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Zhang YY, Li HK, Huang X, Yuan YJ, Zhang XF, Gao XS, Wang XJ, Wei MM, Huang HS, Li W. Heterozygosity analysis of spontaneous 2n female gametes and centromere mapping of the diploid Hevea brasiliensis based on full-sib triploid populations. PLANT REPRODUCTION 2024; 37:47-56. [PMID: 37758937 DOI: 10.1007/s00497-023-00481-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Accepted: 08/28/2023] [Indexed: 09/29/2023]
Abstract
KEY MESSAGE Unreduced megagametophytes via second-division restitution were confirmed through heterozygosity analysis, and four candidate physical centromeres of rubber were located for the first time. The evaluation of maternal heterozygosity restitution (MHR) is vital in identifying the mechanism of 2n gametogenesis and assessing the utilization value of 2n gametes. In this study, three full-sib triploid populations were employed to evaluate the MHR of 2n female gametes of rubber tree clone GT1 and to confirm their genetic derivation. The 2n female gametes of GT1 were derived from second-division restitution (SDR) and transmitted more than half of the parental heterozygosity. In addition, low recombination frequency markers were developed, and four candidate physical centromeres of rubber tree were located for the first time. The confirmation that 2n female gametes of rubber tree clone GT1 are derived from SDR provides insights into the molecular mechanisms of 2n gametogenesis. In addition, the identified centromere location will aid in the development of centromeric markers for the rapid identification of the 2n gametogenesis mechanism.
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Affiliation(s)
- Yuan-Yuan Zhang
- State Key Laboratory of Tropical Crop Breeding, State Centre for Rubber Breeding, Key Laboratory of Biology and Genetic Resources of Rubber Tree, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China.
| | - Hong-Kun Li
- Dehong Institute of Tropical Agricultural Sciences of Yunnan Province, Ruili, 678600, Yunnan, China
| | - Xiao Huang
- State Key Laboratory of Tropical Crop Breeding, State Centre for Rubber Breeding, Key Laboratory of Biology and Genetic Resources of Rubber Tree, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China
| | - Yu-Jiao Yuan
- College of Tropical Crops, Yunnan Agricultural University, Puer, 665099, Yunnan, China
| | - Xiao-Fei Zhang
- State Key Laboratory of Tropical Crop Breeding, State Centre for Rubber Breeding, Key Laboratory of Biology and Genetic Resources of Rubber Tree, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China
| | - Xin-Sheng Gao
- State Key Laboratory of Tropical Crop Breeding, State Centre for Rubber Breeding, Key Laboratory of Biology and Genetic Resources of Rubber Tree, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China
| | - Xiang-Jun Wang
- State Key Laboratory of Tropical Crop Breeding, State Centre for Rubber Breeding, Key Laboratory of Biology and Genetic Resources of Rubber Tree, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China
| | - Ming-Ming Wei
- State Key Laboratory of Tropical Crop Breeding, State Centre for Rubber Breeding, Key Laboratory of Biology and Genetic Resources of Rubber Tree, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China
| | - Hua-Sun Huang
- State Key Laboratory of Tropical Crop Breeding, State Centre for Rubber Breeding, Key Laboratory of Biology and Genetic Resources of Rubber Tree, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China
| | - Weiguo Li
- State Key Laboratory of Tropical Crop Breeding, State Centre for Rubber Breeding, Key Laboratory of Biology and Genetic Resources of Rubber Tree, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China.
