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Thirugnanasambandam PP, Singode A, Thalambedu LP, Athiappan S, Krishnasamy M, Purakkal SV, Govind H, Furtado A, Henry R. Long read transcriptome sequencing of a sugarcane hybrid and its progenitors, Saccharum officinarum and S. spontaneum. FRONTIERS IN PLANT SCIENCE 2023; 14:1199748. [PMID: 37662143 PMCID: PMC10469502 DOI: 10.3389/fpls.2023.1199748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 07/17/2023] [Indexed: 09/05/2023]
Abstract
Commercial sugarcane hybrids are derivatives from Saccharum officinarum and Saccharum spontaneum hybrids containing the full complement of S. officinarum and a few S. spontaneum chromosomes and recombinants with favorable agronomic characters from both the species. The combination of the two sub-genomes in varying proportions in addition to the recombinants presents a challenge in the study of gene expression and regulation in the hybrid. We now report the transcriptome analysis of the two progenitor species and a modern commercial sugarcane hybrid through long read sequencing technology. Transcripts were profiled in the two progenitor species S. officinarum (Black Cheribon), and S. spontaneum (Coimbatore accession) and a recent high yielding, high sugar variety Co 11015. The composition and contribution of the progenitors to a hybrid with respect to sugar, biomass, and disease resistance were established. Sugar related transcripts originated from S. officinarum while several stress and senescence related transcripts were from S. spontaneum in the hybrid. The hybrid had a higher number of transcripts related to sugar transporters, invertases, transcription factors, trehalose, UDP sugars, and cellulose than the two progenitor species. Both S. officinarum and the hybrid had an abundance of novel genes like sugar phosphate translocator, while S. spontaneum had just one. In general, the hybrid shared a larger number of transcripts with S. officinarum than with S. spontaneum, reflecting the genomic contribution, while the progenitors shared very few transcripts between them. The common isoforms among the three genotypes and unique isoforms specific to each genotype indicate that there is a high scope for improvement of the modern hybrids by utilizing novel gene isoforms from the progenitor species.
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Affiliation(s)
| | - Avinash Singode
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Millets Research, Hyderabad, Telangana, India
| | | | - Selvi Athiappan
- Crop Improvement Division, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu, India
| | - Mohanraj Krishnasamy
- Crop Improvement Division, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu, India
| | | | - Hemaprabha Govind
- Crop Improvement Division, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu, India
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Brisbane, QLD, Australia
| | - Robert Henry
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Brisbane, QLD, Australia
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Abstract
Vegetable tannin is widely applied in various industries, in agriculture, and in water treatment as a natural polyphenolic compound; however, little data has been collected concerning the relationship between structure and eco-toxicity. Here, the toxicity of six commercial tannin and three model chemicals was assessed using Photobacterium phosphoreum. Two kinds of hydrolyzed tannin displayed higher bioluminescence inhibition than four kinds of condensed tannin, and the model chemical of hydrolyzed tannin also showed greater toxicity than those of condensed tannin, indicating the structure dependent eco-toxicity of vegetable tannin. The reactive toxicity mechanism was proposed, which was illustrated by molecular simulations based on the model chemicals and luciferase.
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3
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Yang H, Wang T, Yu X, Yang Y, Wang C, Yang Q, Wang X. Enhanced sugar accumulation and regulated plant hormone signalling genes contribute to cold tolerance in hypoploid Saccharum spontaneum. BMC Genomics 2020; 21:507. [PMID: 32698760 PMCID: PMC7376677 DOI: 10.1186/s12864-020-06917-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 07/15/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Wild sugarcane Saccharum spontaneum plants vary in ploidy, which complicates the utilization of its germplasm in sugarcane breeding. Investigations on cold tolerance in relation to different ploidies in S. spontaneum may promote the exploitation of its germplasm and accelerate the improvement of sugarcane varieties. RESULTS A hypoploid clone 12-23 (2n = 54) and hyperploid clone 15-28 (2n = 92) of S. spontaneum were analysed under cold stress from morphological, physiological, and transcriptomic perspectives. Compared with clone 15-28, clone 12-23 plants had lower plant height, leaf length, internode length, stem diameter, and leaf width; depressed stomata and prominent bristles and papillae; and thick leaves with higher bulliform cell groups and thicker adaxial epidermis. Compared with clone 15-28, clone 12-23 showed significantly lower electrical conductivity, significantly higher water content, soluble protein content, and superoxide dismutase activity, and significantly higher soluble sugar content and peroxidase activity. Under cold stress, the number of upregulated genes and downregulated genes of clone 12-23 was higher than clone 15-28, and many stress response genes and pathways were affected and enriched to varying degrees, particularly sugar and starch metabolic pathways and plant hormone signalling pathways. Under cold stress, the activity of 6-phosphate glucose trehalose synthase, trehalose phosphate phosphatase, and brassinosteroid-signalling kinase and the content of trehalose and brassinosteroids of clone 12-23 increased. CONCLUSIONS Compared with hyperploid clone 15-28, hypoploid clone 12-23 maintained a more robust osmotic adjustment system through sugar accumulation and hormonal regulation, which resulted in stronger cold tolerance.
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Affiliation(s)
- Hongli Yang
- Sugarcane Research Institute, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, PR China
| | - Tianju Wang
- Sugarcane Research Institute, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, PR China.,Chuxiong normal university, Chuxiong, 675000, Yunnan Province, PR China
| | - Xinghua Yu
- Sugarcane Research Institute, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, PR China.,Wenshan Academy of Agricultural Sciences, Wenshan, 663000, Yunnan Province, PR China
| | - Yang Yang
- Sugarcane Research Institute, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, PR China
| | - Chunfang Wang
- Sugarcane Research Institute, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, PR China
| | - Qinghui Yang
- Sugarcane Research Institute, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, PR China.
| | - Xianhong Wang
- Sugarcane Research Institute, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, PR China.
