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Chandran D. Co-option of developmentally regulated plant SWEET transporters for pathogen nutrition and abiotic stress tolerance. IUBMB Life 2015; 67:461-71. [PMID: 26179993 DOI: 10.1002/iub.1394] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 06/15/2015] [Indexed: 11/07/2022]
Abstract
Plant sugar will eventually be exported transporter (SWEET) sugar transporters have been implicated in various developmental processes where sugar efflux is essential, including sucrose loading of phloem for long-distance sugar transport, nectar secretion, embryo and pollen nutrition, and maintenance of sugar homeostasis in plant organs. Notably, these transporters are selectively targeted by pathogens to gain access to host sugars. In most cases, when SWEET function is blocked, the growth and virulence of the pathogen is also reduced. There is growing evidence to suggest that the lifestyle of the pathogen may dictate which SWEET or set of SWEET genes are recruited for pathogen growth and proliferation. Furthermore, SWEET transporters may also play a role in abiotic stress tolerance by enabling plant growth under unfavorable environmental conditions. This review provides an overview of the diverse functions of SWEET proteins in plant development, pathogen nutrition, and abiotic stress tolerance. In addition, utility of the model legume Medicago truncatula as a tool to elucidate SWEET function in diverse host-microbe interactions is discussed.
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Affiliation(s)
- Divya Chandran
- Regional Center for Biotechnology, NCR Biotech Science Cluster, Faridabad, Haryana, India
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252
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Rocher S, Jean M, Castonguay Y, Belzile F. Validation of Genotyping-By-Sequencing Analysis in Populations of Tetraploid Alfalfa by 454 Sequencing. PLoS One 2015; 10:e0131918. [PMID: 26115486 PMCID: PMC4482585 DOI: 10.1371/journal.pone.0131918] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 06/08/2015] [Indexed: 02/04/2023] Open
Abstract
Genotyping-by-sequencing (GBS) is a relatively low-cost high throughput genotyping technology based on next generation sequencing and is applicable to orphan species with no reference genome. A combination of genome complexity reduction and multiplexing with DNA barcoding provides a simple and affordable way to resolve allelic variation between plant samples or populations. GBS was performed on ApeKI libraries using DNA from 48 genotypes each of two heterogeneous populations of tetraploid alfalfa (Medicago sativa spp. sativa): the synthetic cultivar Apica (ATF0) and a derived population (ATF5) obtained after five cycles of recurrent selection for superior tolerance to freezing (TF). Nearly 400 million reads were obtained from two lanes of an Illumina HiSeq 2000 sequencer and analyzed with the Universal Network-Enabled Analysis Kit (UNEAK) pipeline designed for species with no reference genome. Following the application of whole dataset-level filters, 11,694 single nucleotide polymorphism (SNP) loci were obtained. About 60% had a significant match on the Medicago truncatula syntenic genome. The accuracy of allelic ratios and genotype calls based on GBS data was directly assessed using 454 sequencing on a subset of SNP loci scored in eight plant samples. Sequencing depth in this study was not sufficient for accurate tetraploid allelic dosage, but reliable genotype calls based on diploid allelic dosage were obtained when using additional quality filtering. Principal Component Analysis of SNP loci in plant samples revealed that a small proportion (<5%) of the genetic variability assessed by GBS is able to differentiate ATF0 and ATF5. Our results confirm that analysis of GBS data using UNEAK is a reliable approach for genome-wide discovery of SNP loci in outcrossed polyploids.
