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Chen Z, Liu Q, Xiao Y, Zhou G, Yu P, Bai J, Huang H, Gong Y. Complete chloroplast genome sequence of Camellia sinensis: genome structure, adaptive evolution, and phylogenetic relationships. J Appl Genet 2023; 64:419-429. [PMID: 37380816 DOI: 10.1007/s13353-023-00767-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 06/13/2023] [Accepted: 06/19/2023] [Indexed: 06/30/2023]
Abstract
The chloroplast (cp) genome holds immense potential for a variety of applications including species identification, phylogenetic analysis, and evolutionary studies. In this study, we utilized Illumina NovaSeq 6000 to sequence the DNA of Camellia sinensis L. cultivar 'Zhuyeqi', followed by the assembly of its chloroplast genome using SPAdes v3.10.1, with subsequent analysis of its features and phylogenetic placement. The results showed that the cp genome of 'Zhuyeqi' was 157,072 bp, with a large single-copy region (LSC, 86,628 bp), a small single-copy region (SSC,18,282 bp), and two inverted repeat regions (IR, 26,081 bp). The total AT and GC contents of the cp genome of 'Zhuyeqi' were observed to be 62.21% and 37.29%, respectively. The cp genome encoded 135 unique genes, including 90 protein-coding genes (CDS), 37 tRNA genes, and 8 rRNA genes. Moreover, 31 codons and 247 simple sequence repeats (SSRs) were identified. The cp genomes of 'Zhuyeqi' were found to be relatively conserved, with conservation observed in the IR region, which showed no evidence of inversions or rearrangements. The five regions with the largest variations were identified, with four regions (rps12, rps19, rps16, and rpl33) located in the LSC region and one divergent region (trnI-GAU) in the IR region. Phylogenetic analysis revealed that Camellia sinensis (KJ996106.1) was closely related to 'Zhuyeqi', indicating a close phylogenetic relationship between these two species. These findings could provide important genetic information for further research into breeding of tea tree, phylogeny, and evolution of Camellia sinensis.
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Affiliation(s)
- Zhiyin Chen
- College of Agriculture & Biotechnology, Hunan University of Humanities, Science & Technology, Loudi, 417000, China
| | - Qing Liu
- College of Agriculture & Biotechnology, Hunan University of Humanities, Science & Technology, Loudi, 417000, China
| | - Ying Xiao
- College of Agriculture & Biotechnology, Hunan University of Humanities, Science & Technology, Loudi, 417000, China
| | - Guihua Zhou
- College of Agriculture & Biotechnology, Hunan University of Humanities, Science & Technology, Loudi, 417000, China
| | - Penghui Yu
- Tea Research Institute, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Jing Bai
- College of Agriculture & Biotechnology, Hunan University of Humanities, Science & Technology, Loudi, 417000, China
| | - Hua Huang
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences; Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou, 510640, People's Republic of China.
| | - Yihui Gong
- College of Agriculture & Biotechnology, Hunan University of Humanities, Science & Technology, Loudi, 417000, China.
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Song M, Wang H, Fan Z, Huang H, Ma H. Advances in sequencing and key character analysis of mango ( Mangifera indica L.). HORTICULTURE RESEARCH 2023; 10:uhac259. [PMID: 37601702 PMCID: PMC10433700 DOI: 10.1093/hr/uhac259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 11/19/2022] [Indexed: 08/22/2023]
Abstract
Mango (Mangifera indica L.) is an important fruit crop in tropical and subtropical countries associated with many agronomic and horticultural problems, such as susceptibility to pathogens, including powdery mildew and anthracnose, poor yield and quality, and short shelf life. Conventional breeding techniques exhibit significant limitations in improving mango quality due to the characteristics of long ripening, self-incompatibility, and high genetic heterozygosity. In recent years, much emphasis has been placed on identification of key genes controlling a certain trait through genomic association analysis and directly breeding new varieties through transgene or genotype selection of offspring. This paper reviews the latest research progress on the genome and transcriptome sequencing of mango fruit. The rapid development of genome sequencing and bioinformatics provides effective strategies for identifying, labeling, cloning, and manipulating many genes related to economically important traits. Preliminary verification of the functions of mango genes has been conducted, including genes related to flowering regulation, fruit development, and polyphenol biosynthesis. Importantly, modern biotechnology can refine existing mango varieties to meet the market demand with high economic benefits.
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Affiliation(s)
- Miaoyu Song
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Haomiao Wang
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Zhiyi Fan
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Hantang Huang
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Huiqin Ma
- College of Horticulture, China Agricultural University, Beijing 100193, China
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100083, China
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Perveen N, Dinesh MR, Sankaran M, Ravishankar KV, Krishnajee HG, Hanur VS, Alamri S, Kesawat MS, Irfan M. Comparative transcriptome analysis provides novel insights into molecular response of salt-tolerant and sensitive polyembryonic mango genotypes to salinity stress at seedling stage. FRONTIERS IN PLANT SCIENCE 2023; 14:1152485. [PMID: 37123820 PMCID: PMC10141464 DOI: 10.3389/fpls.2023.1152485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 03/20/2023] [Indexed: 05/03/2023]
Abstract
Introduction Increased soil salinity in the recent years has adversely affected the productivity of mango globally. Extending the cultivation of mango in salt affected regions warrants the use of salinity tolerant/resistant rootstocks. However, the lack of sufficient genomic and transcriptomic information impedes comprehensive research at the molecular level. Method We employed RNA sequencing-based transcriptome analysis to gain insight into molecular response to salt stress by using two polyembryonic mango genotypes with contrasting response to salt stress viz., salt tolerant Turpentine and salt susceptible Mylepelian. Results RNA sequencing by Novaseq6000 resulted in a total of 2795088, 17535948, 7813704 and 5544894 clean reads in Mylepelian treated (MT), Mylepelian control (MC), Turpentine treated (TT) and Turpentine control (TC) respectively. In total, 7169 unigenes annotated against all the five public databases, including NR, NT, PFAM, KOG, Swissport, KEGG and GO. Further, maximum number of differentially expressed genes were found between MT and MC (2106) followed by MT vs TT (1158) and TT and TC (587). The differentially expressed genes under different treatment levels included transcription factors (bZIP, NAC, bHLH), genes involved in Calcium-dependent protein kinases (CDPKs), ABA biosynthesis, Photosynthesis etc. Expression of few of these genes was experimentally validated through quantitative real-time PCR (qRT-PCR) and contrasting expression pattern of Auxin Response Factor 2 (ARF2), Late Embryogenesis Abundant (LEA) and CDPK genes were observed between Turpentine and Mylepelian. Discussion The results of this study will be useful in understanding the molecular mechanism underlying salt tolerance in mango which can serve as valuable baseline information to generate new targets in mango breeding for salt tolerance.