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Manimekalai R, Suresh G, Govinda Kurup H, Athiappan S, Kandalam M. Role of NGS and SNP genotyping methods in sugarcane improvement programs. Crit Rev Biotechnol 2020; 40:865-880. [PMID: 32508157 DOI: 10.1080/07388551.2020.1765730] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Sugarcane (Saccharum spp.) is one of the most economically significant crops because of its high sucrose content and it is a promising biomass feedstock for biofuel production. Sugarcane genome sequencing and analysis is a difficult task due to its heterozygosity and polyploidy. Long sequence read technologies, PacBio Single-Molecule Real-Time (SMRT) sequencing, the Illumina TruSeq, and the Oxford Nanopore sequencing could solve the problem of genome assembly. On the applications side, next generation sequencing (NGS) technologies played a major role in the discovery of single nucleotide polymorphism (SNP) and the development of low to high throughput genotyping platforms. The two mainstream high throughput genotyping platforms are the SNP microarray and genotyping by sequencing (GBS). This paper reviews the NGS in sugarcane genomics, genotyping methodologies, and the choice of these methods. Array-based SNP genotyping is robust, provides consistent SNPs, and relatively easier downstream data analysis. The GBS method identifies large scale SNPs across the germplasm. A combination of targeted GBS and array-based genotyping methods should be used to increase the accuracy of genomic selection and marker-assisted breeding.
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Affiliation(s)
- Ramaswamy Manimekalai
- Crop Improvement Division, ICAR - Sugarcane Breeding Institute, Indian Council of Agricultural Research (ICAR), Coimbatore, Tamil Nadu, India
| | - Gayathri Suresh
- Crop Improvement Division, ICAR - Sugarcane Breeding Institute, Indian Council of Agricultural Research (ICAR), Coimbatore, Tamil Nadu, India
| | - Hemaprabha Govinda Kurup
- Crop Improvement Division, ICAR - Sugarcane Breeding Institute, Indian Council of Agricultural Research (ICAR), Coimbatore, Tamil Nadu, India
| | - Selvi Athiappan
- Crop Improvement Division, ICAR - Sugarcane Breeding Institute, Indian Council of Agricultural Research (ICAR), Coimbatore, Tamil Nadu, India
| | - Mallikarjuna Kandalam
- Business Development, Asia Pacific Japan region, Thermo Fisher Scientific, Waltham, MA, USA
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Sforça DA, Vautrin S, Cardoso-Silva CB, Mancini MC, Romero-da Cruz MV, Pereira GDS, Conte M, Bellec A, Dahmer N, Fourment J, Rodde N, Van Sluys MA, Vicentini R, Garcia AAF, Forni-Martins ER, Carneiro MS, Hoffmann HP, Pinto LR, Landell MGDA, Vincentz M, Berges H, de Souza AP. Gene Duplication in the Sugarcane Genome: A Case Study of Allele Interactions and Evolutionary Patterns in Two Genic Regions. FRONTIERS IN PLANT SCIENCE 2019; 10:553. [PMID: 31134109 PMCID: PMC6514446 DOI: 10.3389/fpls.2019.00553] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 04/11/2019] [Indexed: 05/25/2023]
Abstract
Sugarcane (Saccharum spp.) is highly polyploid and aneuploid. Modern cultivars are derived from hybridization between S. officinarum and S. spontaneum. This combination results in a genome exhibiting variable ploidy among different loci, a huge genome size (~10 Gb) and a high content of repetitive regions. An approach using genomic, transcriptomic, and genetic mapping can improve our knowledge of the behavior of genetics in sugarcane. The hypothetical HP600 and Centromere Protein C (CENP-C) genes from sugarcane were used to elucidate the allelic expression and genomic and genetic behaviors of this complex polyploid. The physically linked side-by-side genes HP600 and CENP-C were found in two different homeologous chromosome groups with ploidies of eight and ten. The first region (Region01) was a Sorghum bicolor ortholog region with all haplotypes of HP600 and CENP-C expressed, but HP600 exhibited an unbalanced haplotype expression. The second region (Region02) was a scrambled sugarcane sequence formed from different noncollinear genes containing partial duplications of HP600 and CENP-C (paralogs). This duplication resulted in a non-expressed HP600 pseudogene and a recombined fusion version of CENP-C and the orthologous gene Sobic.003G299500 with at least two chimeric gene haplotypes expressed. It was also determined that it occurred before Saccharum genus formation and after the separation of sorghum and sugarcane. A linkage map was constructed using markers from nonduplicated Region01 and for the duplication (Region01 and Region02). We compare the physical and linkage maps, demonstrating the possibility of mapping markers located in duplicated regions with markers in nonduplicated region. Our results contribute directly to the improvement of linkage mapping in complex polyploids and improve the integration of physical and genetic data for sugarcane breeding programs. Thus, we describe the complexity involved in sugarcane genetics and genomics and allelic dynamics, which can be useful for understanding complex polyploid genomes.
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Affiliation(s)
| | - Sonia Vautrin
- Centre National de Ressources Genomiques Vegetales (CNRGV), Institut National de la Recherche Agronomique (INRA), Castanet Tolosan, France
| | | | | | | | | | - Mônica Conte
- Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
| | - Arnaud Bellec
- Centre National de Ressources Genomiques Vegetales (CNRGV), Institut National de la Recherche Agronomique (INRA), Castanet Tolosan, France
| | - Nair Dahmer
- Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
| | - Joelle Fourment
- Centre National de Ressources Genomiques Vegetales (CNRGV), Institut National de la Recherche Agronomique (INRA), Castanet Tolosan, France
| | - Nathalie Rodde
- Centre National de Ressources Genomiques Vegetales (CNRGV), Institut National de la Recherche Agronomique (INRA), Castanet Tolosan, France
| | | | | | | | | | | | - Hermann Paulo Hoffmann
- Centro de Ciências Agrárias, Universidade Federal de São Carlos (UFSCAR), Araras, Brazil
| | | | | | - Michel Vincentz
- Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
| | - Helene Berges
- Centre National de Ressources Genomiques Vegetales (CNRGV), Institut National de la Recherche Agronomique (INRA), Castanet Tolosan, France
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Garsmeur O, Droc G, Antonise R, Grimwood J, Potier B, Aitken K, Jenkins J, Martin G, Charron C, Hervouet C, Costet L, Yahiaoui N, Healey A, Sims D, Cherukuri Y, Sreedasyam A, Kilian A, Chan A, Van Sluys MA, Swaminathan K, Town C, Bergès H, Simmons B, Glaszmann JC, van der Vossen E, Henry R, Schmutz J, D'Hont A. A mosaic monoploid reference sequence for the highly complex genome of sugarcane. Nat Commun 2018; 9:2638. [PMID: 29980662 PMCID: PMC6035169 DOI: 10.1038/s41467-018-05051-5] [Citation(s) in RCA: 179] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 06/13/2018] [Indexed: 01/31/2023] Open
Abstract
Sugarcane (Saccharum spp.) is a major crop for sugar and bioenergy production. Its highly polyploid, aneuploid, heterozygous, and interspecific genome poses major challenges for producing a reference sequence. We exploited colinearity with sorghum to produce a BAC-based monoploid genome sequence of sugarcane. A minimum tiling path of 4660 sugarcane BAC that best covers the gene-rich part of the sorghum genome was selected based on whole-genome profiling, sequenced, and assembled in a 382-Mb single tiling path of a high-quality sequence. A total of 25,316 protein-coding gene models are predicted, 17% of which display no colinearity with their sorghum orthologs. We show that the two species, S. officinarum and S. spontaneum, involved in modern cultivars differ by their transposable elements and by a few large chromosomal rearrangements, explaining their distinct genome size and distinct basic chromosome numbers while also suggesting that polyploidization arose in both lineages after their divergence.