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Affiliation(s)
- Solen Rocher
- Centre de Recherche et de Développement sur les Sols et les Grandes Cultures, Agriculture et agroalimentaire Canada, Quebec City (QC), Canada
| | - Martine Jean
- Département de Phytologie and Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec City (QC), Canada
| | - Yves Castonguay
- Centre de Recherche et de Développement sur les Sols et les Grandes Cultures, Agriculture et agroalimentaire Canada, Quebec City (QC), Canada
- * E-mail:
| | - François Belzile
- Département de Phytologie and Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec City (QC), Canada
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Pellizzaro A, Clochard T, Planchet E, Limami AM, Morère-Le Paven MC. Identification and molecular characterization of Medicago truncatula NRT2 and NAR2 families. PHYSIOLOGIA PLANTARUM 2015; 154:256-69. [PMID: 25430977 DOI: 10.1111/ppl.12314] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2014] [Revised: 11/22/2014] [Accepted: 11/24/2014] [Indexed: 05/24/2023]
Abstract
Nitrate transporters received little attention to legumes probably because these species are able to adapt to N starvation by developing biological N2 fixation. Still it is important to study nitrate transport systems in legumes because nitrate intervenes as a signal in regulation of nodulation probably through nitrate transporters. The aim of this work is to achieve a molecular characterization of nitrate transporter 2 (NRT2) and NAR2 (NRT3) families to allow further work that would unravel their involvement in nitrate transport and signaling. Browsing the latest version of the Medicago truncatula genome annotation (v4 version) revealed three putative NRT2 members that we have named MtNRT2.1 (Medtr4g057890.1), MtNRT2.2 (Medtr4g057865.1) and MtNRT2.3 (Medtr8g069775.1) and two putative NAR2 members we named MtNAR2.1 (Medtr4g104730.1) and MtNAR2.2 (Medtr4g104700.1). The regulation and the spatial expression profiles of MtNRT2.1, the coincidence of its expression with that of MtNAR2.1 and MtNAR2.2 and the size of the encoded protein with 12 transmembrane (TM) spanning regions strongly support the idea that MtNRT2.1 is a nitrate transporter with a major contribution to the high-affinity transport system (HATS), while a very low level of expression characterized MtNRT2.2. Unlike MtNRT2.1, MtNRT2.3 showed a lower level of expression in the root system but was expressed in the shoots and in the nodules thus suggesting an involvement of the encoded protein in nitrate transport inside the plant and/or in nitrate signaling pathways controlling post-inoculation processes that govern nodule functioning.
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Affiliation(s)
- Anthoni Pellizzaro
- Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR4207 QUASAV, 2 Boulevard Lavoisier, F-49045 Angers, France
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, 42 rue Georges Morel, F-49071 Beaucouzé, France
| | - Thibault Clochard
- Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR4207 QUASAV, 2 Boulevard Lavoisier, F-49045 Angers, France
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, 42 rue Georges Morel, F-49071 Beaucouzé, France
| | - Elisabeth Planchet
- Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR4207 QUASAV, 2 Boulevard Lavoisier, F-49045 Angers, France
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, 42 rue Georges Morel, F-49071 Beaucouzé, France
| | - Anis M Limami
- Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR4207 QUASAV, 2 Boulevard Lavoisier, F-49045 Angers, France
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, 42 rue Georges Morel, F-49071 Beaucouzé, France
| | - Marie-Christine Morère-Le Paven
- Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR4207 QUASAV, 2 Boulevard Lavoisier, F-49045 Angers, France
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, 42 rue Georges Morel, F-49071 Beaucouzé, France
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Gentzbittel L, Andersen SU, Ben C, Rickauer M, Stougaard J, Young ND. Naturally occurring diversity helps to reveal genes of adaptive importance in legumes. FRONTIERS IN PLANT SCIENCE 2015; 6:269. [PMID: 25954294 PMCID: PMC4404971 DOI: 10.3389/fpls.2015.00269] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 04/03/2015] [Indexed: 05/05/2023]
Abstract
Environmental changes challenge plants and drive adaptation to new conditions, suggesting that natural biodiversity may be a source of adaptive alleles acting through phenotypic plasticity and/or micro-evolution. Crosses between accessions differing for a given trait have been the most common way to disentangle genetic and environmental components. Interestingly, such man-made crosses may combine alleles that never meet in nature. Another way to discover adaptive alleles, inspired by evolution, is to survey large ecotype collections and to use association genetics to identify loci of interest. Both of these two genetic approaches are based on the use of biodiversity and may eventually help us in identifying the genes that plants use to respond to challenges such as short-term stresses or those due to global climate change. In legumes, two wild species, Medicago truncatula and Lotus japonicus, plus the cultivated soybean (Glycine max) have been adopted as models for genomic studies. In this review, we will discuss the resources, limitations and future plans for a systematic use of biodiversity resources in model legumes to pinpoint genes of adaptive importance in legumes, and their application in breeding.
