcAco3. A phylogenetic study carried on the Aco family in 14 plant species, shows the presence of 5 Aco subfamilies, and that the ancestor of monocot and dicot species shared at least one Aco gene. Real-time RT-PCR expression analyses of the three aconitase citrus genes were performed in pulp tissues along fruit development in acidic and acidless citrus varieties such as mandarins, oranges and lemons. While CcAco3 expression was always low, CcAco1 and CcAco2 genes were generally induced during the rapid phase of fruit growth along with the maximum in acidity and the beginning of the acid reduction. Two exceptions to this general pattern were found: 1) Clemenules mandarin failed inducing CcAco2 although acid levels were rapidly reduced; and 2) the acidless "Sucreña" orange showed unusually high levels of expression of both aconitases, an observation correlating with the acidless phenotype. However, in the acidless "Dulce" lemon aconitase expression was normal suggesting that the acidless trait in this variety is not dependent upon aconitases. CONCLUSIONS Phylogenetic studies showed the occurrence of five different subfamilies of aconitate hydratase in plants and sequence analyses identified three active genes in citrus. The pattern of expression of two of these genes, CcAco1 and CcAco2, was normally associated with the timing of acid content reduction in most genotypes. Two exceptions to this general observation suggest the occurrence of additional regulatory steps of citrate homeostasis in citrus.
Collapse
Affiliation(s)
- Javier Terol
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias, Carretera Moncada - Náquera, Km. 4.5 Moncada (Valencia) E46113, Spain
| | - Guillermo Soler
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias, Carretera Moncada - Náquera, Km. 4.5 Moncada (Valencia) E46113, Spain
| | - Manuel Talon
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias, Carretera Moncada - Náquera, Km. 4.5 Moncada (Valencia) E46113, Spain
| | - Manuel Cercos
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias, Carretera Moncada - Náquera, Km. 4.5 Moncada (Valencia) E46113, Spain
| |
Collapse
|
23
|
Leida C, Terol J, Martí G, Agustí M, Llácer G, Badenes ML, Ríos G. Identification of genes associated with bud dormancy release in Prunus persica by suppression subtractive hybridization. Tree Physiol 2010; 30:655-66. [PMID: 20231169 DOI: 10.1093/treephys/tpq008] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
To better understand the molecular and physiological mechanisms underlying maintenance and release of seasonal bud dormancy in perennial trees, we identified differentially expressed genes during dormancy progression in reproductive buds from peach (Prunus persica [L.] Batsch) by suppression subtractive hybridization (SSH) and microarray hybridization. Four SSH libraries were constructed, which were respectively enriched in cDNA highly expressed in dormant buds (named DR), in dormancy-released buds (RD) and in the cultivars with different chilling requirement, 'Zincal 5' (ZS) and 'Springlady' (SZ), sampled after dormancy release. About 2500 clones picked from the four libraries were loaded on a glass microarray. Hybridization of microarrays with the final products of SSH procedure was performed in order to validate the selected clones that were effectively enriched in their respective sample. Nearly 400 positive clones were sequenced, which corresponded to 101 different unigenes with diverse functional annotation. We obtained DAM4, 5 and 6 genes coding for MADS-box transcription factors previously related to growth cessation and terminal bud formation in the evergrowing mutant of peach. Several other cDNAs are similar to dormancy factors described in other species, and others have been related to bud dormancy for the first time in this study. Quantitative reverse transcription polymerase chain reaction analysis confirmed differential expression of cDNAs coding for a Zn-finger transcription factor, a GRAS-like regulator, a DNA-binding protein and proteins similar to forisome subunits involved in the reversible occlusion of sieve elements in Fabaceae, among others.