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Affiliation(s)
- Nusrat Perveen
- Division of Fruit Crops, ICAR-Indian Institute of Horticultural Research, Hesaraghatta Lakepost, Bengaluru, Karnataka, India
- *Correspondence: Nusrat Perveen, ; K. V. Ravishankar,
| | - M. R. Dinesh
- Division of Fruit Crops, ICAR-Indian Institute of Horticultural Research, Hesaraghatta Lakepost, Bengaluru, Karnataka, India
| | - M. Sankaran
- Division of Fruit Crops, ICAR-Indian Institute of Horticultural Research, Hesaraghatta Lakepost, Bengaluru, Karnataka, India
| | - K. V. Ravishankar
- Division of Biotechnology, ICAR-Indian Institute of Horticultural Research, Hesaraghatta Lakepost, Bengaluru, Karnataka, India
- *Correspondence: Nusrat Perveen, ; K. V. Ravishankar,
| | - Hara Gopal Krishnajee
- Division of Biotechnology, ICAR-Indian Institute of Horticultural Research, Hesaraghatta Lakepost, Bengaluru, Karnataka, India
| | - Vageeshbabu S. Hanur
- Division of Biotechnology, ICAR-Indian Institute of Horticultural Research, Hesaraghatta Lakepost, Bengaluru, Karnataka, India
| | - Saud Alamri
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | | | - Mohammad Irfan
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
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Xin M, Li C, Khoo HE, Li L, He X, Yi P, Tang Y, Sun J. Dynamic Analyses of Transcriptome and Metabolic Profiling: Revealing Molecular Insight of Aroma Synthesis of Mango ( Mangifera indica L. Var. Tainong). FRONTIERS IN PLANT SCIENCE 2021; 12:666805. [PMID: 34025704 PMCID: PMC8138435 DOI: 10.3389/fpls.2021.666805] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 04/09/2021] [Indexed: 05/28/2023]
Abstract
This study aimed to evaluate the changes in aromatic components and other chemical properties of Tainong mango during fruit development, ripening, and storage. As the volatiles of Tainong mango and their related molecular mechanisms remain unclear, volatile profile, metabonomics, and transcriptome analyses were applied to investigate the molecular determinants of the synthesis of aroma components in mango during fruit development and storage. Total acids, total sugar, total carotenoids, enzyme activities of the mango pulp samples were also determined. Volatile components of the mango pulp samples were identified using a gas chromatography-mass spectrometric method. Ribonucleic acid (RNA) sequences of the samples were analyzed by real-time polymerase chain reaction. The results showed that 181 volatiles were isolated and identified in the fruit at seven stages. Compared to the other stages, mango collected on day 8 and day 12 had higher concentrations of 17 volatile components, especially (E,Z)-2,6-nonadienal, 53384 transcripts were also detected through RNA sequencing. The differentially expressed genes analyses included catalytic activity, transferase activity, adenosine diphosphate binding, transcription factor activity, and oxidoreductase activity. α-Pinene content and expression of the differentially expressed genes involved in terpenoid metabolism and enzyme activities in the terpenoid metabolic pathways gradually increased during the maturity of the fruit, and had maximum values at day 8 of storage. Moreover, the integrative analyses revealed potential molecular insights of mango development and aroma formation in the fruit.
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Affiliation(s)
- Ming Xin
- Agro-food Science and Technology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Changbao Li
- Agro-food Science and Technology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Hock Eng Khoo
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin, China
| | - Li Li
- Agro-food Science and Technology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Xuemei He
- Agro-food Science and Technology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Ping Yi
- Guangxi Key Laboratory of Fruits and Vegetables Storage-processing Technology, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Yayuan Tang
- Guangxi Key Laboratory of Fruits and Vegetables Storage-processing Technology, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Jian Sun
- Agro-food Science and Technology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Fruits and Vegetables Storage-processing Technology, Guangxi Academy of Agricultural Sciences, Nanning, China
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Niu Y, Gao C, Liu J. Comparative analysis of the complete plastid genomes of Mangifera species and gene transfer between plastid and mitochondrial genomes. PeerJ 2021; 9:e10774. [PMID: 33614280 PMCID: PMC7881718 DOI: 10.7717/peerj.10774] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 12/22/2020] [Indexed: 01/30/2023] Open
Abstract
Mango is an important commercial fruit crop belonging to the genus Mangifera. In this study, we reported and compared four newly sequenced plastid genomes of the genus Mangifera, which showed high similarities in overall size (157,780–157,853 bp), genome structure, gene order, and gene content. Three mutation hotspots (trnG-psbZ, psbD-trnT, and ycf4-cemA) were identified as candidate DNA barcodes for Mangifera. These three DNA barcode candidate sequences have high species identification ability. We also identified 12 large fragments that were transferred from the plastid genome to the mitochondrial genome, and found that the similarity was more than 99%. The total size of the transferred fragment was 35,652 bp, accounting for 22.6% of the plastid genome. Fifteen intact chloroplast genes, four tRNAs and numerous partial genes and intergenic spacer regions were identified. There are many of these genes transferred from mitochondria to the chloroplast in other species genomes. Phylogenetic analysis based on whole plastid genome data provided a high support value, and the interspecies relationships within Mangifera were resolved well.
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Affiliation(s)
- Yingfeng Niu
- Yunnan Institute of Tropical Crops, Xishuangbanna, China
| | - Chengwen Gao
- The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Jin Liu
- Yunnan Institute of Tropical Crops, Xishuangbanna, China
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Bally ISE, Bombarely A, Chambers AH, Cohen Y, Dillon NL, Innes DJ, Islas-Osuna MA, Kuhn DN, Mueller LA, Ophir R, Rambani A, Sherman A, Yan H. The 'Tommy Atkins' mango genome reveals candidate genes for fruit quality. BMC PLANT BIOLOGY 2021; 21:108. [PMID: 33618672 PMCID: PMC7898432 DOI: 10.1186/s12870-021-02858-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 01/28/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Mango, Mangifera indica L., an important tropical fruit crop, is grown for its sweet and aromatic fruits. Past improvement of this species has predominantly relied on chance seedlings derived from over 1000 cultivars in the Indian sub-continent with a large variation for fruit size, yield, biotic and abiotic stress resistance, and fruit quality among other traits. Historically, mango has been an orphan crop with very limited molecular information. Only recently have molecular and genomics-based analyses enabled the creation of linkage maps, transcriptomes, and diversity analysis of large collections. Additionally, the combined analysis of genomic and phenotypic information is poised to improve mango breeding efficiency. RESULTS This study sequenced, de novo assembled, analyzed, and annotated the genome of the monoembryonic mango cultivar 'Tommy Atkins'. The draft genome sequence was generated using NRGene de-novo Magic on high molecular weight DNA of 'Tommy Atkins', supplemented by 10X Genomics long read sequencing to improve the initial assembly. A hybrid population between 'Tommy Atkins' x 'Kensington Pride' was used to generate phased haplotype chromosomes and a highly resolved phased SNP map. The final 'Tommy Atkins' genome assembly was a consensus sequence that included 20 pseudomolecules representing the 20 chromosomes of mango and included ~ 86% of the ~ 439 Mb haploid mango genome. Skim sequencing identified ~ 3.3 M SNPs using the 'Tommy Atkins' x 'Kensington Pride' mapping population. Repeat masking identified 26,616 genes with a median length of 3348 bp. A whole genome duplication analysis revealed an ancestral 65 MYA polyploidization event shared with Anacardium occidentale. Two regions, one on LG4 and one on LG7 containing 28 candidate genes, were associated with the commercially important fruit size characteristic in the mapping population. CONCLUSIONS The availability of the complete 'Tommy Atkins' mango genome will aid global initiatives to study mango genetics.
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Affiliation(s)
- Ian S E Bally
- Department of Agriculture and Fisheries, Horticulture and Forestry Science, 28 Peters St, Mareeba, QLD, 4880, Australia
| | - Aureliano Bombarely
- Department of Bioscience, University of Milan, Via Celoria 26, 20133, Milan, Italy
- School of Plants and Environmental Sciences, Virginia Tech, Ag Quad Lane, Blacksburg, VA, 24061, USA
| | - Alan H Chambers
- Tropical Research and Education Center, Horticultural Sciences Department, University of Florida, 18905 SW 280th St, Homestead, FL, 33031, USA.