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Roy CB, Goonetilleke SN, Joseph L, Krishnan A, Saha T, Kilian A, Mather DE. Analysis of Genetic Diversity and Resistance to Foliar Pathogens Based on Genotyping-by-Sequencing of a Para Rubber Diversity Panel and Progeny of an Interspecific Cross. PLANTS (BASEL, SWITZERLAND) 2022; 11:3418. [PMID: 36559531 PMCID: PMC9781018 DOI: 10.3390/plants11243418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/19/2022] [Accepted: 11/26/2022] [Indexed: 06/17/2023]
Abstract
Para rubber trees (Hevea brasiliensis) are the largest major source of natural rubber in the world. Its major pathogens are Phytophthora spp., Corynespora cassiicola, and Colletotrichum spp. A rubber diversity panel of 116 clones using over 12,000 single nucleotide polymorphisms (SNPs) from DArTSeq genotyping revealed clear phylogenetic differences in clones that originated from different geographical regions of the world. An integrated linkage map constructed with an F1 progeny of 86 from an interspecific cross between H. brasiliensis and H. benthamiana using 23,978 markers [10,323 SNPs and 13,655 SilicoDArTs] spanned 3947.83 cM with 0.83 cM average marker-interval. The genome scaffolds that were anchored to the linkage map, covering 1.44 Gb of H. brasiliensis reference genome, revealed a high level of collinearity between the genetic map and reference genome. Association analysis identified 12 SNPs significantly associated with the resistance against Phytophthora, Corynespora, and Colletotrichum in six linkage groups: 2, 6, 12, 14, 17, and 18. Kompetitive Allele-Specific PCR marker assays were developed for those 12 SNPs, screened with 178 individuals, and detected clear separation between two genotypes. Within the proximity to those SNPs, 41 potentially key genes that have previously been reported to associate with plant disease resistance were predicted with high confidence.
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Affiliation(s)
- C. Bindu Roy
- Rubber Research Institute of India, Kottayam 686 009, India
| | - Shashi N. Goonetilleke
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Glen Osmond, SA 5064, Australia
| | - Limiya Joseph
- Rubber Research Institute of India, Kottayam 686 009, India
| | - Anu Krishnan
- Rubber Research Institute of India, Kottayam 686 009, India
| | - Thakurdas Saha
- Rubber Research Institute of India, Kottayam 686 009, India
| | - Andrzej Kilian
- Diversity Arrays Technology, Canberra, ACT 2617, Australia
| | - Diane E. Mather
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Glen Osmond, SA 5064, Australia
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Whole genome survey analysis and microsatellite motif identification of Sebastiscus marmoratus. Biosci Rep 2021; 40:222120. [PMID: 32090250 PMCID: PMC7040462 DOI: 10.1042/bsr20192252] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 02/04/2020] [Accepted: 02/13/2020] [Indexed: 01/17/2023] Open
Abstract
The marbled rockfish Sebastiscus marmoratus is an ecologically and economically important marine fish species distributed along the northwestern Pacific coast from Japan to the Philippines. Here, next-generation sequencing was used to generate a whole genome survey dataset to provide fundamental information of its genome and develop genome-wide microsatellite markers for S. marmoratus. The genome size of S. marmoratus was estimated as approximate 800 Mb by using K-mer analyses, and its heterozygosity ratio and repeat sequence ratio were 0.17% and 39.65%, respectively. The preliminary assembled genome was nearly 609 Mb with GC content of 41.3%, and the data were used to develop microsatellite markers. A total of 191,592 microsatellite motifs were identified. The most frequent repeat motif was dinucleotide with a frequency of 76.10%, followed by 19.63% trinucleotide, 3.91% tetranucleotide, and 0.36% pentanucleotide motifs. The AC, GAG, and ATAG repeats were the most abundant motifs of dinucleotide, trinucleotide, and tetranucleotide motifs, respectively. In summary, a wide range of candidate microsatellite markers were identified and characterized in the present study using genome survey analysis. High-quality whole genome sequence based on the “Illumina+PacBio+Hi-C” strategy is warranted for further comparative genomics and evolutionary biology studies in this species.