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Affiliation(s)
- Laurent Gentzbittel
- EcoLab Laboratoire Écologie Fonctionnelle et Environnement, Institut National Polytechnique de Toulouse, Ecole Nationale Supérieure Agronomique de Toulouse, Université Fédérale de ToulouseCastanet Tolosan, France
- EcoLab Laboratoire Écologie Fonctionnelle et Environnement, Centre National de la Recherche ScientifiqueCastanet Tolosan, France
| | - Stig U. Andersen
- Department of Molecular Biology and Genetics, Centre for Carbohydrate Recognition and Signalling, Aarhus UniversityAarhus, Denmark
| | - Cécile Ben
- EcoLab Laboratoire Écologie Fonctionnelle et Environnement, Institut National Polytechnique de Toulouse, Ecole Nationale Supérieure Agronomique de Toulouse, Université Fédérale de ToulouseCastanet Tolosan, France
- EcoLab Laboratoire Écologie Fonctionnelle et Environnement, Centre National de la Recherche ScientifiqueCastanet Tolosan, France
| | - Martina Rickauer
- EcoLab Laboratoire Écologie Fonctionnelle et Environnement, Institut National Polytechnique de Toulouse, Ecole Nationale Supérieure Agronomique de Toulouse, Université Fédérale de ToulouseCastanet Tolosan, France
- EcoLab Laboratoire Écologie Fonctionnelle et Environnement, Centre National de la Recherche ScientifiqueCastanet Tolosan, France
| | - Jens Stougaard
- Department of Molecular Biology and Genetics, Centre for Carbohydrate Recognition and Signalling, Aarhus UniversityAarhus, Denmark
| | - Nevin D. Young
- Department of Plant Pathology, University of MinnesotaSt. Paul, MN, USA
- Department of Plant Biology, University of MinnesotaSt. Paul, MN, USA
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255
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Wong MML, Gujaria-Verma N, Ramsay L, Yuan HY, Caron C, Diapari M, Vandenberg A, Bett KE. Classification and characterization of species within the genus lens using genotyping-by-sequencing (GBS). PLoS One 2015; 10:e0122025. [PMID: 25815480 PMCID: PMC4376907 DOI: 10.1371/journal.pone.0122025] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 02/08/2015] [Indexed: 11/18/2022] Open
Abstract
Lentil (Lens culinaris ssp. culinaris) is a nutritious and affordable pulse with an ancient crop domestication history. The genus Lens consists of seven taxa, however, there are many discrepancies in the taxon and gene pool classification of lentil and its wild relatives. Due to the narrow genetic basis of cultivated lentil, there is a need towards better understanding of the relationships amongst wild germplasm to assist introgression of favourable genes into lentil breeding programs. Genotyping-by-sequencing (GBS) is an easy and affordable method that allows multiplexing of up to 384 samples or more per library to generate genome-wide single nucleotide Polymorphism (SNP) markers. In this study, we aimed to characterize our lentil germplasm collection using a two-enzyme GBS approach. We constructed two 96-plex GBS libraries with a total of 60 accessions where some accessions had several samples and each sample was sequenced in two technical replicates. We developed an automated GBS pipeline and detected a total of 266,356 genome-wide SNPs. After filtering low quality and redundant SNPs based on haplotype information, we constructed a maximum-likelihood tree using 5,389 SNPs. The phylogenetic tree grouped the germplasm collection into their respective taxa with strong support. Based on phylogenetic tree and STRUCTURE analysis, we identified four gene pools, namely L. culinaris/L. orientalis/L. tomentosus, L. lamottei/L. odemensis, L. ervoides and L. nigricans which form primary, secondary, tertiary and quaternary gene pools, respectively. We discovered sequencing bias problems likely due to DNA quality and observed severe run-to-run variation in the wild lentils. We examined the authenticity of the germplasm collection and identified 17% misclassified samples. Our study demonstrated that GBS is a promising and affordable tool for screening by plant breeders interested in crop wild relatives.