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Affiliation(s)
- Olivier Garsmeur
- CIRAD (Centre de Coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, F-34398, Montpellier, France.,AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, 34060, Montpellier, France
| | - Gaetan Droc
- CIRAD (Centre de Coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, F-34398, Montpellier, France.,AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, 34060, Montpellier, France
| | | | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35801, USA
| | - Bernard Potier
- SASRI (South African Sugarcane Research Institute), Mount Edgecombe, 4300, South Africa
| | - Karen Aitken
- CSIRO (Commonwealth Scientific and Industrial Research Organisation), St. Lucia, QLD, 4067, Australia
| | - Jerry Jenkins
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35801, USA
| | - Guillaume Martin
- CIRAD (Centre de Coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, F-34398, Montpellier, France.,AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, 34060, Montpellier, France
| | - Carine Charron
- CIRAD (Centre de Coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, F-34398, Montpellier, France.,AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, 34060, Montpellier, France
| | - Catherine Hervouet
- CIRAD (Centre de Coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, F-34398, Montpellier, France.,AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, 34060, Montpellier, France
| | - Laurent Costet
- CIRAD, UMR PVBMT, F-97410, Saint-Pierre, La Réunion, France
| | - Nabila Yahiaoui
- CIRAD (Centre de Coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, F-34398, Montpellier, France.,AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, 34060, Montpellier, France
| | - Adam Healey
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35801, USA
| | - David Sims
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35801, USA
| | | | | | - Andrzej Kilian
- Diversity Arrays Technology, Yarralumla, ACT, 2600, Australia
| | - Agnes Chan
- J. Craig Venter Institute, Rockville, MD, 20850, USA
| | | | | | | | - Hélène Bergès
- INRA-CNRGV, 31326, Toulouse, Castanet-Tolosan, France
| | - Blake Simmons
- JBEI Joint BioEnergy Institute, Emeryville, CA, 94608, USA
| | - Jean Christophe Glaszmann
- CIRAD (Centre de Coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, F-34398, Montpellier, France.,AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, 34060, Montpellier, France
| | | | - Robert Henry
- QAAFI (Queensland Alliance for Agriculture and Food Innovation), University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35801, USA.,Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Angélique D'Hont
- CIRAD (Centre de Coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, F-34398, Montpellier, France. .,AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, 34060, Montpellier, France.
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7
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Mancini MC, Cardoso-Silva CB, Sforça DA, Pereira de Souza A. "Targeted Sequencing by Gene Synteny," a New Strategy for Polyploid Species: Sequencing and Physical Structure of a Complex Sugarcane Region. FRONTIERS IN PLANT SCIENCE 2018; 9:397. [PMID: 29643861 PMCID: PMC5882829 DOI: 10.3389/fpls.2018.00397] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 03/12/2018] [Indexed: 05/25/2023]
Abstract
Sugarcane exhibits a complex genome mainly due to its aneuploid nature and high ploidy level, and sequencing of its genome poses a great challenge. Closely related species with well-assembled and annotated genomes can be used to help assemble complex genomes. Here, a stable quantitative trait locus (QTL) related to sugar accumulation in sorghum was successfully transferred to the sugarcane genome. Gene sequences related to this QTL were identified in silico from sugarcane transcriptome data, and molecular markers based on these sequences were developed to select bacterial artificial chromosome (BAC) clones from the sugarcane variety SP80-3280. Sixty-eight BAC clones containing at least two gene sequences associated with the sorghum QTL were sequenced using Pacific Biosciences (PacBio) technology. Twenty BAC sequences were found to be related to the syntenic region, of which nine were sufficient to represent this region. The strategy we propose is called "targeted sequencing by gene synteny," which is a simpler approach to understanding the genome structure of complex genomic regions associated with traits of interest.