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4
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Raw transcriptomics data to gene specific SSRs: a validated free bioinformatics workflow for biologists. Sci Rep 2020; 10:18236. [PMID: 33106560 PMCID: PMC7588437 DOI: 10.1038/s41598-020-75270-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 09/21/2020] [Indexed: 02/07/2023] Open
Abstract
Recent advances in next-generation sequencing technologies have paved the path for a considerable amount of sequencing data at a relatively low cost. This has revolutionized the genomics and transcriptomics studies. However, different challenges are now created in handling such data with available bioinformatics platforms both in assembly and downstream analysis performed in order to infer correct biological meaning. Though there are a handful of commercial software and tools for some of the procedures, cost of such tools has made them prohibitive for most research laboratories. While individual open-source or free software tools are available for most of the bioinformatics applications, those components usually operate standalone and are not combined for a user-friendly workflow. Therefore, beginners in bioinformatics might find analysis procedures starting from raw sequence data too complicated and time-consuming with the associated learning-curve. Here, we outline a procedure for de novo transcriptome assembly and Simple Sequence Repeats (SSR) primer design solely based on tools that are available online for free use. For validation of the developed workflow, we used Illumina HiSeq reads of different tissue samples of Santalum album (sandalwood), generated from a previous transcriptomics project. A portion of the designed primers were tested in the lab with relevant samples and all of them successfully amplified the targeted regions. The presented bioinformatics workflow can accurately assemble quality transcriptomes and develop gene specific SSRs. Beginner biologists and researchers in bioinformatics can easily utilize this workflow for research purposes.
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Abstract
The commercial production of high quality natural rubber (NR) solely depends on Hevea brasiliensis Muell. Arg, (Para rubber tree) and accounts for >98% of total production worldwide. NR with its unique properties is an essential commodity for the automobile industry and its synthetic counterparts are in no way substitute to it. The rubber tree genome is very complex and plays an important role in delivering the unique properties of Hevea. But a lack of knowledge on the molecular mechanisms of rubber biosynthesis, disease resistance, etc., in elite clones of rubber still persists. Marker-assisted selection and transgenic techniques were proved to be advantageous in improving the breeding efficiency for latex yield, disease resistance, etc. The suppression subtractive hybridization (SSH), in the form of subtracted cDNA libraries and microarrays, can assist in searching the functions of expressed genes (candidate gene approach). Expressed sequence tags (ESTs) related to various metabolic aspects are well utilized to create EST banks that broadly represent the genes expressed in one tissue, such as latex cells, that assists in the study of gene function and regulation. Transcriptome analysis and gene mapping have been accomplished in Hevea at various stages. However, a selection criterion to delineate high yielding genotypes at the juvenile stage has not been accomplished so far. This is the main pit fall for rubber breeding apart from stock-scion interactions leading to yield differences among a clonally multiplied population. At least four draft genome sequences have been published on Hevea rubber, and all give different genome size and contig lengths-a comprehensive and acceptable genomic map remains unfulfilled. The progress made in molecular markers, latex biosynthesis genes, transcriptome analysis, chloroplast and mitochondrial DNA diversity, paternity identification through Breeding without Breeding (BwB), stimulated latex production and its molecular intricacies, molecular biology of tapping panel dryness, genomics for changed climates and genome mapping are discussed in this review. These information can be utilized to improvise the molecular breeding programs of Hevea in future.