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Affiliation(s)
- Melissa M. L. Wong
- Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Neha Gujaria-Verma
- Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Larissa Ramsay
- Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Hai Ying Yuan
- Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Carolyn Caron
- Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Marwan Diapari
- Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Albert Vandenberg
- Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Kirstin E. Bett
- Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
- * E-mail:
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256
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Jiang C, Chen C, Huang Z, Liu R, Verdier J. ITIS, a bioinformatics tool for accurate identification of transposon insertion sites using next-generation sequencing data. BMC Bioinformatics 2015; 16:72. [PMID: 25887332 PMCID: PMC4351942 DOI: 10.1186/s12859-015-0507-2] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 02/20/2015] [Indexed: 08/30/2023] Open
Abstract
Background Transposable elements constitute an important part of the genome and are essential in adaptive mechanisms. Transposition events associated with phenotypic changes occur naturally or are induced in insertional mutant populations. Transposon mutagenesis results in multiple random insertions and recovery of most/all the insertions is critical for forward genetics study. Using genome next-generation sequencing data and appropriate bioinformatics tool, it is plausible to accurately identify transposon insertion sites, which could provide candidate causal mutations for desired phenotypes for further functional validation. Results We developed a novel bioinformatics tool, ITIS (Identification of Transposon Insertion Sites), for localizing transposon insertion sites within a genome. It takes next-generation genome re-sequencing data (NGS data), transposon sequence, and reference genome sequence as input, and generates a list of highly reliable candidate insertion sites as well as zygosity information of each insertion. Using a simulated dataset and a case study based on an insertional mutant line from Medicago truncatula, we showed that ITIS performed better in terms of sensitivity and specificity than other similar algorithms such as RelocaTE, RetroSeq, TEMP and TIF. With the case study data, we demonstrated the efficiency of ITIS by validating the presence and zygosity of predicted insertion sites of the Tnt1 transposon within a complex plant system, M. truncatula. Conclusion This study showed that ITIS is a robust and powerful tool for forward genetic studies in identifying transposable element insertions causing phenotypes. ITIS is suitable in various systems such as cell culture, bacteria, yeast, insect, mammal and plant. Electronic supplementary material The online version of this article (doi:10.1186/s12859-015-0507-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chuan Jiang
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 201602, China. .,University of Chinese Academy of Sciences, Beijing, 100039, China.
| | - Chao Chen
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 201602, China. .,University of Chinese Academy of Sciences, Beijing, 100039, China.
| | - Ziyue Huang
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 201602, China.
| | - Renyi Liu
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 201602, China.
| | - Jerome Verdier
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 201602, China.
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Abstract
Optical mapping has been widely used to improve de novo plant genome assemblies, including rice, maize, Medicago, Amborella, tomato and wheat, with more genomes in the pipeline. Optical mapping provides long-range information of the genome and can more easily identify large structural variations. The ability of optical mapping to assay long single DNA molecules nicely complements short-read sequencing which is more suitable for the identification of small and short-range variants. Direct use of optical mapping to study population-level genetic diversity is currently limited to microbial strain typing and human diversity studies. Nonetheless, optical mapping shows great promise in the study of plant trait development, domestication and polyploid evolution. Here we review the current applications and future prospects of optical mapping in the field of plant comparative genomics.
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Affiliation(s)
- Haibao Tang
- Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian People's Republic of China ; School of Plant Sciences, iPlant Collaborative, University of Arizona, Tucson, AZ 85721 USA
| | - Eric Lyons
- School of Plant Sciences, iPlant Collaborative, University of Arizona, Tucson, AZ 85721 USA
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Abstract
Optical mapping has been widely used to improve de novo plant genome assemblies, including rice, maize, Medicago, Amborella, tomato and wheat, with more genomes in the pipeline. Optical mapping provides long-range information of the genome and can more easily identify large structural variations. The ability of optical mapping to assay long single DNA molecules nicely complements short-read sequencing which is more suitable for the identification of small and short-range variants. Direct use of optical mapping to study population-level genetic diversity is currently limited to microbial strain typing and human diversity studies. Nonetheless, optical mapping shows great promise in the study of plant trait development, domestication and polyploid evolution. Here we review the current applications and future prospects of optical mapping in the field of plant comparative genomics.