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Affiliation(s)
- Melina C. Mancini
- Center for Molecular Biology and Genetic Engineering, University of Campinas, Campinas, Brazil
| | | | - Danilo A. Sforça
- Center for Molecular Biology and Genetic Engineering, University of Campinas, Campinas, Brazil
| | - Anete Pereira de Souza
- Center for Molecular Biology and Genetic Engineering, University of Campinas, Campinas, Brazil
- Departament Plant Biology, Biology Institute, University of Campinas, Campinas, Brazil
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8
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Basso MF, da Cunha BADB, Ribeiro AP, Martins PK, de Souza WR, de Oliveira NG, Nakayama TJ, Augusto das Chagas Noqueli Casari R, Santiago TR, Vinecky F, Cançado LJ, de Sousa CAF, de Oliveira PA, de Souza SACD, Cançado GMDA, Kobayashi AK, Molinari HBC. Improved Genetic Transformation of Sugarcane (Saccharum spp.) Embryogenic Callus Mediated by Agrobacterium tumefaciens. ACTA ACUST UNITED AC 2018; 2:221-239. [PMID: 31725972 DOI: 10.1002/cppb.20055] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Sugarcane (Saccharum spp.) is a monocotyledonous semi-perennial C4 grass of the Poaceae family. Its capacity to accumulate high content of sucrose and biomass makes it one of the most important crops for sugar and biofuel production. Conventional methods of sugarcane breeding have shown several limitations due to its complex polyploid and aneuploid genome. However, improvement by biotechnological engineering is currently the most promising alternative to introduce economically important traits. In this work, we present an improved protocol for Agrobacterium tumefaciens-mediated transformation of commercial sugarcane hybrids using immature top stalk-derived embryogenic callus cultures. The callus cultures are transformed with preconditioned A. tumefaciens carrying a binary vector that encodes expression cassettes for a gene of interest and the bialaphos resistance gene (bar confers resistance to glufosinate-ammonium herbicide). This protocol has been used to successfully transform a commercial sugarcane cultivar, SP80-3280, highlighting: (i) reduced recalcitrance and oxidation; (ii) high yield of embryogenic callus; (iii) improved selection; and (iv) shoot regeneration and rooting of the transformed plants. Altogether, these improvements generated a transformation efficiency of 2.2%. This protocol provides a reliable tool for a routine procedure for sugarcane improvement by genetic engineering. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Marcos Fernando Basso
- Genetics and Biotechnology Laboratory, National Center for Agroenergy Research (CNPAE), Brazilian Agricultural Research Corporation (EMBRAPA), Brasília, Distrito Federal, Brazil
| | - Bárbara Andrade Dias Brito da Cunha
- Genetics and Biotechnology Laboratory, National Center for Agroenergy Research (CNPAE), Brazilian Agricultural Research Corporation (EMBRAPA), Brasília, Distrito Federal, Brazil
| | - Ana Paula Ribeiro
- Genetics and Biotechnology Laboratory, National Center for Agroenergy Research (CNPAE), Brazilian Agricultural Research Corporation (EMBRAPA), Brasília, Distrito Federal, Brazil
| | - Polyana Kelly Martins
- Genetics and Biotechnology Laboratory, National Center for Agroenergy Research (CNPAE), Brazilian Agricultural Research Corporation (EMBRAPA), Brasília, Distrito Federal, Brazil
| | - Wagner Rodrigo de Souza
- Genetics and Biotechnology Laboratory, National Center for Agroenergy Research (CNPAE), Brazilian Agricultural Research Corporation (EMBRAPA), Brasília, Distrito Federal, Brazil
| | - Nelson Geraldo de Oliveira
- Genetics and Biotechnology Laboratory, National Center for Agroenergy Research (CNPAE), Brazilian Agricultural Research Corporation (EMBRAPA), Brasília, Distrito Federal, Brazil
| | - Thiago Jonas Nakayama
- Genetics and Biotechnology Laboratory, National Center for Agroenergy Research (CNPAE), Brazilian Agricultural Research Corporation (EMBRAPA), Brasília, Distrito Federal, Brazil
| | - Raphael Augusto das Chagas Noqueli Casari
- Genetics and Biotechnology Laboratory, National Center for Agroenergy Research (CNPAE), Brazilian Agricultural Research Corporation (EMBRAPA), Brasília, Distrito Federal, Brazil
| | - Thais Ribeiro Santiago
- Genetics and Biotechnology Laboratory, National Center for Agroenergy Research (CNPAE), Brazilian Agricultural Research Corporation (EMBRAPA), Brasília, Distrito Federal, Brazil
| | - Felipe Vinecky
- Genetics and Biotechnology Laboratory, National Center for Agroenergy Research (CNPAE), Brazilian Agricultural Research Corporation (EMBRAPA), Brasília, Distrito Federal, Brazil
| | - Letícia Jungmann Cançado
- Genetics and Biotechnology Laboratory, National Center for Agroenergy Research (CNPAE), Brazilian Agricultural Research Corporation (EMBRAPA), Brasília, Distrito Federal, Brazil
| | - Carlos Antônio Ferreira de Sousa
- Genetics and Biotechnology Laboratory, National Center for Agroenergy Research (CNPAE), Brazilian Agricultural Research Corporation (EMBRAPA), Brasília, Distrito Federal, Brazil
| | - Patricia Abrão de Oliveira
- Genetics and Biotechnology Laboratory, National Center for Agroenergy Research (CNPAE), Brazilian Agricultural Research Corporation (EMBRAPA), Brasília, Distrito Federal, Brazil
| | | | - Geraldo Magela de Almeida Cançado
- The Joint Research Unit for Genomics Applied to Climate Change (UMIP GenClima), National Center for Agricultural Informatics (CNPTIA), Brazilian Agricultural Research Corporation (EMBRAPA), Campinas, São Paulo, Brazil
| | - Adilson Kenji Kobayashi
- Genetics and Biotechnology Laboratory, National Center for Agroenergy Research (CNPAE), Brazilian Agricultural Research Corporation (EMBRAPA), Brasília, Distrito Federal, Brazil
| | - Hugo Bruno Correa Molinari
- Genetics and Biotechnology Laboratory, National Center for Agroenergy Research (CNPAE), Brazilian Agricultural Research Corporation (EMBRAPA), Brasília, Distrito Federal, Brazil
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9
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Thirugnanasambandam PP, Hoang NV, Henry RJ. The Challenge of Analyzing the Sugarcane Genome. FRONTIERS IN PLANT SCIENCE 2018; 9:616. [PMID: 29868072 PMCID: PMC5961476 DOI: 10.3389/fpls.2018.00616] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 04/18/2018] [Indexed: 05/04/2023]
Abstract
Reference genome sequences have become key platforms for genetics and breeding of the major crop species. Sugarcane is probably the largest crop produced in the world (in weight of crop harvested) but lacks a reference genome sequence. Sugarcane has one of the most complex genomes in crop plants due to the extreme level of polyploidy. The genome of modern sugarcane hybrids includes sub-genomes from two progenitors Saccharum officinarum and S. spontaneum with some chromosomes resulting from recombination between these sub-genomes. Advancing DNA sequencing technologies and strategies for genome assembly are making the sugarcane genome more tractable. Advances in long read sequencing have allowed the generation of a more complete set of sugarcane gene transcripts. This is supporting transcript profiling in genetic research. The progenitor genomes are being sequenced. A monoploid coverage of the hybrid genome has been obtained by sequencing BAC clones that cover the gene space of the closely related sorghum genome. The complete polyploid genome is now being sequenced and assembled. The emerging genome will allow comparison of related genomes and increase understanding of the functioning of this polyploidy system. Sugarcane breeding for traditional sugar and new energy and biomaterial uses will be enhanced by the availability of these genomic resources.