Collapse
Affiliation(s)
- Carmen Leida
- Instituto Valenciano de Investigaciones Agrarias, E-46113, Moncada, Valencia, Spain
| | | | | | | | | | | | | |
Collapse
|
24
|
Terol J, Naranjo MA, Ollitrault P, Talon M. Development of genomic resources for Citrus clementina: characterization of three deep-coverage BAC libraries and analysis of 46,000 BAC end sequences. BMC Genomics 2008; 9:423. [PMID: 18801166 PMCID: PMC2561056 DOI: 10.1186/1471-2164-9-423] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2008] [Accepted: 09/18/2008] [Indexed: 11/24/2022] Open
Abstract
Background Citrus species constitute one of the major tree fruit crops of the subtropical regions with great economic importance. However, their peculiar reproductive characteristics, low genetic diversity and the long-term nature of tree breeding mostly impair citrus variety improvement. In woody plants, genomic science holds promise of improvements and in the Citrus genera the development of genomic tools may be crucial for further crop improvements. In this work we report the characterization of three BAC libraries from Clementine (Citrus clementina), one of the most relevant citrus fresh fruit market cultivars, and the analyses of 46.000 BAC end sequences. Clementine is a diploid plant with an estimated haploid genome size of 367 Mb and 2n = 18 chromosomes, which makes feasible the use of genomics tools to boost genetic improvement. Results Three genomic BAC libraries of Citrus clementina were constructed through EcoRI, MboI and HindIII digestions and 56,000 clones, representing an estimated genomic coverage of 19.5 haploid genome-equivalents, were picked. BAC end sequencing (BES) of 28,000 clones produced 28.1 Mb of genomic sequence that allowed the identification of the repetitive fraction (12.5% of the genome) and estimation of gene content (31,000 genes) of this species. BES analyses identified 3,800 SSRs and 6,617 putative SNPs. Comparative genomic studies showed that citrus gene homology and microsyntheny with Populus trichocarpa was rather higher than with Arabidopsis thaliana, a species phylogenetically closer to citrus. Conclusion In this work, we report the characterization of three BAC libraries from C. clementina, and a new set of genomic resources that may be useful for isolation of genes underlying economically important traits, physical mapping and eventually crop improvement in Citrus species. In addition, BAC end sequencing has provided a first insight on the basic structure and organization of the citrus genome and has yielded valuable molecular markers for genetic mapping and cloning of genes of agricultural interest. Paired end sequences also may be very helpful for whole-genome sequencing programs.
Collapse
Affiliation(s)
- Javier Terol
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias, Carretera Moncada, Náquera, Km. 4,5 Moncada, Valencia, E46113, Spain.
| | | | | | | |
Collapse
|
25
|
Luro FL, Costantino G, Terol J, Argout X, Allario T, Wincker P, Talon M, Ollitrault P, Morillon R. Transferability of the EST-SSRs developed on Nules clementine (Citrus clementina Hort ex Tan) to other Citrus species and their effectiveness for genetic mapping. BMC Genomics 2008; 9:287. [PMID: 18558001 PMCID: PMC2435559 DOI: 10.1186/1471-2164-9-287] [Citation(s) in RCA: 144] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2008] [Accepted: 06/16/2008] [Indexed: 11/16/2022] Open
Abstract
Background During the last decade, numerous microsatellite markers were developed for genotyping and to identify closely related plant genotypes. In citrus, previously developed microsatellite markers were arisen from genomic libraries and more often located in non coding DNA sequences. To optimize the use of these EST-SSRs as genetic markers in genome mapping programs and citrus systematic analysis, we have investigated their polymorphism related to the type (di or trinucleotide) or their position in the coding sequences. Results Among 11000 unigenes from a Clementine EST library, we have found at least one microsatellite sequence (repeated units size ranged from 2 to 6 nucleotides) in 1500 unigenes (13.6%). More than 95% of these SSRs were di or trinucleotides. If trinucleotide microsatellites were encountered trough all part of EST sequences, dinucleotide microsatellites were preferentially (50%) concentrated in the 5' 100th nucleotides. We assessed the polymorphism of 41 EST-SSR, by PCR amplification droved with flanking primers among ten Citrus species plus 3 from other genera. More than 90% of EST-SSR markers were polymorphic. Furthermore, dinucleotide microsatellite markers were more polymorphic than trinucleotide ones, probably related to their distribution that was more often located in the 5' UnTranslated Region (UTR). We obtained a good agreement of diversity relationships between the citrus species and relatives assessed with EST-SSR markers with the established taxonomy and phylogeny. To end, the heterozygosity of each genotype and all dual combinations were studied to evaluate the percentage of mappable markers. Higher values (> 45%) were observed for putative Citrus inter-specific hybrids (lime lemon, or sour orange) than for Citrus basic true species (mandarin, pummelo and citron) (<30%). Most favorable combinations for genome mapping were observed in those involving interspecific hybrid genotypes. Those gave higher levels of mappable markers (>70%) with a significant proportion suitable for synteny analysis. Conclusion Fourty one new EST-SSR markers were produced and were available for citrus genetic studies. Whatever the position of the SSR in the ESTs the EST-SSR markers we developed are powerful to investigate genetic diversity and genome mapping in citrus.