| | - Yuval Cohen
- Department of Fruit Tree Sciences, Volcani Research Center, Derech Hamacabim 68, P.O. Box 15159, 7528809, Rishon Le'Zion, Israel
| | - Natalie L Dillon
- Department of Agriculture and Fisheries, Horticulture and Forestry Science, 28 Peters St, Mareeba, QLD, 4880, Australia
| | - David J Innes
- Department of Agriculture and Fisheries, Horticulture and Forestry Science, EcoSciences Precinct, 41 Boggo Rd, Dutton Park, QLD, 4102, Australia
| | - María A Islas-Osuna
- Centro de Investigación en Alimentación y Desarrollo, A.C, Carretera Gustavo Enrique Astiazarán Rosas 46, Col. La Victoria, 83304, Hermosillo, Sonora, Mexico
| | - David N Kuhn
- Subtropical Horticulture Research Station, USDA-ARS, 13601 Old Cutler Rd, Coral Gables, FL, 33158, USA
| | - Lukas A Mueller
- Boyce Thompson Institute, 533 Tower Road, Ithaca, NY, 14853, USA
| | - Ron Ophir
- Department of Fruit Tree Sciences, Volcani Research Center, Derech Hamacabim 68, P.O. Box 15159, 7528809, Rishon Le'Zion, Israel
| | - Aditi Rambani
- Boyce Thompson Institute, 533 Tower Road, Ithaca, NY, 14853, USA
| | - Amir Sherman
- Department of Fruit Tree Sciences, Volcani Research Center, Derech Hamacabim 68, P.O. Box 15159, 7528809, Rishon Le'Zion, Israel
| | - Haidong Yan
- School of Plants and Environmental Sciences, Virginia Tech, Ag Quad Lane, Blacksburg, VA, 24061, USA
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Dong F, Lin Z, Lin J, Ming R, Zhang W. Chloroplast Genome of Rambutan and Comparative Analyses in Sapindaceae. PLANTS 2021; 10:plants10020283. [PMID: 33540810 PMCID: PMC7912957 DOI: 10.3390/plants10020283] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 01/28/2021] [Accepted: 01/29/2021] [Indexed: 02/03/2023]
Abstract
Rambutan (Nephelium lappaceum L.) is an important fruit tree that belongs to the family Sapindaceae and is widely cultivated in Southeast Asia. We sequenced its chloroplast genome for the first time and assembled 161,321 bp circular DNA. It is characterized by a typical quadripartite structure composed of a large (86,068 bp) and small (18,153 bp) single-copy region interspersed by two identical inverted repeats (IRs) (28,550 bp). We identified 132 genes including 78 protein-coding genes, 29 tRNA and 4 rRNA genes, with 21 genes duplicated in the IRs. Sixty-three simple sequence repeats (SSRs) and 98 repetitive sequences were detected. Twenty-nine codons showed biased usage and 49 potential RNA editing sites were predicted across 18 protein-coding genes in the rambutan chloroplast genome. In addition, coding gene sequence divergence analysis suggested that ccsA, clpP, rpoA, rps12, psbJ and rps19 were under positive selection, which might reflect specific adaptations of N. lappaceum to its particular living environment. Comparative chloroplast genome analyses from nine species in Sapindaceae revealed that a higher similarity was conserved in the IR regions than in the large single-copy (LSC) and small single-copy (SSC) regions. The phylogenetic analysis showed that N. lappaceum chloroplast genome has the closest relationship with that of Pometia tomentosa. The understanding of the chloroplast genomics of rambutan and comparative analysis of Sapindaceae species would provide insight into future research on the breeding of rambutan and Sapindaceae evolutionary studies.
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Affiliation(s)
- Fei Dong
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; or
| | - Zhicong Lin
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; or
| | - Jing Lin
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Fujian Agriculture and Forestry University, Fuzhou 350002, China; or
| | - Ray Ming
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Correspondence: (R.M.); (W.Z.); Tel.: +1-217-333-1221 (R.M.); Tel.: +86-15-8006-2379 (W.Z.)
| | - Wenping Zhang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Fujian Agriculture and Forestry University, Fuzhou 350002, China; or
- Correspondence: (R.M.); (W.Z.); Tel.: +1-217-333-1221 (R.M.); Tel.: +86-15-8006-2379 (W.Z.)
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Khanum Z, Tiznado-Hernández ME, Ali A, Musharraf SG, Shakeel M, Khan IA. Adaptation mechanism of mango fruit ( Mangifera indica L. cv. Chaunsa White) to heat suggest modulation in several metabolic pathways. RSC Adv 2020; 10:35531-35544. [PMID: 35515688 PMCID: PMC9056917 DOI: 10.1039/d0ra01223h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 08/13/2020] [Indexed: 01/02/2023] Open
Abstract
Climate change is becoming a global problem because of its harmful effects on crop productivity. In this regard, it is crucial to carry out studies to determine crops' response to heatwave stress. Response molecular mechanisms during the development and ripening of mango fruit (Mangifera indica L. cv. Chaunsa White) under extreme heatwaves were studied. Mango flowers were tagged and fruits 18, 34, 62, 79, 92 days after flowering (DAF) as well as fruits on 10 and 15 days of postharvest shelf life were studied through RNA-Seq and metabolome of the fruit mesocarp. The environmental temperature was recorded during the experiment. Roughly, 2 000 000 clean reads were generated and assembled into 12 876 redundant transcripts and 2674 non-redundant transcripts. The expression of genes playing a role in oxidative stress, circadian rhythm, senescence, glycolysis, secondary metabolite biosynthesis, flavonoid biosynthesis and monoterpenoid biosynthesis was quantified as well as reactive oxygen species. Higher expressions of six abiotic stress genes and a senescent associated gene was found at 79 DAF (recorded temperature 44 °C). Higher expressions of nucleoredoxin and glutathione S-transferase 1 family protein were also recorded. Activation of the GABA-shunt pathway was detected by the glutamate decarboxylase transcript expression at 79 DAF. Larger energy demands at the beginning of fruit ripening were indicated by an increase in fructose-bisphosphate aldolase gene expression. Finally, the radical-scavenging effect of mango fruit inflorescence and fruit pulp extracts showed decline upon heatwave exposure. We recorded a broad genetic response of mango fruit suggesting the activation of several metabolic pathways which indicated the occurrence of genetic and metabolic crosstalks in response to intense heatwaves. Collectively, this study presents experimental evidence to help in the elucidation of the molecular mechanism of crops response to heat stress which in turn will help in the designing of protocols to increase crop productivity in the face of climate change.
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Affiliation(s)
- Zainab Khanum
- Jamil-ur-Rahman Center for Genome Research, Dr Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi Karachi-75270 Pakistan
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi Karachi-75270 Pakistan
| | - Martín E Tiznado-Hernández
- Coordinación de Tecnología de Alimentos de Origen Vegetal, Centro de Investigación en Alimentación y Desarrollo A. C. Hermosillo Sonora Mexico
| | - Arslan Ali
- Jamil-ur-Rahman Center for Genome Research, Dr Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi Karachi-75270 Pakistan
| | - Syed Ghulam Musharraf
- Jamil-ur-Rahman Center for Genome Research, Dr Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi Karachi-75270 Pakistan
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi Karachi-75270 Pakistan
| | - Muhammad Shakeel
- Jamil-ur-Rahman Center for Genome Research, Dr Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi Karachi-75270 Pakistan
| | - Ishtiaq Ahmad Khan
- Jamil-ur-Rahman Center for Genome Research, Dr Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi Karachi-75270 Pakistan
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Li L, Wu HX, Ma XW, Xu WT, Liang QZ, Zhan RL, Wang SB. Transcriptional mechanism of differential sugar accumulation in pulp of two contrasting mango (Mangifera indica L.) cultivars. Genomics 2020; 112:4505-4515. [PMID: 32735916 DOI: 10.1016/j.ygeno.2020.07.038] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 07/20/2020] [Accepted: 07/24/2020] [Indexed: 02/06/2023]
Abstract
Temporal transcriptome analysis combined with targeted metabolomics was employed to investigate the mechanisms of high sugar accumulation in fruit pulp of two contrasting mango cultivars. Ten sugar metabolites were identified in mango pulp with the most dominant being d-glucose. Analysis of the gene expression patterns revealed that the high-sugar cultivar prioritized the conversion of sucrose to d-glucose by up-regulating invertases and β-glucosidases and increased other genes directly contributing to the synthesis of sucrose and d-glucose. In contrast, it repressed the expression of genes converting sucrose, d-glucose and other sugars into intermediates compounds for downstream processes. It also strongly increased the expression of alpha-amylases which may promote high degradation of starch into d-glucose. Besides, ¾ of the sugar transporters was strongly up-regulated, indicative of their preponderant role in sugar accumulation in mango fruit. Overall, this study provides a good insight into the regulation pattern of high sugar accumulation in mango pulp.