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259
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Argyris JM, Ruiz-Herrera A, Madriz-Masis P, Sanseverino W, Morata J, Pujol M, Ramos-Onsins SE, Garcia-Mas J. Use of targeted SNP selection for an improved anchoring of the melon (Cucumis melo L.) scaffold genome assembly. BMC Genomics 2015; 16:4. [PMID: 25612459 PMCID: PMC4316794 DOI: 10.1186/s12864-014-1196-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 12/22/2014] [Indexed: 01/01/2023] Open
Abstract
Background The genome of the melon (Cucumis melo L.) double-haploid line DHL92 was recently sequenced, with 87.5 and 80.8% of the scaffold assembly anchored and oriented to the 12 linkage groups, respectively. However, insufficient marker coverage and a lack of recombination left several large, gene rich scaffolds unanchored, and some anchored scaffolds unoriented. To improve the anchoring and orientation of the melon genome assembly, we used resequencing data between the parental lines of DHL92 to develop a new set of SNP markers from unanchored scaffolds. Results A high-resolution genetic map composed of 580 SNPs was used to anchor 354.8 Mb of sequence, contained in 141 scaffolds (average size 2.5 Mb) and corresponding to 98.2% of the scaffold assembly, to the 12 melon chromosomes. Over 325.4 Mb (90%) of the assembly was oriented. The genetic map revealed regions of segregation distortion favoring SC alleles as well as recombination suppression regions coinciding with putative centromere, 45S, and 5S rDNA sites. New chromosome-scale pseudomolecules were created by incorporating to the previous v3.5 version an additional 38.3 Mb of anchored sequence representing 1,837 predicted genes contained in 55 scaffolds. Using fluorescent in situ hybridization (FISH) with BACs that produced chromosome-specific signals, melon chromosomes that correspond to the twelve linkage groups were identified, and a standardized karyotype of melon inbred line T111 was developed. Conclusions By utilizing resequencing data and targeted SNP selection combined with a large F2 mapping population, we significantly improved the quantity of anchored and oriented melon scaffold genome assembly. Using genome information combined with FISH mapping provided the first cytogenetic map of an inodorus melon type. With these results it was possible to make inferences on melon chromosome structure by relating zones of recombination suppression to centromeres and 45S and 5S heterochromatic regions. This study represents the first steps towards the integration of the high-resolution genetic and cytogenetic maps with the genomic sequence in melon that will provide more information on genome organization and allow for the improvement of the melon genome draft sequence. Electronic supplementary material The online version of this article (doi:10.1186/s12864-014-1196-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jason M Argyris
- IRTA, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, 08193, Barcelona, Spain.
| | - Aurora Ruiz-Herrera
- Departament de Biologia Cellular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Campus UAB, 08193, Barcelona, Spain. .,Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona, Campus UAB, 08193, Barcelona, Spain.
| | - Pablo Madriz-Masis
- IRTA, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, 08193, Barcelona, Spain.
| | - Walter Sanseverino
- IRTA, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, 08193, Barcelona, Spain. .,Present Address: Sequentia Biotech, Campus UAB - Edifici CRAG, Bellaterra - Cerdanyola del Vallès, 08193, Barcelona, Spain.
| | - Jordi Morata
- IRTA, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, 08193, Barcelona, Spain.
| | - Marta Pujol
- IRTA, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, 08193, Barcelona, Spain.
| | | | - Jordi Garcia-Mas
- IRTA, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, 08193, Barcelona, Spain.
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260
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Tang H, Zhang X, Miao C, Zhang J, Ming R, Schnable JC, Schnable PS, Lyons E, Lu J. ALLMAPS: robust scaffold ordering based on multiple maps. Genome Biol 2015; 16:3. [PMID: 25583564 PMCID: PMC4305236 DOI: 10.1186/s13059-014-0573-1] [Citation(s) in RCA: 240] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2014] [Accepted: 12/15/2014] [Indexed: 11/29/2022] Open
Abstract
The ordering and orientation of genomic scaffolds to reconstruct chromosomes is an essential step during de novo genome assembly. Because this process utilizes various mapping techniques that each provides an independent line of evidence, a combination of multiple maps can improve the accuracy of the resulting chromosomal assemblies. We present ALLMAPS, a method capable of computing a scaffold ordering that maximizes colinearity across a collection of maps. ALLMAPS is robust against common mapping errors, and generates sequences that are maximally concordant with the input maps. ALLMAPS is a useful tool in building high-quality genome assemblies. ALLMAPS is available at: https://github.com/tanghaibao/jcvi/wiki/ALLMAPS.