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6
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Zhang S, Zhang X, Chen X, Xu T, Wang M, Qin Q, Zhong L, Jiang H, Zhu X, Liu H, Shao J, Zhu Z, Shi Q, Bian W, You X. Construction of a High-Density Linkage Map and QTL Fine Mapping for Growth- and Sex-Related Traits in Channel Catfish ( Ictalurus punctatus). Front Genet 2019; 10:251. [PMID: 30984241 PMCID: PMC6448050 DOI: 10.3389/fgene.2019.00251] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 03/06/2019] [Indexed: 12/11/2022] Open
Abstract
A high-density genetic linkage map is of particular importance in the fine mapping for important economic traits and whole genome assembly in aquaculture species. The channel catfish (Ictalurus punctatus), a species native to North America, is one of the most important commercial freshwater fish in the world. Outside of the United States, China has become the major producer and consumer of channel catfish after experiencing rapid development in the past three decades. In this study, based on restriction site associated DNA sequencing (RAD-seq), a high-density genetic linkage map of channel catfish was constructed by using single nucleotide polymorphisms (SNPs) in a F1 family composed of 156 offspring and their two parental individuals. A total of 4,768 SNPs were assigned to 29 linkage groups (LGs), and the length of the linkage map reached 2,480.25 centiMorgans (cM) with an average distance of 0.55 cM between loci. Based on this genetic linkage map, 223 genomic scaffolds were anchored to the 29 LGs of channel catfish, and a total length of 704.66 Mb was assembled. Quantitative trait locus (QTL) mapping and genome-wide association analysis identified 10 QTLs of sex-related and six QTLs of growth-related traits at LG17 and LG28, respectively. Candidate genes associated with sex dimorphism, including spata2, spata5, sf3, zbtb38, and fox, were identified within QTL intervals on the LG17. A sex-linked marker with simple sequence repeats (SSR) in zbtb38 gene of the LG17 was validated for practical verification of sex in the channel catfish. Thus, the LG17 was considered as a sex-related LG. Potential growth-related genes were also identified, including important regulators such as megf9, npffr1, and gas1. In a word, we constructed the high-density genetic linkage map and developed the sex-linked marker in channel catfish, which are important genetic resources for future marker-assisted selection (MAS) of this economically important teleost.
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Affiliation(s)
- Shiyong Zhang
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China.,The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
| | - Xinhui Zhang
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Beijing Genomics Institute, Shenzhen, China
| | - Xiaohui Chen
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China.,The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
| | - Tengfei Xu
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Beijing Genomics Institute, Shenzhen, China
| | - Minghua Wang
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China.,The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
| | - Qin Qin
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China.,The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
| | - Liqiang Zhong
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China.,The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
| | - Hucheng Jiang
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China.,The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
| | - Xiaohua Zhu
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China
| | - Hongyan Liu
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China
| | - Junjie Shao
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China
| | - Zhifei Zhu
- BGI-Zhenjiang Institute of Hydrobiology, Zhenjiang, China
| | - Qiong Shi
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Beijing Genomics Institute, Shenzhen, China
| | - Wenji Bian
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China.,The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
| | - Xinxin You
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Beijing Genomics Institute, Shenzhen, China
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7
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Men X, Wang F, Chen GQ, Zhang HB, Xian M. Biosynthesis of Natural Rubber: Current State and Perspectives. Int J Mol Sci 2018; 20:E50. [PMID: 30583567 PMCID: PMC6337083 DOI: 10.3390/ijms20010050] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Revised: 12/17/2018] [Accepted: 12/19/2018] [Indexed: 12/12/2022] Open
Abstract
Natural rubber is a kind of indispensable biopolymers with great use and strategic importance in human society. However, its production relies almost exclusively on rubber-producing plants Hevea brasiliensis, which have high requirements for growth conditions, and the mechanism of natural rubber biosynthesis remains largely unknown. In the past two decades, details of the rubber chain polymerization and proteins involved in natural rubber biosynthesis have been investigated intensively. Meanwhile, omics and other advanced biotechnologies bring new insight into rubber production and development of new rubber-producing plants. This review summarizes the achievements of the past two decades in understanding the biosynthesis of natural rubber, especially the massive information obtained from the omics analyses. Possibilities of natural rubber biosynthesis in vitro or in genetically engineered microorganisms are also discussed.
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Affiliation(s)
- Xiao Men
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.189 Songling Road, Laoshan District, Qingdao 266101, China.
| | - Fan Wang
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.189 Songling Road, Laoshan District, Qingdao 266101, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Guo-Qiang Chen
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.189 Songling Road, Laoshan District, Qingdao 266101, China.
| | - Hai-Bo Zhang
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.189 Songling Road, Laoshan District, Qingdao 266101, China.
| | - Mo Xian
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.189 Songling Road, Laoshan District, Qingdao 266101, China.