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Affiliation(s)
- Prathima P. Thirugnanasambandam
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
- ICAR - Sugarcane Breeding Institute, Coimbatore, India
- *Correspondence: Prathima P. Thirugnanasambandam,
| | - Nam V. Hoang
- College of Agriculture and Forestry, Hue University, Hue, Vietnam
| | - Robert J. Henry
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
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10
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Yang X, Song J, You Q, Paudel DR, Zhang J, Wang J. Mining sequence variations in representative polyploid sugarcane germplasm accessions. BMC Genomics 2017; 18:594. [PMID: 28793856 PMCID: PMC5551020 DOI: 10.1186/s12864-017-3980-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 08/01/2017] [Indexed: 11/10/2022] Open
Abstract
Background Sugarcane (Saccharum spp.) is one of the most important economic crops because of its high sugar production and biofuel potential. Due to the high polyploid level and complex genome of sugarcane, it has been a huge challenge to investigate genomic sequence variations, which are critical for identifying alleles contributing to important agronomic traits. In order to mine the genetic variations in sugarcane, genotyping by sequencing (GBS), was used to genotype 14 representative Saccharum complex accessions. GBS is a method to generate a large number of markers, enabled by next generation sequencing (NGS) and the genome complexity reduction using restriction enzymes. Results To use GBS for high throughput genotyping highly polyploid sugarcane, the GBS analysis pipelines in 14 Saccharum complex accessions were established by evaluating different alignment methods, sequence variants callers, and sequence depth for single nucleotide polymorphism (SNP) filtering. By using the established pipeline, a total of 76,251 non-redundant SNPs, 5642 InDels, 6380 presence/absence variants (PAVs), and 826 copy number variations (CNVs) were detected among the 14 accessions. In addition, non-reference based universal network enabled analysis kit and Stacks de novo called 34,353 and 109,043 SNPs, respectively. In the 14 accessions, the percentages of single dose SNPs ranged from 38.3% to 62.3% with an average of 49.6%, much more than the portions of multiple dosage SNPs. Concordantly called SNPs were used to evaluate the phylogenetic relationship among the 14 accessions. The results showed that the divergence time between the Erianthus genus and the Saccharum genus was more than 10 million years ago (MYA). The Saccharum species separated from their common ancestors ranging from 0.19 to 1.65 MYA. Conclusions The GBS pipelines including the reference sequences, alignment methods, sequence variant callers, and sequence depth were recommended and discussed for the Saccharum complex and other related species. A large number of sequence variations were discovered in the Saccharum complex, including SNPs, InDels, PAVs, and CNVs. Genome-wide SNPs were further used to illustrate sequence features of polyploid species and demonstrated the divergence of different species in the Saccharum complex. The results of this study showed that GBS was an effective NGS-based method to discover genomic sequence variations in highly polyploid and heterozygous species.
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Affiliation(s)
- Xiping Yang
- Department of Agronomy, University of Florida, Gainesville, FL, 32610, USA
| | - Jian Song
- Department of Agronomy, University of Florida, Gainesville, FL, 32610, USA
| | - Qian You
- Department of Agronomy, University of Florida, Gainesville, FL, 32610, USA
| | - Dev R Paudel
- Department of Agronomy, University of Florida, Gainesville, FL, 32610, USA
| | - Jisen Zhang
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Haixia Institute of Science and Techonology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Jianping Wang
- Department of Agronomy, University of Florida, Gainesville, FL, 32610, USA. .,FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Haixia Institute of Science and Techonology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China. .,Genetics Institute, Plant Molecular and Biology Program, University of Florida, Gainesville, FL, 32610, USA.
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11
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Hoang NV, Furtado A, Mason PJ, Marquardt A, Kasirajan L, Thirugnanasambandam PP, Botha FC, Henry RJ. A survey of the complex transcriptome from the highly polyploid sugarcane genome using full-length isoform sequencing and de novo assembly from short read sequencing. BMC Genomics 2017; 18:395. [PMID: 28532419 PMCID: PMC5440902 DOI: 10.1186/s12864-017-3757-8] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 05/03/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Despite the economic importance of sugarcane in sugar and bioenergy production, there is not yet a reference genome available. Most of the sugarcane transcriptomic studies have been based on Saccharum officinarum gene indices (SoGI), expressed sequence tags (ESTs) and de novo assembled transcript contigs from short-reads; hence knowledge of the sugarcane transcriptome is limited in relation to transcript length and number of transcript isoforms. RESULTS The sugarcane transcriptome was sequenced using PacBio isoform sequencing (Iso-Seq) of a pooled RNA sample derived from leaf, internode and root tissues, of different developmental stages, from 22 varieties, to explore the potential for capturing full-length transcript isoforms. A total of 107,598 unique transcript isoforms were obtained, representing about 71% of the total number of predicted sugarcane genes. The majority of this dataset (92%) matched the plant protein database, while just over 2% was novel transcripts, and over 2% was putative long non-coding RNAs. About 56% and 23% of total sequences were annotated against the gene ontology and KEGG pathway databases, respectively. Comparison with de novo contigs from Illumina RNA-Sequencing (RNA-Seq) of the internode samples from the same experiment and public databases showed that the Iso-Seq method recovered more full-length transcript isoforms, had a higher N50 and average length of largest 1,000 proteins; whereas a greater representation of the gene content and RNA diversity was captured in RNA-Seq. Only 62% of PacBio transcript isoforms matched 67% of de novo contigs, while the non-matched proportions were attributed to the inclusion of leaf/root tissues and the normalization in PacBio, and the representation of more gene content and RNA classes in the de novo assembly, respectively. About 69% of PacBio transcript isoforms and 41% of de novo contigs aligned with the sorghum genome, indicating the high conservation of orthologs in the genic regions of the two genomes. CONCLUSIONS The transcriptome dataset should contribute to improved sugarcane gene models and sugarcane protein predictions; and will serve as a reference database for analysis of transcript expression in sugarcane.