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Affiliation(s)
- Li Li
- Key Laboratory of Tropical Fruit Biology of Ministry of Agriculture, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China
| | - Hong-Xia Wu
- Key Laboratory of Tropical Fruit Biology of Ministry of Agriculture, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China
| | - Xiao-Wei Ma
- Key Laboratory of Tropical Fruit Biology of Ministry of Agriculture, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China
| | - Wen-Tian Xu
- Key Laboratory of Tropical Fruit Biology of Ministry of Agriculture, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China
| | - Qing-Zhi Liang
- Key Laboratory of Tropical Fruit Biology of Ministry of Agriculture, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China
| | - Ru-Lin Zhan
- Haikou Experimental Station (Institute of Tropical Fruit Tree), Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Song-Biao Wang
- Key Laboratory of Tropical Fruit Biology of Ministry of Agriculture, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China.
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Zhang Y, Ou KW, Huang GD, Lu YF, Yang GQ, Pang XH. The complete chloroplast genome sequence of Mangifera sylvatica Roxb. (Anacardiaceae) and its phylogenetic analysis. MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:738-739. [PMID: 33366727 PMCID: PMC7748516 DOI: 10.1080/23802359.2020.1715286] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
In this study, we firstly reported the complete chloroplast (cp) genome sequences of the Mangifera sylvatica from Nanning, Guangxi province, China. The complete wild mango cp genome size is 158063 bp with a typical small single-copy region (SSC, 18340 bp), a large single-copy region (LSC, 87008 bp) and a pair of inverted repeats (IRs, 26379 bp and 26379 bp respectively). Out of 112 unique annotated genes in mango cp genome, 78 found to be protein coding, 30 to be tRNA and 4 rRNA genes. Besides, we found 51 microsatellite sequences (SSRs) in the cp genome. Sequence alignment and ML analysis of 29 full plastome data revealed M. sylvatica shares the closest relationship with cultivated mango (M. indica) and form a sister group with Rhus chinensis within Anacardiaceae.
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Affiliation(s)
- Yu Zhang
- Guangxi Subtropical Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Ke-Wei Ou
- Guangxi Subtropical Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Guo-Di Huang
- Guangxi Subtropical Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Ye-Fei Lu
- Guangxi Subtropical Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Guo-Qian Yang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Xin-Hua Pang
- Guangxi Subtropical Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
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Chabikwa TG, Barbier FF, Tanurdzic M, Beveridge CA. De novo transcriptome assembly and annotation for gene discovery in avocado, macadamia and mango. Sci Data 2020; 7:9. [PMID: 31913298 PMCID: PMC6949230 DOI: 10.1038/s41597-019-0350-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 11/26/2019] [Indexed: 01/03/2023] Open
Abstract
Avocado (Persea americana Mill.), macadamia (Macadamia integrifolia L.) and mango (Mangifera indica L.) are important subtropical tree species grown for their edible fruits and nuts. Despite their commercial and nutritional importance, the genomic information for these species is largely lacking. Here we report the generation of avocado, macadamia and mango transcriptome assemblies from pooled leaf, stem, bud, root, floral and fruit/nut tissue. Using normalized cDNA libraries, we generated comprehensive RNA-Seq datasets from which we assembled 63420, 78871 and 82198 unigenes of avocado, macadamia and mango, respectively using a combination of de novo transcriptome assembly and redundancy reduction. These unigenes were functionally annotated using Basic Local Alignment Search Tool (BLAST) to query the Universal Protein Resource Knowledgebase (UniProtKB). A workflow encompassing RNA extraction, library preparation, transcriptome assembly, redundancy reduction, assembly validation and annotation is provided. This study provides avocado, macadamia and mango transcriptome and annotation data, which is valuable for gene discovery and gene expression profiling experiments as well as ongoing and future genome annotation and marker development applications.
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Affiliation(s)
- Tinashe G Chabikwa
- School of Biological Sciences, The University of Queensland, St. Lucia, Brisbane, Queensland, 4072, Australia
| | - Francois F Barbier
- School of Biological Sciences, The University of Queensland, St. Lucia, Brisbane, Queensland, 4072, Australia
| | - Milos Tanurdzic
- School of Biological Sciences, The University of Queensland, St. Lucia, Brisbane, Queensland, 4072, Australia.
| | - Christine A Beveridge
- School of Biological Sciences, The University of Queensland, St. Lucia, Brisbane, Queensland, 4072, Australia.
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Brisbane, Queensland, 4072, Australia.
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12
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Villas Boas GR, Rodrigues Lemos JM, de Oliveira MW, Dos Santos RC, Stefanello da Silveira AP, Bacha FB, Aguero Ito CN, Cornelius EB, Lima FB, Sachilarid Rodrigues AM, Costa NB, Bittencourt FF, Freitas de Lima F, Paes MM, Gubert P, Oesterreich SA. Preclinical safety evaluation of the aqueous extract from Mangifera indica Linn. (Anacardiaceae): genotoxic, clastogenic and cytotoxic assessment in experimental models of genotoxicity in rats to predict potential human risks. JOURNAL OF ETHNOPHARMACOLOGY 2019; 243:112086. [PMID: 31310830 DOI: 10.1016/j.jep.2019.112086] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 06/22/2019] [Accepted: 07/12/2019] [Indexed: 06/10/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Medicinal plants widely used by the population contain significant concentrations of biologically active compounds and, although they have proven pharmacological properties, can cause DNA damage and develop fatal diseases. AIM OF THE STUDY The present study aimed to evaluate the genotoxic, cytotoxic potential and clastogenic effects of the aqueous extract from Mangifera indica leaves (EAMI) on rats submitted to experimental genotoxicity models and through the SMART test performed in Drosophila melanogaster. MATERIAL AND METHODS The comet assay and the micronucleus test were performed on peripheral and bone marrow blood, respectively, of Wistar rats, orally treated with EAMI at doses of 125, 250, 500 and 1000 mg/kg/bw for 28 days. In the SMART test, the standard cross between three mutant D. melanogaster strains was used. Larvae were treated with EAMI at different concentrations, and the wings of adult flies were evaluated for the presence/frequency of mutant spots and compared to the negative control group. RESULTS Phytochemical analysis of EAMI indicated high levels of flavonoids. The tests performed in rats showed that EAMI did not present significant genotoxic or clastogenic effects. The results showed a critical dose-dependent cytoprotective effect exerted by EAMI. This result was attributed to the high content of polyphenols and flavonoids. The biotransformation metabolites of EAMI did not present genotoxic activity, as demonstrated by the SMART test. CONCLUSIONS These results are relevant since they provide safety information about a plant species of great therapeutic, economical, nutritious and ethnopharmacological value for the population.
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Affiliation(s)
- Gustavo Roberto Villas Boas
- Research Group on Development of Pharmaceutical Products (P&DProFar), Center for Biological and Health Sciences, Federal University of Western Bahia, Barreiras, Bahia, Brazil.
| | | | | | - Rafael Claudino Dos Santos
- Faculty of Health Sciences, Federal University of Grande Dourados, Dourados, Mato Grosso do Sul, Brazil.
| | | | - Flávia Barbieri Bacha
- Faculty of Health Sciences, University Center of Grande Dourados, Dourados, Mato Grosso do Sul, Brazil.
| | - Caren Naomi Aguero Ito
- Faculty of Health Sciences, University Center of Grande Dourados, Dourados, Mato Grosso do Sul, Brazil.
| | | | - Fernanda Brioli Lima
- Faculty of Health Sciences, University Center of Grande Dourados, Dourados, Mato Grosso do Sul, Brazil.
| | | | - Nathália Belmal Costa
- Faculty of Health Sciences, University Center of Grande Dourados, Dourados, Mato Grosso do Sul, Brazil.
| | | | - Fernando Freitas de Lima
- Faculty of Health Sciences, Federal University of Grande Dourados, Dourados, Mato Grosso do Sul, Brazil.
| | - Marina Meirelles Paes
- Research Group on Development of Pharmaceutical Products (P&DProFar), Center for Biological and Health Sciences, Federal University of Western Bahia, Barreiras, Bahia, Brazil.
| | - Priscila Gubert
- Research Group on Development of Pharmaceutical Products (P&DProFar), Center for Biological and Health Sciences, Federal University of Western Bahia, Barreiras, Bahia, Brazil.