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Wang C, Zhu J, Liu M, Yang Q, Wu J, Li Z. De novo sequencing and transcriptome assembly of Arisaema heterophyllum Blume and identification of genes involved in isoflavonoid biosynthesis. Sci Rep 2018; 8:17643. [PMID: 30518768 PMCID: PMC6281570 DOI: 10.1038/s41598-018-35664-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 11/09/2018] [Indexed: 01/24/2023] Open
Abstract
Arisaema heterophyllum Blume (AhBl) is one of the valued medicinal plants. However, its genetic information is limited, which impedes further studies of this valuable resource. To investigate the genes involved in the isoflavonoid biosynthesis, we deeply performed transcriptome sequencing for AhBl. An average of 10.98 Gb clean reads were obtained based on root, tuber and leaf tissues, and 109,937 unigenes were yielded after de novo assembly. In total, 72,287 of those unigenes were annotated in at least one public database. The numbers of expressed unigenes in each tissue were 35,686, 43,363 and 47,783, respectively. The overall expression levels of transcripts in leaf were higher than those in root and tuber. Differentially expressed genes analysis indicated that a total of 12,448 shared unigenes were detected in all three tissues, 10,215 of which were higher expressed in tuber than that in root and leaf. Besides, 87 candidate unigenes that encode for enzymes involved in biosynthesis of isoflavonoid were identified and analyzed, and some key enzyme genes were experimentally validated by quantitative Real-Time PCR (qRT-PCR). This study provides a unique dataset for the systematic analysis of AhBl functional genes and expression characteristics, and facilitates the future study of the pharmacological mechanism of AhBl.
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Affiliation(s)
- Chenkai Wang
- Anhui University of Chinese Medicine and Anhui Academy of Chinese Medicine, Hefei, 230038, China
- Key Laboratory of Xin'an Medicine, Ministry of Education, Anhui University of Chinese Medicine, Hefei, 230038, China
| | - Jinhang Zhu
- Anhui Medical University, Hefei, 230032, China
| | - Miaomiao Liu
- Anhui University of Chinese Medicine and Anhui Academy of Chinese Medicine, Hefei, 230038, China
- Key Laboratory of Xin'an Medicine, Ministry of Education, Anhui University of Chinese Medicine, Hefei, 230038, China
| | - Qingshan Yang
- Anhui University of Chinese Medicine and Anhui Academy of Chinese Medicine, Hefei, 230038, China
- Synergetic Innovation Center of Anhui Authentic Chinese Medicine Quality Improvement, Hefei, 230012, China
| | - Jiawen Wu
- Anhui University of Chinese Medicine and Anhui Academy of Chinese Medicine, Hefei, 230038, China.
- Key Laboratory of Xin'an Medicine, Ministry of Education, Anhui University of Chinese Medicine, Hefei, 230038, China.
- Synergetic Innovation Center of Anhui Authentic Chinese Medicine Quality Improvement, Hefei, 230012, China.
| | - Zegeng Li
- Anhui University of Chinese Medicine and Anhui Academy of Chinese Medicine, Hefei, 230038, China.
- The First Affiliated Hospital of Anhui University of traditional Chinese Medicine, Anhui, 230038, China.
- Key Laboratory of Respiratory Diseases, State Administration of Traditional Chinese Medicine of the People's Republic of China, Anhui, 230038, China.