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Affiliation(s)
- Nam V Hoang
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Room 2.245, Level 2, The John Hay Building, Queensland Biosciences Precinct [#80], 306 Carmody Road, St. Lucia, QLD, 4072, Australia.,College of Agriculture and Forestry, Hue University, Hue, Vietnam
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Room 2.245, Level 2, The John Hay Building, Queensland Biosciences Precinct [#80], 306 Carmody Road, St. Lucia, QLD, 4072, Australia
| | - Patrick J Mason
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Room 2.245, Level 2, The John Hay Building, Queensland Biosciences Precinct [#80], 306 Carmody Road, St. Lucia, QLD, 4072, Australia
| | - Annelie Marquardt
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Room 2.245, Level 2, The John Hay Building, Queensland Biosciences Precinct [#80], 306 Carmody Road, St. Lucia, QLD, 4072, Australia.,Sugar Research Australia, Indooroopilly, QLD, 4068, Australia
| | - Lakshmi Kasirajan
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Room 2.245, Level 2, The John Hay Building, Queensland Biosciences Precinct [#80], 306 Carmody Road, St. Lucia, QLD, 4072, Australia.,ICAR - Sugarcane Breeding Institute, Coimbatore, Tamil Nadu, India
| | - Prathima P Thirugnanasambandam
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Room 2.245, Level 2, The John Hay Building, Queensland Biosciences Precinct [#80], 306 Carmody Road, St. Lucia, QLD, 4072, Australia.,ICAR - Sugarcane Breeding Institute, Coimbatore, Tamil Nadu, India
| | - Frederik C Botha
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Room 2.245, Level 2, The John Hay Building, Queensland Biosciences Precinct [#80], 306 Carmody Road, St. Lucia, QLD, 4072, Australia.,Sugar Research Australia, Indooroopilly, QLD, 4068, Australia
| | - Robert J Henry
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Room 2.245, Level 2, The John Hay Building, Queensland Biosciences Precinct [#80], 306 Carmody Road, St. Lucia, QLD, 4072, Australia.
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12
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Okura VK, de Souza RSC, de Siqueira Tada SF, Arruda P. BAC-Pool Sequencing and Assembly of 19 Mb of the Complex Sugarcane Genome. FRONTIERS IN PLANT SCIENCE 2016; 7:342. [PMID: 27047520 PMCID: PMC4804495 DOI: 10.3389/fpls.2016.00342] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Accepted: 03/06/2016] [Indexed: 05/18/2023]
Abstract
Sequencing plant genomes are often challenging because of their complex architecture and high content of repetitive sequences. Sugarcane has one of the most complex genomes. It is highly polyploid, preserves intact homeologous chromosomes from its parental species and contains >55% repetitive sequences. Although bacterial artificial chromosome (BAC) libraries have emerged as an alternative for accessing the sugarcane genome, sequencing individual clones is laborious and expensive. Here, we present a strategy for sequencing and assembly reads produced from the DNA of pooled BAC clones. A set of 178 BAC clones, randomly sampled from the SP80-3280 sugarcane BAC library, was pooled and sequenced using the Illumina HiSeq2000 and PacBio platforms. A hybrid assembly strategy was used to generate 2,451 scaffolds comprising 19.2 MB of assembled genome sequence. Scaffolds of ≥20 Kb corresponded to 80% of the assembled sequences, and the full sequences of forty BACs were recovered in one or two contigs. Alignment of the BAC scaffolds with the chromosome sequences of sorghum showed a high degree of collinearity and gene order. The alignment of the BAC scaffolds to the 10 sorghum chromosomes suggests that the genome of the SP80-3280 sugarcane variety is ∼19% contracted in relation to the sorghum genome. In conclusion, our data show that sequencing pools composed of high numbers of BAC clones may help to construct a reference scaffold map of the sugarcane genome.
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Affiliation(s)
- Vagner Katsumi Okura
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de CampinasCampinas, Brazil
- Laboratório Central de Tecnologias de Alto Desempenho em Ciências da Vida, Universidade Estadual de CampinasCampinas, Brazil
| | - Rafael S. C. de Souza
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de CampinasCampinas, Brazil
| | - Susely F. de Siqueira Tada
- Laboratório Central de Tecnologias de Alto Desempenho em Ciências da Vida, Universidade Estadual de CampinasCampinas, Brazil
| | - Paulo Arruda
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de CampinasCampinas, Brazil
- Departamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de CampinasCampinas, Brazil
- *Correspondence: Paulo Arruda,
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Hoang NV, Furtado A, Botha FC, Simmons BA, Henry RJ. Potential for Genetic Improvement of Sugarcane as a Source of Biomass for Biofuels. Front Bioeng Biotechnol 2015; 3:182. [PMID: 26636072 PMCID: PMC4646955 DOI: 10.3389/fbioe.2015.00182] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Accepted: 10/26/2015] [Indexed: 11/13/2022] Open
Abstract
Sugarcane (Saccharum spp. hybrids) has great potential as a major feedstock for biofuel production worldwide. It is considered among the best options for producing biofuels today due to an exceptional biomass production capacity, high carbohydrate (sugar + fiber) content, and a favorable energy input/output ratio. To maximize the conversion of sugarcane biomass into biofuels, it is imperative to generate improved sugarcane varieties with better biomass degradability. However, unlike many diploid plants, where genetic tools are well developed, biotechnological improvement is hindered in sugarcane by our current limited understanding of the large and complex genome. Therefore, understanding the genetics of the key biofuel traits in sugarcane and optimization of sugarcane biomass composition will advance efficient conversion of sugarcane biomass into fermentable sugars for biofuel production. The large existing phenotypic variation in Saccharum germplasm and the availability of the current genomics technologies will allow biofuel traits to be characterized, the genetic basis of critical differences in biomass composition to be determined, and targets for improvement of sugarcane for biofuels to be established. Emerging options for genetic improvement of sugarcane for the use as a bioenergy crop are reviewed. This will better define the targets for potential genetic manipulation of sugarcane biomass composition for biofuels.