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Bajpai A, Khan K, Muthukumar M, Rajan S, Singh NK. Molecular analysis of anthocyanin biosynthesis pathway genes and their differential expression in mango peel. Genome 2018; 61:157-166. [PMID: 29338343 DOI: 10.1139/gen-2017-0205] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Mango fruit is cherished by masses for its taste and nutrition, contributed by color, flavor, and aroma. Among these, peel color is an important trait contributing to fruit quality and market value. We attempted to elucidate the role of key genes of the anthocyanin biosynthesis pathway related to fruit peel color from the leaf transcriptome of mango cultivar Amrapali. A total of 108 mined transcript sequences were assigned to the phenylpropanoid-flavonoid pathway from which 15 contigs representing anthocyanin biosynthesis genes were annotated. Alternate splice variants were identified by mapping against genes of Citrus clementina and Vitis vinifera (closest relatives) and protein subcellular localization was determined. Phylogenetic analysis of these pathway genes clustered them into distinct groups aligning with homologous genes of Magnifera indica, C. clementina, and V. vinifera. Expression profiling revealed higher relative fold expressions in mature fruit peel of red-colored varieties (Arunika, Ambika, and Tommy Atkins) in comparison with the green-peeled Amrapali. MiCHS, MiCHI, and MiF3H alternate splice variants revealed differential gene expression. Functionally divergent variants indicate availability of an allelic pool programmed to play critical roles in peel color. This study provides insight into the molecular genetic basis of peel color and offers scope for development of biomarkers in varietal improvement programs.
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Affiliation(s)
- Anju Bajpai
- a ICAR-Central Institute for Subtropical Horticulture, Lucknow-226101, India
| | - Kasim Khan
- a ICAR-Central Institute for Subtropical Horticulture, Lucknow-226101, India
| | - M Muthukumar
- a ICAR-Central Institute for Subtropical Horticulture, Lucknow-226101, India
| | - S Rajan
- a ICAR-Central Institute for Subtropical Horticulture, Lucknow-226101, India
| | - N K Singh
- b ICAR-National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi-110012, India
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14
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Jo S, Kim HW, Kim YK, Sohn JY, Cheon SH, Kim KJ. The complete plastome sequences of Mangifera indica L. (Anacardiaceae). Mitochondrial DNA B Resour 2017; 2:698-700. [PMID: 33473951 PMCID: PMC7800470 DOI: 10.1080/23802359.2017.1390407] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 10/06/2017] [Indexed: 11/18/2022] Open
Abstract
In this study, we determined the complete plastome sequence of Mangifera indica L. (Anacardiaceae) (NCBI acc. no. KX871231). The complete plastome is 157,780 bp in length, and consists of a large single copy of 86,673 bp and a small single copy of 18,349 bp, separated by two inverted repeats of 25,792 bp. The plastome contains 112 genes, of which 78 are protein-coding genes, 30 are tRNA genes, and four are rRNA genes. Sixteen genes contain one intron and two genes have two introns. The average A-T content of the plastome is 62.1%. The M. indica plastome has approximately 15 kb inversion between trnT-UGU and trnT-GGU. We identify a palindromic repeat of 18 bp (ATTCTTTTTTTTTTTTTT/AAAAAAAAAAAAAAGAAT) near the inversion breakpoints of M. indica plastome. Phylogenetic analysis revealed that M. indica is a sister group of Rhus chinensis with 100% bootstrap support. Anacardiaceae clade is a sister group of Boswellia sacra (Burseraceae) with 100% bootstrap support.
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Affiliation(s)
- Sangjin Jo
- Division of Life Sciences, Korea University, Seoul, Korea
| | - Hoe-Won Kim
- Division of Life Sciences, Korea University, Seoul, Korea
| | - Young-Kee Kim
- Division of Life Sciences, Korea University, Seoul, Korea
| | - Jung-Yeon Sohn
- Division of Life Sciences, Korea University, Seoul, Korea
| | - Se-Hwan Cheon
- Division of Life Sciences, Korea University, Seoul, Korea
| | - Ki-Joong Kim
- Division of Life Sciences, Korea University, Seoul, Korea
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15
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Deshpande AB, Anamika K, Jha V, Chidley HG, Oak PS, Kadoo NY, Pujari KH, Giri AP, Gupta VS. Transcriptional transitions in Alphonso mango (Mangifera indica L.) during fruit development and ripening explain its distinct aroma and shelf life characteristics. Sci Rep 2017; 7:8711. [PMID: 28821734 PMCID: PMC5562913 DOI: 10.1038/s41598-017-08499-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 07/10/2017] [Indexed: 01/27/2023] Open
Abstract
Alphonso is known as the “King of mangos” due to its unique flavor, attractive color, low fiber pulp and long shelf life. We analyzed the transcriptome of Alphonso mango through Illumina sequencing from seven stages of fruit development and ripening as well as flower. Total transcriptome data from these stages ranged between 65 and 143 Mb. Importantly, 20,755 unique transcripts were annotated and 4,611 were assigned enzyme commission numbers, which encoded 142 biological pathways. These included ethylene and flavor related secondary metabolite biosynthesis pathways, as well as those involved in metabolism of starch, sucrose, amino acids and fatty acids. Differential regulation (p-value ≤ 0.05) of thousands of transcripts was evident in various stages of fruit development and ripening. Novel transcripts for biosynthesis of mono-terpenes, sesqui-terpenes, di-terpenes, lactones and furanones involved in flavor formation were identified. Large number of transcripts encoding cell wall modifying enzymes was found to be steady in their expression, while few were differentially regulated through these stages. Novel 79 transcripts of inhibitors of cell wall modifying enzymes were simultaneously detected throughout Alphonso fruit development and ripening, suggesting controlled activity of these enzymes involved in fruit softening.
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Affiliation(s)
- Ashish B Deshpande
- Plant Molecular Biology Group, Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, 411008, Maharashtra, India
| | - Krishanpal Anamika
- Labs, Persistent Systems Limited, Pingala-Aryabhata, Erandwane, Pune, 411004, India
| | - Vineet Jha
- Labs, Persistent Systems Limited, Pingala-Aryabhata, Erandwane, Pune, 411004, India
| | - Hemangi G Chidley
- Plant Molecular Biology Group, Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, 411008, Maharashtra, India
| | - Pranjali S Oak
- Plant Molecular Biology Group, Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, 411008, Maharashtra, India
| | - Narendra Y Kadoo
- Plant Molecular Biology Group, Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, 411008, Maharashtra, India
| | - Keshav H Pujari
- Dr. Balasaheb Sawant Konkan Agriculture University, Dapoli, 415712, Maharashtra, India
| | - Ashok P Giri
- Plant Molecular Biology Group, Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, 411008, Maharashtra, India
| | - Vidya S Gupta
- Plant Molecular Biology Group, Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, 411008, Maharashtra, India.