Collapse
Affiliation(s)
- François L Luro
- INRA, Unité de Recherche GEQA, INRA San Giuliano, 20230 San Nicolao, France.
| | | | | | | | | | | | | | | | | |
Collapse
|
26
|
Götz S, García-Gómez JM, Terol J, Williams TD, Nagaraj SH, Nueda MJ, Robles M, Talón M, Dopazo J, Conesa A. High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Res 2008; 36:3420-35. [PMID: 18445632 PMCID: PMC2425479 DOI: 10.1093/nar/gkn176] [Citation(s) in RCA: 2867] [Impact Index Per Article: 179.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Functional genomics technologies have been widely adopted in the biological research of both model and non-model species. An efficient functional annotation of DNA or protein sequences is a major requirement for the successful application of these approaches as functional information on gene products is often the key to the interpretation of experimental results. Therefore, there is an increasing need for bioinformatics resources which are able to cope with large amount of sequence data, produce valuable annotation results and are easily accessible to laboratories where functional genomics projects are being undertaken. We present the Blast2GO suite as an integrated and biologist-oriented solution for the high-throughput and automatic functional annotation of DNA or protein sequences based on the Gene Ontology vocabulary. The most outstanding Blast2GO features are: (i) the combination of various annotation strategies and tools controlling type and intensity of annotation, (ii) the numerous graphical features such as the interactive GO-graph visualization for gene-set function profiling or descriptive charts, (iii) the general sequence management features and (iv) high-throughput capabilities. We used the Blast2GO framework to carry out a detailed analysis of annotation behaviour through homology transfer and its impact in functional genomics research. Our aim is to offer biologists useful information to take into account when addressing the task of functionally characterizing their sequence data.
Collapse
Affiliation(s)
- Stefan Götz
- Bioinformatics Department, Centro de Investigación Principe Felipe, Valencia, Spain
| | | | | | | | | | | | | | | | | | | |
Collapse
|
27
|
Abstract
The homeotic Antennapedia gene, cloned from the genomic DNA of D. subobscura, was localized on the polytene chromosomes of nine species of the Drosophila obscura group. In all of them, the probe used hybridized on chromosomes equivalent to the E element of Müller's terminology. These results are consistent with the idea that single copy genes do not move around the genome and that chromosomal elements have conserved their genetic identity during evolution.
Collapse
Affiliation(s)
- J Terol
- Departament de Genètica, Facultat de Ciències Biològiques, Universitat de València, Spain
| | | | | |
Collapse
|
28
|
Terol J, Domingo C, Talón M. The GH3 family in plants: genome wide analysis in rice and evolutionary history based on EST analysis. Gene 2006; 371:279-90. [PMID: 16488558 DOI: 10.1016/j.gene.2005.12.014] [Citation(s) in RCA: 104] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2005] [Revised: 12/12/2005] [Accepted: 12/16/2005] [Indexed: 12/30/2022]
Abstract
The GH3 gene family in Arabidopsis, implicated in hormonal homeostasis through the conjugation of indolacetic and jasmonic acids to amino acids, is involved in a broad range of plant growth and development processes. In this work, the analysis of the GH3 family in the genome of Oryza sativa identified 13 hypothetical ORFs. EST analysis and RT-PCR assays demonstrated that 12 of them were active genes. An extensive EST analysis of the GH3 family performed on 26 plant species was used to estimate the minimum number of GH3 genes en each one. The data indicated that the members of the GH3 family progressively increased in the different plant divisions from Chlorophyta (0), Bryophyta (3), and Coniferophyta (4), to Magnoliophyta (7-19). Phylogenetic analyses showed a high degree of conservation between Arabidopsis and rice GH3 proteins and, in general, in the plant kingdom. The data revealed a homology clustering consistent with the functional classification of the Arabidopsis proteins, since most of the 110 sequences analyzed grouped into 2 main clusters, corresponding to the Arabidopsis functional groups I (jasmonic acid adenylation) and II (indolacetic acid adenylation). And additional cluster including group III (non-adenylation ability) was exclusively composed of proteins from Arabidopsis thaliana, Brassica napus and Gossypium hirsutum.
Collapse
Affiliation(s)
- Javier Terol
- Departamento de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra. Moncada Náquera Km 4,5, Moncada (Valencia) 46113, Spain.