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Affiliation(s)
- Haibao Tang
- Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian Province, China. .,School of Plant Sciences, iPlant Collaborative, University of Arizona, Tucson, AZ, 85721, USA. .,Data2Bio LLC, 2079 Roy J. Carver Co-Lab, Ames, Iowa, 50011, USA.
| | - Xingtan Zhang
- J. Craig Venter Institute, 9704 Medical Center Dr, Rockville, MD, 20850, USA.
| | - Chenyong Miao
- Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian Province, China.
| | - Jisen Zhang
- Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian Province, China.
| | - Ray Ming
- Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian Province, China.
| | - James C Schnable
- Data2Bio LLC, 2079 Roy J. Carver Co-Lab, Ames, Iowa, 50011, USA. .,Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68588, USA.
| | - Patrick S Schnable
- Data2Bio LLC, 2079 Roy J. Carver Co-Lab, Ames, Iowa, 50011, USA. .,Department of Agronomy, Iowa State University, Ames, IA, 50011, USA.
| | - Eric Lyons
- School of Plant Sciences, iPlant Collaborative, University of Arizona, Tucson, AZ, 85721, USA.
| | - Jianguo Lu
- Heilongjiang River Fisheries Research Institute, Harbin, 150070, China.
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261
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Krishnakumar V, Kim M, Rosen BD, Karamycheva S, Bidwell SL, Tang H, Town CD. MTGD: The Medicago truncatula genome database. PLANT & CELL PHYSIOLOGY 2015; 56:e1. [PMID: 25432968 DOI: 10.1093/pcp/pcu179] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Medicago truncatula, a close relative of alfalfa (Medicago sativa), is a model legume used for studying symbiotic nitrogen fixation, mycorrhizal interactions and legume genomics. J. Craig Venter Institute (JCVI; formerly TIGR) has been involved in M. truncatula genome sequencing and annotation since 2002 and has maintained a web-based resource providing data to the community for this entire period. The website (http://www.MedicagoGenome.org) has seen major updates in the past year, where it currently hosts the latest version of the genome (Mt4.0), associated data and legacy project information, presented to users via a rich set of open-source tools. A JBrowse-based genome browser interface exposes tracks for visualization. Mutant gene symbols originally assembled and curated by the Frugoli lab are now hosted at JCVI and tie into our community annotation interface, Medicago EuCAP (to be integrated soon with our implementation of WebApollo). Literature pertinent to M. truncatula is indexed and made searchable via the Textpresso search engine. The site also implements MedicMine, an instance of InterMine that offers interconnectivity with other plant 'mines' such as ThaleMine and PhytoMine, and other model organism databases (MODs). In addition to these new features, we continue to provide keyword- and locus identifier-based searches served via a Chado-backed Tripal Instance, a BLAST search interface and bulk downloads of data sets from the iPlant Data Store (iDS). Finally, we maintain an E-mail helpdesk, facilitated by a JIRA issue tracking system, where we receive and respond to questions about the website and requests for specific data sets from the community.
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Affiliation(s)
- Vivek Krishnakumar
- Plant Genomics Group, J. Craig Venter Institute, 9704 Medical Center Dr, Rockville, MD 20850, USA
| | - Maria Kim
- Plant Genomics Group, J. Craig Venter Institute, 9704 Medical Center Dr, Rockville, MD 20850, USA
| | - Benjamin D Rosen
- Plant Genomics Group, J. Craig Venter Institute, 9704 Medical Center Dr, Rockville, MD 20850, USA
| | - Svetlana Karamycheva
- Plant Genomics Group, J. Craig Venter Institute, 9704 Medical Center Dr, Rockville, MD 20850, USA
| | - Shelby L Bidwell
- Plant Genomics Group, J. Craig Venter Institute, 9704 Medical Center Dr, Rockville, MD 20850, USA
| | - Haibao Tang
- Plant Genomics Group, J. Craig Venter Institute, 9704 Medical Center Dr, Rockville, MD 20850, USA
| | - Christopher D Town
- Plant Genomics Group, J. Craig Venter Institute, 9704 Medical Center Dr, Rockville, MD 20850, USA