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Affiliation(s)
- Nam V. Hoang
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
- College of Agriculture and Forestry, Hue University, Hue, Vietnam
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
| | - Frederik C. Botha
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
- Sugar Research Australia, Indooroopilly, QLD, Australia
| | - Blake A. Simmons
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
- Joint BioEnergy Institute, Emeryville, CA, USA
| | - Robert J. Henry
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
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14
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Santos AA, Penha HA, Bellec A, Munhoz CDF, Pedrosa-Harand A, Bergès H, Vieira MLC. Begin at the beginning: A BAC-end view of the passion fruit (Passiflora) genome. BMC Genomics 2014; 15:816. [PMID: 25260959 PMCID: PMC4189760 DOI: 10.1186/1471-2164-15-816] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 09/22/2014] [Indexed: 12/16/2022] Open
Abstract
Background The passion fruit (Passiflora edulis) is a tropical crop of economic importance both for juice production and consumption as fresh fruit. The juice is also used in concentrate blends that are consumed worldwide. However, very little is known about the genome of the species. Therefore, improving our understanding of passion fruit genomics is essential and to some degree a pre-requisite if its genetic resources are to be used more efficiently. In this study, we have constructed a large-insert BAC library and provided the first view on the structure and content of the passion fruit genome, using BAC-end sequence (BES) data as a major resource. Results The library consisted of 82,944 clones and its levels of organellar DNA were very low. The library represents six haploid genome equivalents, and the average insert size was 108 kb. To check its utility for gene isolation, successful macroarray screening experiments were carried out with probes complementary to eight Passiflora gene sequences available in public databases. BACs harbouring those genes were used in fluorescent in situ hybridizations and unique signals were detected for four BACs in three chromosomes (n = 9). Then, we explored 10,000 BES and we identified reads likely to contain repetitive mobile elements (19.6% of all BES), simple sequence repeats and putative proteins, and to estimate the GC content (~42%) of the reads. Around 9.6% of all BES were found to have high levels of similarity to plant genes and ontological terms were assigned to more than half of the sequences analysed (940). The vast majority of the top-hits made by our sequences were to Populus trichocarpa (24.8% of the total occurrences), Theobroma cacao (21.6%), Ricinus communis (14.3%), Vitis vinifera (6.5%) and Prunus persica (3.8%). Conclusions We generated the first large-insert library for a member of Passifloraceae. This BAC library provides a new resource for genetic and genomic studies, as well as it represents a valuable tool for future whole genome study. Remarkably, a number of BAC-end pair sequences could be mapped to intervals of the sequenced Arabidopsis thaliana, V. vinifera and P. trichocarpa chromosomes, and putative collinear microsyntenic regions were identified. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-816) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | - Maria Lucia Carneiro Vieira
- Departamento de Genética, Universidade de São Paulo, Escola Superior de Agricultura "Luiz de Queiroz", P,O, Box 83, 13400-970 Piracicaba, Brazil.
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15
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de Setta N, Monteiro-Vitorello CB, Metcalfe CJ, Cruz GMQ, Del Bem LE, Vicentini R, Nogueira FTS, Campos RA, Nunes SL, Turrini PCG, Vieira AP, Ochoa Cruz EA, Corrêa TCS, Hotta CT, de Mello Varani A, Vautrin S, da Trindade AS, de Mendonça Vilela M, Lembke CG, Sato PM, de Andrade RF, Nishiyama MY, Cardoso-Silva CB, Scortecci KC, Garcia AAF, Carneiro MS, Kim C, Paterson AH, Bergès H, D'Hont A, de Souza AP, Souza GM, Vincentz M, Kitajima JP, Van Sluys MA. Building the sugarcane genome for biotechnology and identifying evolutionary trends. BMC Genomics 2014; 15:540. [PMID: 24984568 PMCID: PMC4122759 DOI: 10.1186/1471-2164-15-540] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Accepted: 06/19/2014] [Indexed: 01/24/2023] Open
Abstract
Background Sugarcane is the source of sugar in all tropical and subtropical countries and is becoming increasingly important for bio-based fuels. However, its large (10 Gb), polyploid, complex genome has hindered genome based breeding efforts. Here we release the largest and most diverse set of sugarcane genome sequences to date, as part of an on-going initiative to provide a sugarcane genomic information resource, with the ultimate goal of producing a gold standard genome. Results Three hundred and seventeen chiefly euchromatic BACs were sequenced. A reference set of one thousand four hundred manually-annotated protein-coding genes was generated. A small RNA collection and a RNA-seq library were used to explore expression patterns and the sRNA landscape. In the sucrose and starch metabolism pathway, 16 non-redundant enzyme-encoding genes were identified. One of the sucrose pathway genes, sucrose-6-phosphate phosphohydrolase, is duplicated in sugarcane and sorghum, but not in rice and maize. A diversity analysis of the s6pp duplication region revealed haplotype-structured sequence composition. Examination of hom(e)ologous loci indicate both sequence structural and sRNA landscape variation. A synteny analysis shows that the sugarcane genome has expanded relative to the sorghum genome, largely due to the presence of transposable elements and uncharacterized intergenic and intronic sequences. Conclusion This release of sugarcane genomic sequences will advance our understanding of sugarcane genetics and contribute to the development of molecular tools for breeding purposes and gene discovery. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-540) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Marie-Anne Van Sluys
- Departamento de Botânica - Instituto de Biociências, Universidade de São Paulo, Rua do Matão 277, São Paulo 05508-090, SP, Brazil.
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Characterization of rubber tree microRNA in phytohormone response using large genomic DNA libraries, promoter sequence and gene expression analysis. Mol Genet Genomics 2014; 289:921-33. [PMID: 24859131 DOI: 10.1007/s00438-014-0862-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 05/05/2014] [Indexed: 10/25/2022]
Abstract
The para rubber tree is the most widely cultivated tree species for producing natural rubber (NR) latex. Unfortunately, rubber tree characteristics such as a long life cycle, heterozygous genetic backgrounds, and poorly understood genetic profiles are the obstacles to breeding new rubber tree varieties, such as those with improved NR yields. Recent evidence has revealed the potential importance of controlling microRNA (miRNA) decay in some aspects of NR regulation. To gain a better understanding of miRNAs and their relationship with rubber tree gene regulation networks, large genomic DNA insert-containing libraries were generated to complement the incomplete draft genome sequence and applied as a new powerful tool to predict a function of interested genes. Bacterial artificial chromosome and fosmid libraries, containing a total of 120,576 clones with an average insert size of 43.35 kb, provided approximately 2.42 haploid genome equivalents of coverage based on the estimated 2.15 gb rubber tree genome. Based on these library sequences, the precursors of 1 member of rubber tree-specific miRNAs and 12 members of conserved miRNAs were successfully identified. A panel of miRNAs was characterized for phytohormone response by precisely identifying phytohormone-responsive motifs in their promoter sequences. Furthermore, the quantitative real-time PCR on ethylene stimulation of rubber trees was performed to demonstrate that the miR2118, miR159, miR164 and miR166 are responsive to ethylene, thus confirmed the prediction by genomic DNA analysis. The cis-regulatory elements identified in the promoter regions of these miRNA genes help augment our understanding of miRNA gene regulation and provide a foundation for further investigation of the regulation of rubber tree miRNAs.