| | | | | |
Collapse
|
29
|
Muñoz-Descalzo S, Terol J, Paricio N. Cabut, a C2H2 zinc finger transcription factor, is required during Drosophila dorsal closure downstream of JNK signaling. Dev Biol 2005; 287:168-79. [PMID: 16198331 DOI: 10.1016/j.ydbio.2005.08.048] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2005] [Revised: 08/29/2005] [Accepted: 08/31/2005] [Indexed: 11/29/2022]
Abstract
During dorsal closure, the lateral epithelia on each side of the embryo migrate dorsally over the amnioserosa and fuse at the dorsal midline. Detailed genetic studies have revealed that many molecules are involved in this epithelial sheet movement, either with a signaling function or as structural or motor components of the process. Here, we report the characterization of cabut (cbt), a new Drosophila gene involved in dorsal closure. cbt is expressed in the yolk sac nuclei and in the lateral epidermis. The Cbt protein contains three C2H2-type zinc fingers and a serine-rich domain, suggesting that it functions as a transcription factor. cbt mutants die as embryos with dorsal closure defects. Such embryos show defects in the elongation of the dorsal-most epidermal cells as well as in the actomyosin cable assembly at the leading edge. A combination of molecular and genetic analyses demonstrates that cbt expression is dependent on the JNK cascade during dorsal closure, and it functions downstream of Jun regulating dpp expression in the leading edge cells.
Collapse
Affiliation(s)
- Silvia Muñoz-Descalzo
- Departamento de Genética, Facultad CC Biológicas, University of Valencia, Dr. Moliner 50, 46100 Burjasot, Spain
| | | | | |
Collapse
|
30
|
Conesa A, Götz S, García-Gómez JM, Terol J, Talón M, Robles M. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 2005; 21:3674-3676. [PMID: 16081474 DOI: 10.1093/bioinformatics/bti610%jbioinformatics] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023] Open
Abstract
SUMMARY We present here Blast2GO (B2G), a research tool designed with the main purpose of enabling Gene Ontology (GO) based data mining on sequence data for which no GO annotation is yet available. B2G joints in one application GO annotation based on similarity searches with statistical analysis and highlighted visualization on directed acyclic graphs. This tool offers a suitable platform for functional genomics research in non-model species. B2G is an intuitive and interactive desktop application that allows monitoring and comprehension of the whole annotation and analysis process. AVAILABILITY Blast2GO is freely available via Java Web Start at http://www.blast2go.de. SUPPLEMENTARY MATERIAL http://www.blast2go.de -> Evaluation.
Collapse
Affiliation(s)
- Ana Conesa
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias, Moncada, Valencia, Spain.
| | | | | | | | | | | |
Collapse
|
31
|
Conesa A, Götz S, García-Gómez JM, Terol J, Talón M, Robles M. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 2005; 21:3674-6. [PMID: 16081474 DOI: 10.1093/bioinformatics/bti610] [Citation(s) in RCA: 8009] [Impact Index Per Article: 421.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
SUMMARY We present here Blast2GO (B2G), a research tool designed with the main purpose of enabling Gene Ontology (GO) based data mining on sequence data for which no GO annotation is yet available. B2G joints in one application GO annotation based on similarity searches with statistical analysis and highlighted visualization on directed acyclic graphs. This tool offers a suitable platform for functional genomics research in non-model species. B2G is an intuitive and interactive desktop application that allows monitoring and comprehension of the whole annotation and analysis process. AVAILABILITY Blast2GO is freely available via Java Web Start at http://www.blast2go.de. SUPPLEMENTARY MATERIAL http://www.blast2go.de -> Evaluation.
Collapse
Affiliation(s)
- Ana Conesa
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias, Moncada, Valencia, Spain.
| | | | | | | | | | | |
Collapse
|
32
|
Forment J, Gadea J, Huerta L, Abizanda L, Agusti J, Alamar S, Alos E, Andres F, Arribas R, Beltran JP, Berbel A, Blazquez MA, Brumos J, Canas LA, Cercos M, Colmenero-Flores JM, Conesa A, Estables B, Gandia M, Garcia-Martinez JL, Gimeno J, Gisbert A, Gomez G, Gonzalez-Candelas L, Granell A, Guerri J, Lafuente MT, Madueno F, Marcos JF, Marques MC, Martinez F, Martinez-Godoy MA, Miralles S, Moreno P, Navarro L, Pallas V, Perez-Amador MA, Perez-Valle J, Pons C, Rodrigo I, Rodriguez PL, Royo C, Serrano R, Soler G, Tadeo F, Talon M, Terol J, Trenor M, Vaello L, Vicente O, Vidal C, Zacarias L, Conejero V. Development of a citrus genome-wide EST collection and cDNA microarray as resources for genomic studies. Plant Mol Biol 2005; 57:375-91. [PMID: 15830128 DOI: 10.1007/s11103-004-7926-1] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2004] [Accepted: 12/20/2004] [Indexed: 05/20/2023]
Abstract
A functional genomics project has been initiated to approach the molecular characterization of the main biological and agronomical traits of citrus. As a key part of this project, a citrus EST collection has been generated from 25 cDNA libraries covering different tissues, developmental stages and stress conditions. The collection includes a total of 22,635 high-quality ESTs, grouped in 11,836 putative unigenes, which represent at least one third of the estimated number of genes in the citrus genome. Functional annotation of unigenes which have Arabidopsis orthologues (68% of all unigenes) revealed gene representation in every major functional category, suggesting that a genome-wide EST collection was obtained. A Citrus clementina Hort. ex Tan. cv. Clemenules genomic library, that will contribute to further characterization of relevant genes, has also been constructed. To initiate the analysis of citrus transcriptome, we have developed a cDNA microarray containing 12,672 probes corresponding to 6875 putative unigenes of the collection. Technical characterization of the microarray showed high intra- and inter-array reproducibility, as well as a good range of sensitivity. We have also validated gene expression data achieved with this microarray through an independent technique such as RNA gel blot analysis.