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16
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Moazzzam Jazi M, Seyedi SM, Ebrahimie E, Ebrahimi M, De Moro G, Botanga C. A genome-wide transcriptome map of pistachio (Pistacia vera L.) provides novel insights into salinity-related genes and marker discovery. BMC Genomics 2017; 18:627. [PMID: 28814265 PMCID: PMC5559799 DOI: 10.1186/s12864-017-3989-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 08/01/2017] [Indexed: 12/18/2022] Open
Abstract
Background Pistachio (Pistacia vera L.) is one of the most important commercial nut crops worldwide. It is a salt-tolerant and long-lived tree, with the largest cultivation area in Iran. Climate change and subsequent increased soil salt content have adversely affected the pistachio yield in recent years. However, the lack of genomic/global transcriptomic sequences on P. vera impedes comprehensive researches at the molecular level. Hence, whole transcriptome sequencing is required to gain insight into functional genes and pathways in response to salt stress. Results RNA sequencing of a pooled sample representing 24 different tissues of two pistachio cultivars with contrasting salinity tolerance under control and salt treatment by Illumina Hiseq 2000 platform resulted in 368,953,262 clean 100 bp paired-ends reads (90 Gb). Following creating several assemblies and assessing their quality from multiple perspectives, we found that using the annotation-based metrics together with the length-based parameters allows an improved assessment of the transcriptome assembly quality, compared to the solely use of the length-based parameters. The generated assembly by Trinity was adopted for functional annotation and subsequent analyses. In total, 29,119 contigs annotated against all of five public databases, including NR, UniProt, TAIR10, KOG and InterProScan. Among 279 KEGG pathways supported by our assembly, we further examined the pathways involved in the plant hormone biosynthesis and signaling as well as those to be contributed to secondary metabolite biosynthesis due to their importance under salinity stress. In total, 11,337 SSRs were also identified, which the most abundant being dinucleotide repeats. Besides, 13,097 transcripts as candidate stress-responsive genes were identified. Expression of some of these genes experimentally validated through quantitative real-time PCR (qRT-PCR) that further confirmed the accuracy of the assembly. From this analysis, the contrasting expression pattern of NCED3 and SOS1 genes were observed between salt-sensitive and salt-tolerant cultivars. Conclusion This study, as the first report on the whole transcriptome survey of P. vera, provides important resources and paves the way for functional and comparative genomic studies on this major tree to discover the salinity tolerance-related markers and stress response mechanisms for breeding of new pistachio cultivars with more salinity tolerance. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3989-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Maryam Moazzzam Jazi
- Plant Biotechnology Department, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Seyed Mahdi Seyedi
- Plant Biotechnology Department, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran.
| | - Esmaeil Ebrahimie
- School of Medicine, The University of Adelaide, Adelaide, Australia.,Institute of Biotechnology, Shiraz University, Shiraz, Iran.,Division of Information Technology, Engineering and the Environment, School of Information Technology and Mathematical Sciences, University of South Australia, Adelaide, Australia.,School of Biological Sciences, Faculty of Science and Engineering, Flinders University, Adelaide, Australia
| | | | - Gianluca De Moro
- Center of Marine Sciences (CCMAR), University of Algarve, Faro, Portugal
| | - Christopher Botanga
- Department of Biological Sciences, Chicago State University, Chicago, IL, USA
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17
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Li YH, Zhang HN, Wu QS, Muday GK. Transcriptional sequencing and analysis of major genes involved in the adventitious root formation of mango cotyledon segments. PLANTA 2017; 245:1193-1213. [PMID: 28303391 DOI: 10.1007/s00425-017-2677-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 03/09/2017] [Indexed: 05/12/2023]
Abstract
A total of 74,745 unigenes were generated and 1975 DEGs were identified. Candidate genes that may be involved in the adventitious root formation of mango cotyledon segment were revealed. Adventitious root formation is a crucial step in plant vegetative propagation, but the molecular mechanism of adventitious root formation remains unclear. Adventitious roots formed only at the proximal cut surface (PCS) of mango cotyledon segments, whereas no roots were formed on the opposite, distal cut surface (DCS). To identify the transcript abundance changes linked to adventitious root development, RNA was isolated from PCS and DCS at 0, 4 and 7 days after culture, respectively. Illumina sequencing of libraries generated from these samples yielded 62.36 Gb high-quality reads that were assembled into 74,745 unigenes with an average sequence length of 807 base pairs, and 33,252 of the assembled unigenes at least had homologs in one of the public databases. Comparative analysis of these transcriptome databases revealed that between the different time points at PCS there were 1966 differentially expressed genes (DEGs), while there were only 51 DEGs for the PCS vs. DCS when time-matched samples were compared. Of these DEGs, 1636 were assigned to gene ontology (GO) classes, the majority of that was involved in cellular processes, metabolic processes and single-organism processes. Candidate genes that may be involved in the adventitious root formation of mango cotyledon segment are predicted to encode polar auxin transport carriers, auxin-regulated proteins, cell wall remodeling enzymes and ethylene-related proteins. In order to validate RNA-sequencing results, we further analyzed the expression profiles of 20 genes by quantitative real-time PCR. This study expands the transcriptome information for Mangifera indica and identifies candidate genes involved in adventitious root formation in cotyledon segments of mango.
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Affiliation(s)
- Yun-He Li
- South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Sciences, No. 1 Huxiu Road, Zhanjiang, 524091, China.
- Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture, Zhanjiang, 524091, China.
- Department of Biology, Wake Forest University, Winston-Salem, NC, 27109, USA.
| | - Hong-Na Zhang
- South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Sciences, No. 1 Huxiu Road, Zhanjiang, 524091, China
| | - Qing-Song Wu
- South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Sciences, No. 1 Huxiu Road, Zhanjiang, 524091, China
| | - Gloria K Muday
- Department of Biology, Wake Forest University, Winston-Salem, NC, 27109, USA
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18
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Kuhn DN, Bally ISE, Dillon NL, Innes D, Groh AM, Rahaman J, Ophir R, Cohen Y, Sherman A. Genetic Map of Mango: A Tool for Mango Breeding. FRONTIERS IN PLANT SCIENCE 2017; 8:577. [PMID: 28473837 PMCID: PMC5397511 DOI: 10.3389/fpls.2017.00577] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 03/30/2017] [Indexed: 05/27/2023]
Abstract
Mango (Mangifera indica) is an economically and nutritionally important tropical/subtropical tree fruit crop. Most of the current commercial cultivars are selections rather than the products of breeding programs. To improve the efficiency of mango breeding, molecular markers have been used to create a consensus genetic map that identifies all 20 linkage groups in seven mapping populations. Polyembryony is an important mango trait, used for clonal propagation of cultivars and rootstocks. In polyembryonic mango cultivars, in addition to a zygotic embryo, several apomictic embryos develop from maternal tissue surrounding the fertilized egg cell. This trait has been associated with linkage group 8 in our consensus genetic map and has been validated in two of the seven mapping populations. In addition, we have observed a significant association between trait and single nucleotide polymorphism (SNP) markers for the vegetative trait of branch habit and the fruit traits of bloom, ground skin color, blush intensity, beak shape, and pulp color.
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Affiliation(s)
- David N. Kuhn
- Subtropical Horticulture Research Station, United States Department of Agriculture—Agriculture Research ServiceMiami, FL, USA
| | - Ian S. E. Bally
- Department of Agriculture and Fisheries, Centre for Tropical Agriculture, Horticulture and Forestry ScienceBrisbane, QLD, Australia
| | - Natalie L. Dillon
- Department of Agriculture and Fisheries, Centre for Tropical Agriculture, Horticulture and Forestry ScienceBrisbane, QLD, Australia
| | - David Innes
- Department of Agriculture and Fisheries, Centre for Tropical Agriculture, Horticulture and Forestry ScienceBrisbane, QLD, Australia
| | - Amy M. Groh
- International Center for Tropical Botany, Florida International UniversityMiami, FL, USA
| | - Jordon Rahaman
- International Center for Tropical Botany, Florida International UniversityMiami, FL, USA
| | - Ron Ophir
- Department of Fruit Tree Sciences, Plant Sciences Institute, Agriculture Research OrganizationRishon Letzion, Israel
| | - Yuval Cohen
- Department of Fruit Tree Sciences, Plant Sciences Institute, Agriculture Research OrganizationRishon Letzion, Israel
| | - Amir Sherman
- Department of Fruit Tree Sciences, Plant Sciences Institute, Agriculture Research OrganizationRishon Letzion, Israel
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Leaf Transcriptome Sequencing for Identifying Genic-SSR Markers and SNP Heterozygosity in Crossbred Mango Variety 'Amrapali' (Mangifera indica L.). PLoS One 2016; 11:e0164325. [PMID: 27736892 PMCID: PMC5063295 DOI: 10.1371/journal.pone.0164325] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Accepted: 09/25/2016] [Indexed: 12/13/2022] Open
Abstract
Mango (Mangifera indica L.) is called “king of fruits” due to its sweetness, richness of taste, diversity, large production volume and a variety of end usage. Despite its huge economic importance genomic resources in mango are scarce and genetics of useful horticultural traits are poorly understood. Here we generated deep coverage leaf RNA sequence data for mango parental varieties ‘Neelam’, ‘Dashehari’ and their hybrid ‘Amrapali’ using next generation sequencing technologies. De-novo sequence assembly generated 27,528, 20,771 and 35,182 transcripts for the three genotypes, respectively. The transcripts were further assembled into a non-redundant set of 70,057 unigenes that were used for SSR and SNP identification and annotation. Total 5,465 SSR loci were identified in 4,912 unigenes with 288 type I SSR (n ≥ 20 bp). One hundred type I SSR markers were randomly selected of which 43 yielded PCR amplicons of expected size in the first round of validation and were designated as validated genic-SSR markers. Further, 22,306 SNPs were identified by aligning high quality sequence reads of the three mango varieties to the reference unigene set, revealing significantly enhanced SNP heterozygosity in the hybrid Amrapali. The present study on leaf RNA sequencing of mango varieties and their hybrid provides useful genomic resource for genetic improvement of mango.