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Li Z, Jiang H, Zhou L, Deng L, Lin Y, Peng X, Yan H, Cheng B. Molecular evolution of the HD-ZIP I gene family in legume genomes. Gene 2013; 533:218-28. [PMID: 24095777 DOI: 10.1016/j.gene.2013.09.084] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Revised: 09/22/2013] [Accepted: 09/24/2013] [Indexed: 11/26/2022]
Abstract
Homeodomain leucine zipper I (HD-ZIP I) genes were used to increase the plasticity of plants by mediating external signals and regulating growth in response to environmental conditions. The way genomic histories drove the evolution of the HD-ZIP I family in legume species was described; HD-ZIP I genes were searched in Lotus japonicus, Medicago truncatula, Cajanus cajan and Phaseolus vulgaris, and then divided into five clades through phylogenetic analysis. Microsynteny analysis was made based on genomic segments containing the HD-ZIP I genes. Some pairs turned out to conform with syntenic genome regions, while others corresponded to those that were inverted, expanded, or contracted after the divergence of legumes. Besides, we dated their duplications by Ks analysis and demonstrated that all the blocks were formed after the monocot-dicot split; we observed Ka/Ks ratios representing strong purifying selections in the four legume species which might have been followed by gene loss and rearrangement.
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Affiliation(s)
- Zhen Li
- Key Lab of Crop Biology, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
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de Siqueira Ferreira S, Nishiyama MY, Paterson AH, Souza GM. Biofuel and energy crops: high-yield Saccharinae take center stage in the post-genomics era. Genome Biol 2013; 14:210. [PMID: 23805917 PMCID: PMC3707038 DOI: 10.1186/gb-2013-14-6-210] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The Saccharinae, especially sugarcane, Miscanthus and sorghum, present remarkable characteristics for bioenergy production. Biotechnology of these plants will be important for a sustainable feedstock supply. Herein, we review knowledge useful for their improvement and synergies gained by their parallel study.
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Affiliation(s)
- Savio de Siqueira Ferreira
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, 05508-000 São Paulo, SP, Brazil
| | - Milton Yutaka Nishiyama
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, 05508-000 São Paulo, SP, Brazil
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
| | - Glaucia Mendes Souza
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, 05508-000 São Paulo, SP, Brazil
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Kim C, Lee TH, Compton RO, Robertson JS, Pierce GJ, Paterson AH. A genome-wide BAC end-sequence survey of sugarcane elucidates genome composition, and identifies BACs covering much of the euchromatin. PLANT MOLECULAR BIOLOGY 2013; 81:139-47. [PMID: 23161199 DOI: 10.1007/s11103-012-9987-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Accepted: 11/07/2012] [Indexed: 05/09/2023]
Abstract
BAC-end sequences (BESs) of hybrid sugarcane cultivar R570 are presented. A total of 66,990 informative BESs were obtained from 43,874 BAC clones. Similarity search using a variety of public databases revealed that 13.5 and 42.8 % of BESs match known gene-coding and repeat regions, respectively. That 11.7 % of BESs are still unmatched to any nucleotide sequences in the current public databases despite the fact that a close relative, sorghum, is fully sequenced, indicates that there may be many sugarcane-specific or lineage-specific sequences. We found 1,742 simple sequence repeat motifs in 1,585 BESs, spanning 27,383 bp in length. As simple sequence repeat markers derived from BESs have some advantages over randomly generated markers, these may be particularly useful for comparing BAC-based physical maps with genetic maps. BES and overgo hybridization information was used for anchoring sugarcane BAC clones to the sorghum genome sequence. While sorghum and sugarcane have extensive similarity in terms of genomic structure, only 2,789 BACs (6.4 %) could be confidently anchored to the sorghum genome at the stringent threshold of having both-end information (BESs or overgos) within 300 Kb. This relatively low rate of anchoring may have been caused in part by small- or large-scale genomic rearrangements in the Saccharum genus after two rounds of whole genome duplication since its divergence from the sorghum lineage about 7.8 million years ago. Limiting consideration to only low-copy matches, 1,245 BACs were placed to 1,503 locations, covering ~198 Mb of the sorghum genome or about 78 % of the estimated 252 Mb of euchromatin. BESs and their analyses presented here may provide an early profile of the sugarcane genome as well as a basis for BAC-by-BAC sequencing of much of the basic gene set of sugarcane.
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Affiliation(s)
- Changsoo Kim
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
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Asamizu E, Shirasawa K, Hirakawa H, Sato S, Tabata S, Yano K, Ariizumi T, Shibata D, Ezura H. Mapping of Micro-Tom BAC-End Sequences to the Reference Tomato Genome Reveals Possible Genome Rearrangements and Polymorphisms. INTERNATIONAL JOURNAL OF PLANT GENOMICS 2012; 2012:437026. [PMID: 23227037 PMCID: PMC3514829 DOI: 10.1155/2012/437026] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Accepted: 10/18/2012] [Indexed: 05/29/2023]
Abstract
A total of 93,682 BAC-end sequences (BESs) were generated from a dwarf model tomato, cv. Micro-Tom. After removing repetitive sequences, the BESs were similarity searched against the reference tomato genome of a standard cultivar, "Heinz 1706." By referring to the "Heinz 1706" physical map and by eliminating redundant or nonsignificant hits, 28,804 "unique pair ends" and 8,263 "unique ends" were selected to construct hypothetical BAC contigs. The total physical length of the BAC contigs was 495, 833, 423 bp, covering 65.3% of the entire genome. The average coverage of euchromatin and heterochromatin was 58.9% and 67.3%, respectively. From this analysis, two possible genome rearrangements were identified: one in chromosome 2 (inversion) and the other in chromosome 3 (inversion and translocation). Polymorphisms (SNPs and Indels) between the two cultivars were identified from the BLAST alignments. As a result, 171,792 polymorphisms were mapped on 12 chromosomes. Among these, 30,930 polymorphisms were found in euchromatin (1 per 3,565 bp) and 140,862 were found in heterochromatin (1 per 2,737 bp). The average polymorphism density in the genome was 1 polymorphism per 2,886 bp. To facilitate the use of these data in Micro-Tom research, the BAC contig and polymorphism information are available in the TOMATOMICS database.
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Affiliation(s)
- Erika Asamizu
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8572, Japan
| | - Kenta Shirasawa
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu 292-0818, Japan
| | - Hideki Hirakawa
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu 292-0818, Japan
| | - Shusei Sato
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu 292-0818, Japan
| | - Satoshi Tabata
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu 292-0818, Japan
| | - Kentaro Yano
- School of Agriculture, Meiji University, 1-1-1 Higashi-mita, Tama-ku, Kawasaki 214-8571, Japan
| | - Tohru Ariizumi
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8572, Japan
| | - Daisuke Shibata
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu 292-0818, Japan
| | - Hiroshi Ezura
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8572, Japan
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