Collapse
Affiliation(s)
- J Forment
- Instituto de Biologíia Molecular y Celular de Plantas (IBMCP), Universidad Politécnica de Valencia, Laboratorio de Genómica, Spain
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
33
|
Morales JM, Rodriguez M, Terol J, Torres A, Alvarez J. Nursing Records With Standardized Nursing Language in Prehospital Emergency Care: From Utopia to Reality. ACTA ACUST UNITED AC 2003. [DOI: 10.1111/j.1744-618x.2003.032_9.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
34
|
|
35
|
Terol J, Bargues M, Carrasco P, Pérez-Alonso M, Paricio N. Molecular characterization and evolution of the protein phosphatase 2A B' regulatory subunit family in plants. Plant Physiol 2002; 129:808-22. [PMID: 12068121 PMCID: PMC161703 DOI: 10.1104/pp.020004] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Type 2A serine/threonine protein phosphatases (PP2A) are important components in the reversible protein phosphorylation events in plants and other organisms. PP2A proteins are oligomeric complexes constituted by a catalytic subunit and several regulatory subunits that modulate the activity of these phosphatases. The analysis of the complete genome of Arabidopsis allowed us to characterize four novel genes, AtB'epsilon, AtB'zeta, AtB'eta, and AtB'theta;, belonging to the PP2A B' regulatory subunit family. Because four genes of this type had been described previously, this family is composed of eight members. Reverse transcriptase-polymerase chain reaction experiments showed that AtB'epsilon mRNAs are present in all Arabidopsis tissues analyzed, and their levels do not respond significantly to heat stress. Expressed sequence tags corresponding to AtB'zeta, AtB'eta, and AtB'theta; have been identified, indicating that the new genes are actively transcribed. The genomic organization of this family of PP2A regulatory subunits is reported, as well as its chromosomal location. An extensive survey of the family has been carried out in plants, characterizing B' subunits in a number of different species, and performing a phylogenetic study that included several B' regulatory proteins from animals. Our results indicate that the animal and plant proteins have evolved independently, that there is a relationship between the number of B' isoforms and the complexity of the organism, and that there are at least three main subfamilies of regulatory subunits in plants, which we have named alpha, eta, and kappa.
Collapse
Affiliation(s)
- Javier Terol
- Departament de Genetica, Universitat de València, Doctor Moliner 50, 46100 Burjassot, Spain
| | | | | | | | | |
Collapse
|
36
|
Terol J, Mascarell R, Fernandez-Pedrosa V, Pérez-Alonso M. Statistical validation of the identification of tuna species: bootstrap analysis of mitochondrial DNA sequences. J Agric Food Chem 2002; 50:963-969. [PMID: 11853465 DOI: 10.1021/jf011032o] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Sequencing of the mitochondrial cytochrome b gene has been used to differentiate three tuna species: Thunnus albacares (yellowfin tuna), Thunnus obesus (bigeye tuna), and Katsuwonus pelamis (skipjack). A PCR amplified 528 bp fragment from 30 frozen samples and a 171 bp fragment from 26 canned samples of the three species were analyzed to determine the intraspecific variation and the positions with diagnostic value. Polymorphic sites between the species that did not present intraspecific variation were given a diagnostic value. The genetic distance between the sequences was calculated, and a phylogenetic tree was constructed, showing that the sequences belonging to the same species clustered together. The bootstrap test of confidence was used to determine the statistical validation of the species assignation, allowing for the first time a quantification of the certainty of the species assignation. The bootstrap values obtained from these results indicate that the sequencing of the cytochrome b fragments allows a correct species assignation with a probability > or =95%.