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20
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Comparative transcriptome analysis of unripe and mid-ripe fruit of Mangifera indica (var. "Dashehari") unravels ripening associated genes. Sci Rep 2016; 6:32557. [PMID: 27586495 PMCID: PMC5009307 DOI: 10.1038/srep32557] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 08/09/2016] [Indexed: 01/18/2023] Open
Abstract
Ripening in mango is under a complex control of ethylene. In an effort to understand the complex spatio-temporal control of ripening we have made use of a popular N. Indian variety “Dashehari” This variety ripens from the stone inside towards the peel outside and forms jelly in the pulp in ripe fruits. Through a combination of 454 and Illumina sequencing, a transcriptomic analysis of gene expression from unripe and midripe stages have been performed in triplicates. Overall 74,312 unique transcripts with ≥1 FPKM were obtained. The transcripts related to 127 pathways were identified in “Dashehari” mango transcriptome by the KEGG analysis. These pathways ranged from detoxification, ethylene biosynthesis, carbon metabolism and aromatic amino acid degradation. The transcriptome study reveals differences not only in expression of softening associated genes but also those that govern ethylene biosynthesis and other nutritional characteristics. This study could help to develop ripening related markers for selective breeding to reduce the problems of excess jelly formation during softening in the “Dashehari” variety.
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Sherman A, Rubinstein M, Eshed R, Benita M, Ish-Shalom M, Sharabi-Schwager M, Rozen A, Saada D, Cohen Y, Ophir R. Mango (Mangifera indica L.) germplasm diversity based on single nucleotide polymorphisms derived from the transcriptome. BMC PLANT BIOLOGY 2015; 15:277. [PMID: 26573148 PMCID: PMC4647706 DOI: 10.1186/s12870-015-0663-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 11/04/2015] [Indexed: 05/29/2023]
Abstract
BACKGROUND Germplasm collections are an important source for plant breeding, especially in fruit trees which have a long duration of juvenile period. Thus, efforts have been made to study the diversity of fruit tree collections. Even though mango is an economically important crop, most of the studies on diversity in mango collections have been conducted with a small number of genetic markers. RESULTS We describe a de novo transcriptome assembly from mango cultivar 'Keitt'. Variation discovery was performed using Illumina resequencing of 'Keitt' and 'Tommy Atkins' cultivars identified 332,016 single-nucleotide polymorphisms (SNPs) and 1903 simple-sequence repeats (SSRs). Most of the SSRs (70.1%) were of trinucleotide with the preponderance of motif (GGA/AAG)n and only 23.5% were di-nucleotide SSRs with the mostly of (AT/AT)n motif. Further investigation of the diversity in the Israeli mango collection was performed based on a subset of 293 SNPs. Those markers have divided the Israeli mango collection into two major groups: one group included mostly mango accessions from Southeast Asia (Malaysia, Thailand, Indonesia) and India and the other with mainly of Floridian and Israeli mango cultivars. The latter group was more polymorphic (FS=-0.1 on the average) and was more of an admixture than the former group. A slight population differentiation was detected (FST=0.03), suggesting that if the mango accessions of the western world apparently was originated from Southeast Asia, as has been previously suggested, the duration of cultivation was not long enough to develop a distinct genetic background. CONCLUSIONS Whole-transcriptome reconstruction was used to significantly broaden the mango's genetic variation resources, i.e., SNPs and SSRs. The set of SNP markers described in this study is novel. A subset of SNPs was sampled to explore the Israeli mango collection and most of them were polymorphic in many mango accessions. Therefore, we believe that these SNPs will be valuable as they recapitulate and strengthen the history of mango diversity.
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Affiliation(s)
- Amir Sherman
- Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel.
| | - Mor Rubinstein
- Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel.
| | - Ravit Eshed
- Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel.
| | - Miri Benita
- Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel.
| | - Mazal Ish-Shalom
- Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel.
| | - Michal Sharabi-Schwager
- Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel.
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel.
| | - Ada Rozen
- Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel.
| | - David Saada
- Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel.
| | - Yuval Cohen
- Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel.
| | - Ron Ophir
- Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel.
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22
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Ibarra-Laclette E, Méndez-Bravo A, Pérez-Torres CA, Albert VA, Mockaitis K, Kilaru A, López-Gómez R, Cervantes-Luevano JI, Herrera-Estrella L. Deep sequencing of the Mexican avocado transcriptome, an ancient angiosperm with a high content of fatty acids. BMC Genomics 2015; 16:599. [PMID: 26268848 PMCID: PMC4533766 DOI: 10.1186/s12864-015-1775-y] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 07/14/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Avocado (Persea americana) is an economically important tropical fruit considered to be a good source of fatty acids. Despite its importance, the molecular and cellular characterization of biochemical and developmental processes in avocado is limited due to the lack of transcriptome and genomic information. RESULTS The transcriptomes of seeds, roots, stems, leaves, aerial buds and flowers were determined using different sequencing platforms. Additionally, the transcriptomes of three different stages of fruit ripening (pre-climacteric, climacteric and post-climacteric) were also analyzed. The analysis of the RNAseqatlas presented here reveals strong differences in gene expression patterns between different organs, especially between root and flower, but also reveals similarities among the gene expression patterns in other organs, such as stem, leaves and aerial buds (vegetative organs) or seed and fruit (storage organs). Important regulators, functional categories, and differentially expressed genes involved in avocado fruit ripening were identified. Additionally, to demonstrate the utility of the avocado gene expression atlas, we investigated the expression patterns of genes implicated in fatty acid metabolism and fruit ripening. CONCLUSIONS A description of transcriptomic changes occurring during fruit ripening was obtained in Mexican avocado, contributing to a dynamic view of the expression patterns of genes involved in fatty acid biosynthesis and the fruit ripening process.
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Affiliation(s)
- Enrique Ibarra-Laclette
- Laboratorio Nacional de Genómica para la Biodiversidad-Langebio/Unidad de Genómica Avanzada UGA, Centro de Investigación y Estudios Avanzados del IPN, 36500, Irapuato, Guanajuato, Mexico.,Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C., 91070, Xalapa, Veracruz, Mexico
| | - Alfonso Méndez-Bravo
- Laboratorio Nacional de Genómica para la Biodiversidad-Langebio/Unidad de Genómica Avanzada UGA, Centro de Investigación y Estudios Avanzados del IPN, 36500, Irapuato, Guanajuato, Mexico.,Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C., 91070, Xalapa, Veracruz, Mexico
| | - Claudia Anahí Pérez-Torres
- Laboratorio Nacional de Genómica para la Biodiversidad-Langebio/Unidad de Genómica Avanzada UGA, Centro de Investigación y Estudios Avanzados del IPN, 36500, Irapuato, Guanajuato, Mexico.,Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C., 91070, Xalapa, Veracruz, Mexico.,Investigador Cátedra CONACyT en el Instituto de Ecología A.C., Veracruz, Mexico
| | - Victor A Albert
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, 14260, USA
| | - Keithanne Mockaitis
- Department of Biology and Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN, 47405, USA
| | - Aruna Kilaru
- Department of Biological Sciences, East Tennessee State University, Johnson City, TN, 37614, USA.,Department of Biomedical Sciences, East Tennessee State University, Johnson City, TN, 37614, USA
| | - Rodolfo López-Gómez
- Instituto de Investigaciones Químico-Biológicas (IIQB), Universidad Michoacana de San Nicolás de Hidalgo, 58030, Morelia, Michoacán, Mexico
| | - Jacob Israel Cervantes-Luevano
- Laboratorio Nacional de Genómica para la Biodiversidad-Langebio/Unidad de Genómica Avanzada UGA, Centro de Investigación y Estudios Avanzados del IPN, 36500, Irapuato, Guanajuato, Mexico
| | - Luis Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad-Langebio/Unidad de Genómica Avanzada UGA, Centro de Investigación y Estudios Avanzados del IPN, 36500, Irapuato, Guanajuato, Mexico.