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Ogilvie HA, Imin N, Djordjevic MA. Diversification of the C-TERMINALLY ENCODED PEPTIDE (CEP) gene family in angiosperms, and evolution of plant-family specific CEP genes. BMC Genomics 2014; 15:870. [PMID: 25287121 PMCID: PMC4197245 DOI: 10.1186/1471-2164-15-870] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 09/24/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Small, secreted signaling peptides work in parallel with phytohormones to control important aspects of plant growth and development. Genes from the C-TERMINALLY ENCODED PEPTIDE (CEP) family produce such peptides which negatively regulate plant growth, especially under stress, and affect other important developmental processes. To illuminate how the CEP gene family has evolved within the plant kingdom, including its emergence, diversification and variation between lineages, a comprehensive survey was undertaken to identify and characterize CEP genes in 106 plant genomes. RESULTS Using a motif-based system developed for this study to identify canonical CEP peptide domains, a total of 916 CEP genes and 1,223 CEP domains were found in angiosperms and for the first time in gymnosperms. This defines a narrow band for the emergence of CEP genes in plants, from the divergence of lycophytes to the angiosperm/gymnosperm split. Both CEP genes and domains were found to have diversified in angiosperms, particularly in the Poaceae and Solanaceae plant families. Multispecies orthologous relationships were determined for 22% of identified CEP genes, and further analysis of those groups found selective constraints upon residues within the CEP peptide and within the previously little-characterized variable region. An examination of public Oryza sativa RNA-Seq datasets revealed an expression pattern that links OsCEP5 and OsCEP6 to panicle development and flowering, and CEP gene trees reveal these emerged from a duplication event associated with the Poaceae plant family. CONCLUSIONS The characterization of the plant-family specific CEP genes OsCEP5 and OsCEP6, the association of CEP genes with angiosperm-specific development processes like panicle development, and the diversification of CEP genes in angiosperms provides further support for the hypothesis that CEP genes have been integral to the evolution of novel traits within the angiosperm lineage. Beyond these findings, the comprehensive set of CEP genes and their properties reported here will be a resource for future research on CEP genes and peptides.
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Affiliation(s)
- Huw A Ogilvie
- Research School of Biology, The Australian National University, Canberra, ACT 0200 Australia
| | - Nijat Imin
- Research School of Biology, The Australian National University, Canberra, ACT 0200 Australia
| | - Michael A Djordjevic
- Research School of Biology, The Australian National University, Canberra, ACT 0200 Australia
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Formey D, Sallet E, Lelandais-Brière C, Ben C, Bustos-Sanmamed P, Niebel A, Frugier F, Combier JP, Debellé F, Hartmann C, Poulain J, Gavory F, Wincker P, Roux C, Gentzbittel L, Gouzy J, Crespi M. The small RNA diversity from Medicago truncatula roots under biotic interactions evidences the environmental plasticity of the miRNAome. Genome Biol 2014; 15:457. [PMID: 25248950 PMCID: PMC4212123 DOI: 10.1186/s13059-014-0457-4] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 09/01/2014] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Legume roots show a remarkable plasticity to adapt their architecture to biotic and abiotic constraints, including symbiotic interactions. However, global analysis of miRNA regulation in roots is limited, and a global view of the evolution of miRNA-mediated diversification in different ecotypes is lacking. RESULTS In the model legume Medicago truncatula, we analyze the small RNA transcriptome of roots submitted to symbiotic and pathogenic interactions. Genome mapping and a computational pipeline identify 416 miRNA candidates, including known and novel variants of 78 miRNA families present in miRBase. Stringent criteria of pre-miRNA prediction yield 52 new mtr-miRNAs, including 27 miRtrons. Analyzing miRNA precursor polymorphisms in 26 M. truncatula ecotypes identifies higher sequence polymorphism in conserved rather than Medicago-specific miRNA precursors. An average of 19 targets, mainly involved in environmental responses and signalling, is predicted per novel miRNA. We identify miRNAs responsive to bacterial and fungal pathogens or symbionts as well as their related Nod and Myc-LCO symbiotic signals. Network analyses reveal modules of new and conserved co-expressed miRNAs that regulate distinct sets of targets, highlighting potential miRNA-regulated biological pathways relevant to pathogenic and symbiotic interactions. CONCLUSIONS We identify 52 novel genuine miRNAs and large plasticity of the root miRNAome in response to the environment, and also in response to purified Myc/Nod signaling molecules. The new miRNAs identified and their sequence variation across M. truncatula ecotypes may be crucial to understand the adaptation of root growth to the soil environment, notably in the agriculturally important legume crops.