Collapse
Affiliation(s)
- Javier Terol
- Departamento de Genética, Universidad de Valencia, Dr. Moliner 50, Burjasot E46100, Spain
| | | | | | | |
Collapse
|
37
|
Terol J, Castillo MC, Bargues M, Pérez-Alonso M, de Frutos R. Structural and evolutionary analysis of the copia-like elements in the Arabidopsis thaliana genome. Mol Biol Evol 2001; 18:882-92. [PMID: 11319272 DOI: 10.1093/oxfordjournals.molbev.a003870] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The analysis of 460 kb of genomic sequence of Arabidopsis thaliana chromosome III allowed us to identify two new transposable elements named AtC1 and AtC2. AtC1 shows identical long terminal repeats (LTRs) and all the structural features characteristic of the copia-like active elements. AtC2 is also a full copia-like element, but a putative stop codon in the open reading frame (ORF) would produce a truncated protein. In order to identify the copia-like fraction of the A. thaliana genome, a careful computer-based analysis of the available sequences (which correspond to 92% of the genome) was performed. Approximately 300 nonredundant copia-like sequences homologous to AtC1 and AtC2 were detected, which showed an extreme heterogeneity in size and degree of conservation. This number of copies would correspond to approximately 1% of the A. thaliana genome. Seventy-one sequences were selected for further analysis, with 23 of them being full complete elements. Five corresponded to previously described ones, and the remaining ones, named AtC3 to AtC18 are new elements described in this work. Most of these elements presented a putative functional ORF, nearly identical LTRs, and the other elements necessary for retrotransposon activity. Phylogenetic trees, supported by high bootstrap values, indicated that these 23 elements could be considered separate families. In turn, these 23 families could be clustered into six major lineages, named copia I-VI. Most of the 71 analyzed sequences clustered into these six main clades. The widespread presence of these copia-like superfamilies throughout plant genomes is discussed.
Collapse
Affiliation(s)
- J Terol
- Departamento de Genética, Facultad de Ciencias Biológicas, Universitat de València, Valencia, Spain
| | | | | | | | | |
Collapse
|
38
|
Abstract
We describe a new subfamily of WD repeat proteins characterised by the presence of a C3H zinc finger at the N-terminal part of the protein associated with seven WD40 repeats. We have identified four members of this subfamily in Arabidopsis thaliana, one of them with associated expressed sequence tags (ESTs). We have also identified homologous ESTs in rice, cotton, maize, poplar, pine tree and the ice plant. We do not observe animal homologues, suggesting that this subfamily could be specific for plants. Our data suggest an important role for these proteins. Based on the high sequence conservation within the conserved domains, we suggest that these proteins could have a regulatory function.
Collapse
Affiliation(s)
- J Terol
- Departamento de Genética, Universitat de València, Dr. Moliner 50, 46100, Burjassot, Spain.
| | | | | |
Collapse
|
39
|
Salanoubat M, Lemcke K, Rieger M, Ansorge W, Unseld M, Fartmann B, Valle G, Blöcker H, Perez-Alonso M, Obermaier B, Delseny M, Boutry M, Grivell LA, Mache R, Puigdomènech P, De Simone V, Choisne N, Artiguenave F, Robert C, Brottier P, Wincker P, Cattolico L, Weissenbach J, Saurin W, Quétier F, Schäfer M, Müller-Auer S, Gabel C, Fuchs M, Benes V, Wurmbach E, Drzonek H, Erfle H, Jordan N, Bangert S, Wiedelmann R, Kranz H, Voss H, Holland R, Brandt P, Nyakatura G, Vezzi A, D'Angelo M, Pallavicini A, Toppo S, Simionati B, Conrad A, Hornischer K, Kauer G, Löhnert TH, Nordsiek G, Reichelt J, Scharfe M, Schön O, Bargues M, Terol J, Climent J, Navarro P, Collado C, Perez-Perez A, Ottenwälder B, Duchemin D, Cooke R, Laudie M, Berger-Llauro C, Purnelle B, Masuy D, de Haan M, Maarse AC, Alcaraz JP, Cottet A, Casacuberta E, Monfort A, Argiriou A, flores M, Liguori R, Vitale D, Mannhaupt G, Haase D, Schoof H, Rudd S, Zaccaria P, Mewes HW, Mayer KF, Kaul S, Town CD, Koo HL, Tallon LJ, Jenkins J, Rooney T, Rizzo M, Walts A, Utterback T, Fujii CY, Shea TP, Creasy TH, Haas B, Maiti R, Wu D, Peterson J, Van Aken S, Pai G, Militscher J, Sellers P, Gill JE, Feldblyum TV, Preuss D, Lin X, Nierman WC, Salzberg SL, White O, Venter JC, Fraser CM, Kaneko T, Nakamura Y, Sato S, Kato T, Asamizu E, Sasamoto S, Kimura T, Idesawa K, Kawashima K, Kishida Y, Kiyokawa C, Kohara M, Matsumoto M, Matsuno A, Muraki A, Nakayama S, Nakazaki N, Shinpo S, Takeuchi C, Wada T, Watanabe A, Yamada M, Yasuda M, Tabata S. Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana. Nature 2000; 408:820-2. [PMID: 11130713 DOI: 10.1038/35048706] [Citation(s) in RCA: 142] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Arabidopsis thaliana is an important model system for plant biologists. In 1996 an international collaboration (the Arabidopsis Genome Initiative) was formed to sequence the whole genome of Arabidopsis and in 1999 the sequence of the first two chromosomes was reported. The sequence of the last three chromosomes and an analysis of the whole genome are reported in this issue. Here we present the sequence of chromosome 3, organized into four sequence segments (contigs). The two largest (13.5 and 9.2 Mb) correspond to the top (long) and the bottom (short) arms of chromosome 3, and the two small contigs are located in the genetically defined centromere. This chromosome encodes 5,220 of the roughly 25,500 predicted protein-coding genes in the genome. About 20% of the predicted proteins have significant homology to proteins in eukaryotic genomes for which the complete sequence is available, pointing to important conserved cellular functions among eukaryotes.