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23
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Hoang VLT, Innes DJ, Shaw PN, Monteith GR, Gidley MJ, Dietzgen RG. Sequence diversity and differential expression of major phenylpropanoid-flavonoid biosynthetic genes among three mango varieties. BMC Genomics 2015; 16:561. [PMID: 26220670 PMCID: PMC4518526 DOI: 10.1186/s12864-015-1784-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2015] [Accepted: 07/17/2015] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Mango fruits contain a broad spectrum of phenolic compounds which impart potential health benefits; their biosynthesis is catalysed by enzymes in the phenylpropanoid-flavonoid (PF) pathway. The aim of this study was to reveal the variability in genes involved in the PF pathway in three different mango varieties Mangifera indica L., a member of the family Anacardiaceae: Kensington Pride (KP), Irwin (IW) and Nam Doc Mai (NDM) and to determine associations with gene expression and mango flavonoid profiles. RESULTS A close evolutionary relationship between mango genes and those from the woody species poplar of the Salicaceae family (Populus trichocarpa) and grape of the Vitaceae family (Vitis vinifera), was revealed through phylogenetic analysis of PF pathway genes. We discovered 145 SNPs in total within coding sequences with an average frequency of one SNP every 316 bp. Variety IW had the highest SNP frequency (one SNP every 258 bp) while KP and NDM had similar frequencies (one SNP every 369 bp and 360 bp, respectively). The position in the PF pathway appeared to influence the extent of genetic diversity of the encoded enzymes. The entry point enzymes phenylalanine lyase (PAL), cinnamate 4-mono-oxygenase (C4H) and chalcone synthase (CHS) had low levels of SNP diversity in their coding sequences, whereas anthocyanidin reductase (ANR) showed the highest SNP frequency followed by flavonoid 3'-hydroxylase (F3'H). Quantitative PCR revealed characteristic patterns of gene expression that differed between mango peel and flesh, and between varieties. CONCLUSIONS The combination of mango expressed sequence tags and availability of well-established reference PF biosynthetic genes from other plant species allowed the identification of coding sequences of genes that may lead to the formation of important flavonoid compounds in mango fruits and facilitated characterisation of single nucleotide polymorphisms between varieties. We discovered an association between the extent of sequence variation and position in the pathway for up-stream genes. The high expression of PAL, C4H and CHS genes in mango peel compared to flesh is associated with high amounts of total phenolic contents in peels, which suggest that these genes have an influence on total flavonoid levels in mango fruit peel and flesh. In addition, the particularly high expression levels of ANR in KP and NDM peels compared to IW peel and the significant accumulation of its product epicatechin gallate (ECG) in those extracts reflects the rate-limiting role of ANR on ECG biosynthesis in mango.
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Affiliation(s)
- Van L T Hoang
- School of Pharmacy, The University of Queensland, Brisbane, Queensland, Australia.
- Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Queensland, Australia.
| | - David J Innes
- Department of Agriculture and Fisheries, Agri-Science Queensland, Brisbane, Queensland, Australia.
| | - P Nicholas Shaw
- School of Pharmacy, The University of Queensland, Brisbane, Queensland, Australia.
- Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Queensland, Australia.
| | - Gregory R Monteith
- School of Pharmacy, The University of Queensland, Brisbane, Queensland, Australia.
| | - Michael J Gidley
- Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Queensland, Australia.
| | - Ralf G Dietzgen
- School of Pharmacy, The University of Queensland, Brisbane, Queensland, Australia.
- Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Queensland, Australia.
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24
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Dautt-Castro M, Ochoa-Leyva A, Contreras-Vergara CA, Pacheco-Sanchez MA, Casas-Flores S, Sanchez-Flores A, Kuhn DN, Islas-Osuna MA. Mango (Mangifera indica L.) cv. Kent fruit mesocarp de novo transcriptome assembly identifies gene families important for ripening. FRONTIERS IN PLANT SCIENCE 2015; 6:62. [PMID: 25741352 PMCID: PMC4332321 DOI: 10.3389/fpls.2015.00062] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 01/24/2015] [Indexed: 05/04/2023]
Abstract
Fruit ripening is a physiological and biochemical process genetically programmed to regulate fruit quality parameters like firmness, flavor, odor and color, as well as production of ethylene in climacteric fruit. In this study, a transcriptomic analysis of mango (Mangifera indica L.) mesocarp cv. "Kent" was done to identify key genes associated with fruit ripening. Using the Illumina sequencing platform, 67,682,269 clean reads were obtained and a transcriptome of 4.8 Gb. A total of 33,142 coding sequences were predicted and after functional annotation, 25,154 protein sequences were assigned with a product according to Swiss-Prot database and 32,560 according to non-redundant database. Differential expression analysis identified 2,306 genes with significant differences in expression between mature-green and ripe mango [1,178 up-regulated and 1,128 down-regulated (FDR ≤ 0.05)]. The expression of 10 genes evaluated by both qRT-PCR and RNA-seq data was highly correlated (R = 0.97), validating the differential expression data from RNA-seq alone. Gene Ontology enrichment analysis, showed significantly represented terms associated to fruit ripening like "cell wall," "carbohydrate catabolic process" and "starch and sucrose metabolic process" among others. Mango genes were assigned to 327 metabolic pathways according to Kyoto Encyclopedia of Genes and Genomes database, among them those involved in fruit ripening such as plant hormone signal transduction, starch and sucrose metabolism, galactose metabolism, terpenoid backbone, and carotenoid biosynthesis. This study provides a mango transcriptome that will be very helpful to identify genes for expression studies in early and late flowering mangos during fruit ripening.
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Affiliation(s)
- Mitzuko Dautt-Castro
- Laboratorio de Genética y Biología Molecular de Plantas, Centro de Investigación en Alimentación y DesarrolloHermosillo, Sonora, Mexico
| | - Adrian Ochoa-Leyva
- Instituto Nacional de Medicina Genómica, Unidad de Genómica de Poblaciones, Aplicada a la Salud, Facultad de Qumica UNAM, DelegaciónTlalpan, Mexico DF
| | - Carmen A. Contreras-Vergara
- Laboratorio de Genética y Biología Molecular de Plantas, Centro de Investigación en Alimentación y DesarrolloHermosillo, Sonora, Mexico
| | - Magda A. Pacheco-Sanchez
- Laboratorio de Genética y Biología Molecular de Plantas, Centro de Investigación en Alimentación y DesarrolloHermosillo, Sonora, Mexico
| | - Sergio Casas-Flores
- Laboratorio de Genómica Funcional y Comparativa, División de Biología Molecular, Instituto Potosino de Investigación Científica y TecnológicaSan Luis Potosí (SLP), Mexico
| | - Alejandro Sanchez-Flores
- Unidad Universitaria de Secuenciación Masiva de DNA, Instituto de Biotecnología/Universidad Nacional Autónoma de MéxicoCuernavaca, Morelos, Mexico
| | - David N. Kuhn
- United States Department of Agriculture – Agricultural Research Service, Subtropical Horticulture Research StationMiami, FL, USA
| | - Maria A. Islas-Osuna
- Laboratorio de Genética y Biología Molecular de Plantas, Centro de Investigación en Alimentación y DesarrolloHermosillo, Sonora, Mexico
- *Correspondence: Maria A. Islas-Osuna, Laboratorio de Genética y Biología Molecular de Plantas, Centro de Investigación en Alimentación y Desarrollo, Carretera Ejido La Victoria Km 0.6, Hermosillo, Sonora 83304, Mexico e-mail:
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