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Shen C, Yue R, Yang Y, Zhang L, Sun T, Xu L, Tie S, Wang H. Genome-wide identification and expression profiling analysis of the Aux/IAA gene family in Medicago truncatula during the early phase of Sinorhizobium meliloti infection. PLoS One 2014; 9:e107495. [PMID: 25226164 PMCID: PMC4166667 DOI: 10.1371/journal.pone.0107495] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Accepted: 08/12/2014] [Indexed: 12/18/2022] Open
Abstract
Background Auxin/indoleacetic acid (Aux/IAA) genes, coding a family of short-lived nuclear proteins, play key roles in wide variety of plant developmental processes, including root system regulation and responses to environmental stimulus. However, how they function in auxin signaling pathway and symbiosis with rhizobial in Medicago truncatula are largely unknown. The present study aims at gaining deeper insight on distinctive expression and function features of Aux/IAA family genes in Medicago truncatula during nodule formation. Principal Findings Using the latest updated draft of the full Medicago truncatula genome, a comprehensive identification and analysis of IAA genes were performed. The data indicated that MtIAA family genes are distributed in all the M. truncatula chromosomes except chromosome 6. Most of MtIAA genes are responsive to exogenous auxin and express in tissues-specific manner. To understand the biological functions of MtIAA genes involved in nodule formation, quantitative real-time polymerase chain reaction (qRT-PCR) was used to test the expression profiling of MtIAA genes during the early phase of Sinorhizobium meliloti (S. meliloti) infection. The expression patterns of most MtIAA genes were down-regulated in roots and up-regulated in shoots by S. meliloti infection. The differences in expression responses between roots and shoots caused by S. meliloti infection were alleviated by 1-NOA application. Conclusion The genome-wide identification, evolution and expression pattern analysis of MtIAA genes were performed in this study. The data helps us to understand the roles of MtIAA-mediated auxin signaling in nodule formation during the early phase of S. meliloti infection.
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Affiliation(s)
- Chenjia Shen
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- * E-mail: (CS); (ST); (HW)
| | - Runqing Yue
- Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Yanjun Yang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Lei Zhang
- Department of Plant Pathology, Washington State University, Pullman, Washington, United States of America
| | - Tao Sun
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Luqin Xu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Shuanggui Tie
- Henan Academy of Agricultural Sciences, Zhengzhou, China
- * E-mail: (CS); (ST); (HW)
| | - Huizhong Wang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- * E-mail: (CS); (ST); (HW)
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265
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Bohra A, Jha UC, Kishor PBK, Pandey S, Singh NP. Genomics and molecular breeding in lesser explored pulse crops: current trends and future opportunities. Biotechnol Adv 2014; 32:1410-28. [PMID: 25196916 DOI: 10.1016/j.biotechadv.2014.09.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Revised: 08/29/2014] [Accepted: 09/01/2014] [Indexed: 12/17/2022]
Abstract
Pulses are multipurpose crops for providing income, employment and food security in the underprivileged regions, notably the FAO-defined low-income food-deficit countries. Owing to their intrinsic ability to endure environmental adversities and the least input/management requirements, these crops remain central to subsistence farming. Given their pivotal role in rain-fed agriculture, substantial research has been invested to boost the productivity of these pulse crops. To this end, genomic tools and technologies have appeared as the compelling supplement to the conventional breeding. However, the progress in minor pulse crops including dry beans (Vigna spp.), lupins, lablab, lathyrus and vetches has remained unsatisfactory, hence these crops are often labeled as low profile or lesser researched. Nevertheless, recent scientific and technological breakthroughs particularly the next generation sequencing (NGS) are radically transforming the scenario of genomics and molecular breeding in these minor crops. NGS techniques have allowed de novo assembly of whole genomes in these orphan crops. Moreover, the availability of a reference genome sequence would promote re-sequencing of diverse genotypes to unlock allelic diversity at a genome-wide scale. In parallel, NGS has offered high-resolution genetic maps or more precisely, a robust genetic framework to implement whole-genome strategies for crop improvement. As has already been demonstrated in lupin, sequencing-based genotyping of the representative sample provided access to a number of functionally-relevant markers that could be deployed straight away in crop breeding programs. This article attempts to outline the recent progress made in genomics of these lesser explored pulse crops, and examines the prospects of genomics assisted integrated breeding to enhance and stabilize crop yields.
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Affiliation(s)
- Abhishek Bohra
- Indian Institute of Pulses Research (IIPR), Kanpur 208024, India.
| | - Uday Chand Jha
- Indian Institute of Pulses Research (IIPR), Kanpur 208024, India
| | - P B Kavi Kishor
- Department of Genetics, Osmania University, Hyderabad 500007, India
| | | | - Narendra P Singh
- Indian Institute of Pulses Research (IIPR), Kanpur 208024, India
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