Collapse
Affiliation(s)
- M Salanoubat
- Genoscope and CNRS FRE2231, Evry, France. salanou@genoscope. cns.fr
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
40
|
Mayer K, Schüller C, Wambutt R, Murphy G, Volckaert G, Pohl T, Düsterhöft A, Stiekema W, Entian KD, Terryn N, Harris B, Ansorge W, Brandt P, Grivell L, Rieger M, Weichselgartner M, de Simone V, Obermaier B, Mache R, Müller M, Kreis M, Delseny M, Puigdomenech P, Watson M, Schmidtheini T, Reichert B, Portatelle D, Perez-Alonso M, Boutry M, Bancroft I, Vos P, Hoheisel J, Zimmermann W, Wedler H, Ridley P, Langham SA, McCullagh B, Bilham L, Robben J, Van der Schueren J, Grymonprez B, Chuang YJ, Vandenbussche F, Braeken M, Weltjens I, Voet M, Bastiaens I, Aert R, Defoor E, Weitzenegger T, Bothe G, Ramsperger U, Hilbert H, Braun M, Holzer E, Brandt A, Peters S, van Staveren M, Dirske W, Mooijman P, Klein Lankhorst R, Rose M, Hauf J, Kötter P, Berneiser S, Hempel S, Feldpausch M, Lamberth S, Van den Daele H, De Keyser A, Buysshaert C, Gielen J, Villarroel R, De Clercq R, Van Montagu M, Rogers J, Cronin A, Quail M, Bray-Allen S, Clark L, Doggett J, Hall S, Kay M, Lennard N, McLay K, Mayes R, Pettett A, Rajandream MA, Lyne M, Benes V, Rechmann S, Borkova D, Blöcker H, Scharfe M, Grimm M, Löhnert TH, Dose S, de Haan M, Maarse A, Schäfer M, Müller-Auer S, Gabel C, Fuchs M, Fartmann B, Granderath K, Dauner D, Herzl A, Neumann S, Argiriou A, Vitale D, Liguori R, Piravandi E, Massenet O, Quigley F, Clabauld G, Mündlein A, Felber R, Schnabl S, Hiller R, Schmidt W, Lecharny A, Aubourg S, Chefdor F, Cooke R, Berger C, Montfort A, Casacuberta E, Gibbons T, Weber N, Vandenbol M, Bargues M, Terol J, Torres A, Perez-Perez A, Purnelle B, Bent E, Johnson S, Tacon D, Jesse T, Heijnen L, Schwarz S, Scholler P, Heber S, Francs P, Bielke C, Frishman D, Haase D, Lemcke K, Mewes HW, Stocker S, Zaccaria P, Bevan M, Wilson RK, de la Bastide M, Habermann K, Parnell L, Dedhia N, Gnoj L, Schutz K, Huang E, Spiegel L, Sehkon M, Murray J, Sheet P, Cordes M, Abu-Threideh J, Stoneking T, Kalicki J, Graves T, Harmon G, Edwards J, Latreille P, Courtney L, Cloud J, Abbott A, Scott K, Johnson D, Minx P, Bentley D, Fulton B, Miller N, Greco T, Kemp K, Kramer J, Fulton L, Mardis E, Dante M, Pepin K, Hillier L, Nelson J, Spieth J, Ryan E, Andrews S, Geisel C, Layman D, Du H, Ali J, Berghoff A, Jones K, Drone K, Cotton M, Joshu C, Antonoiu B, Zidanic M, Strong C, Sun H, Lamar B, Yordan C, Ma P, Zhong J, Preston R, Vil D, Shekher M, Matero A, Shah R, Swaby IK, O'Shaughnessy A, Rodriguez M, Hoffmann J, Till S, Granat S, Shohdy N, Hasegawa A, Hameed A, Lodhi M, Johnson A, Chen E, Marra M, Martienssen R, McCombie WR. Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana. Nature 1999; 402:769-77. [PMID: 10617198 DOI: 10.1038/47134] [Citation(s) in RCA: 313] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The higher plant Arabidopsis thaliana (Arabidopsis) is an important model for identifying plant genes and determining their function. To assist biological investigations and to define chromosome structure, a coordinated effort to sequence the Arabidopsis genome was initiated in late 1996. Here we report one of the first milestones of this project, the sequence of chromosome 4. Analysis of 17.38 megabases of unique sequence, representing about 17% of the genome, reveals 3,744 protein coding genes, 81 transfer RNAs and numerous repeat elements. Heterochromatic regions surrounding the putative centromere, which has not yet been completely sequenced, are characterized by an increased frequency of a variety of repeats, new repeats, reduced recombination, lowered gene density and lowered gene expression. Roughly 60% of the predicted protein-coding genes have been functionally characterized on the basis of their homology to known genes. Many genes encode predicted proteins that are homologous to human and Caenorhabditis elegans proteins.
Collapse
Affiliation(s)
- K Mayer
- GSF-Forschungszentrum f. Umwelt u. Gesundheit, Munich Information Center for Protein Sequences am Max-Planck-Institut f. Biochemie, Germany
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
41
|
Medina J, Bargues M, Terol J, Pérez-Alonso M, Salinas J. The Arabidopsis CBF gene family is composed of three genes encoding AP2 domain-containing proteins whose expression Is regulated by low temperature but not by abscisic acid or dehydration. Plant Physiol 1999; 119:463-70. [PMID: 9952441 PMCID: PMC32122 DOI: 10.1104/pp.119.2.463] [Citation(s) in RCA: 264] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
We have identified two genes from Arabidopsis that show high similarity with CBF1, a gene encoding an AP2 domain-containing transcriptional activator that binds to the low-temperature-responsive element CCGAC and induces the expression of some cold-regulated genes, increasing plant freezing tolerance. These two genes, which we have named CBF2 and CBF3, also encode proteins containing AP2 DNA-binding motifs. Furthermore, like CBF1, CBF2 and CBF3 proteins also include putative nuclear-localization signals and potential acidic activation domains. The CBF2 and CBF3 genes are linked to CBF1, constituting a cluster on the bottom arm of chromosome IV. The high level of similarity among the three CBF genes, their tandem organization, and the fact that they have the same transcriptional orientation all suggest a common origin. CBF1, CBF2, and CBF3 show identical expression patterns, being induced very rapidly by low-temperature treatment. However, in contrast to most of the cold-induced plant genes characterized, they are not responsive to abscisic acid or dehydration. Taken together, all of these data suggest that CBF2 and CBF3 may function as transcriptional activators, controlling the level of low-temperature gene expression and promoting freezing tolerance through an abscisic acid-independent pathway.
Collapse
Affiliation(s)
- J Medina
- Departamento de Mejora Genética y Biotecnología, Instituto Nacional de Investigaciones Agrarias y Alimentarias, Carretera de la Coruña, Km. 7, 28040 Madrid, Spain
| | | | | | | | | |
Collapse
|
42
|
Abstract
We have characterized at the molecular level the zerknüllt (zen) region of the Drosophila subobscura Antennapedia complex. The sequence comparison between D. subobscura and D. melanogaster shows an irregular distribution of the conserved and diverged regions, with the homeobox and a putative activating domain completely conserved. Comparisons of the promoter sequence and pattern of expression of the gene during development suggest that the regulation of zen has been conserved during evolution. The conservation of zen expression in a subpopulation of the polar cells indicates the existence of an important role in such cells. We describe a transitory segmented pattern of expression of zen in both species, suggesting the existence of interactions with a pair rule gene. Some indirect clues indicate that the z2 gene might be absent from the D. subobscura genome. A chromosome walk initiated to reach the proboscipedia gene of D. subobscura reveals that the distance between pb and zen is at least four times the one described for D. melanogaster and for D. pseudoobscura. Finally, we present cytological evidence showing that the ANT-C is inverted in D. subobscura as compared to D. melanogaster.
Collapse
Affiliation(s)
- J Terol
- Department of Biochemistry, Imperial College, London, UK
| | | | | |
Collapse
|
43
|
|