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Conson ARO, Taniguti CH, Amadeu RR, Andreotti IAA, de Souza LM, dos Santos LHB, Rosa JRBF, Mantello CC, da Silva CC, José Scaloppi Junior E, Ribeiro RV, Le Guen V, Garcia AAF, Gonçalves PDS, de Souza AP. High-Resolution Genetic Map and QTL Analysis of Growth-Related Traits of Hevea brasiliensis Cultivated Under Suboptimal Temperature and Humidity Conditions. FRONTIERS IN PLANT SCIENCE 2018; 9:1255. [PMID: 30197655 PMCID: PMC6117502 DOI: 10.3389/fpls.2018.01255] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 08/08/2018] [Indexed: 06/02/2023]
Abstract
Rubber tree (Hevea brasiliensis) cultivation is the main source of natural rubber worldwide and has been extended to areas with suboptimal climates and lengthy drought periods; this transition affects growth and latex production. High-density genetic maps with reliable markers support precise mapping of quantitative trait loci (QTL), which can help reveal the complex genome of the species, provide tools to enhance molecular breeding, and shorten the breeding cycle. In this study, QTL mapping of the stem diameter, tree height, and number of whorls was performed for a full-sibling population derived from a GT1 and RRIM701 cross. A total of 225 simple sequence repeats (SSRs) and 186 single-nucleotide polymorphism (SNP) markers were used to construct a base map with 18 linkage groups and to anchor 671 SNPs from genotyping by sequencing (GBS) to produce a very dense linkage map with small intervals between loci. The final map was composed of 1,079 markers, spanned 3,779.7 cM with an average marker density of 3.5 cM, and showed collinearity between markers from previous studies. Significant variation in phenotypic characteristics was found over a 59-month evaluation period with a total of 38 QTLs being identified through a composite interval mapping method. Linkage group 4 showed the greatest number of QTLs (7), with phenotypic explained values varying from 7.67 to 14.07%. Additionally, we estimated segregation patterns, dominance, and additive effects for each QTL. A total of 53 significant effects for stem diameter were observed, and these effects were mostly related to additivity in the GT1 clone. Associating accurate genome assemblies and genetic maps represents a promising strategy for identifying the genetic basis of phenotypic traits in rubber trees. Then, further research can benefit from the QTLs identified herein, providing a better understanding of the key determinant genes associated with growth of Hevea brasiliensis under limiting water conditions.
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Affiliation(s)
- André R. O. Conson
- Molecular Biology and Genetic Engineering Center, University of Campinas, Campinas, Brazil
| | - Cristiane H. Taniguti
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Rodrigo R. Amadeu
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | | | - Livia M. de Souza
- Molecular Biology and Genetic Engineering Center, University of Campinas, Campinas, Brazil
| | | | - João R. B. F. Rosa
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
- FTS Sementes S.A., Research and Development Center, Ponta Grossa, Brazil
| | - Camila C. Mantello
- Molecular Biology and Genetic Engineering Center, University of Campinas, Campinas, Brazil
- National Institute of Agricultural Botany (NIAB), Cambridge, United Kingdom
| | - Carla C. da Silva
- Molecular Biology and Genetic Engineering Center, University of Campinas, Campinas, Brazil
| | | | - Rafael V. Ribeiro
- Department of Plant Biology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Vincent Le Guen
- French Agricultural Research Centre for International Development (CIRAD), UMR AGAP, Montpellier, France
| | - Antonio A. F. Garcia
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | | | - Anete P. de Souza
- Molecular Biology and Genetic Engineering Center, University of Campinas, Campinas, Brazil
- Department of Plant Biology, Institute of Biology, University of Campinas, Campinas, Brazil
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10
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de Souza LM, dos Santos LHB, Rosa JRBF, da Silva CC, Mantello CC, Conson ARO, Scaloppi EJ, Fialho JDF, de Moraes MLT, Gonçalves PDS, Margarido GRA, Garcia AAF, Le Guen V, de Souza AP. Linkage Disequilibrium and Population Structure in Wild and Cultivated Populations of Rubber Tree ( Hevea brasiliensis). FRONTIERS IN PLANT SCIENCE 2018; 9:815. [PMID: 30018620 PMCID: PMC6037771 DOI: 10.3389/fpls.2018.00815] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 05/28/2018] [Indexed: 05/20/2023]
Abstract
Among rubber tree species, which belong to the Hevea genus of the Euphorbiaceae family, Hevea brasiliensis (Willd. ex Adr.de Juss.) Muell. Arg. is the main commercial source of natural rubber production worldwide. Knowledge of the population structure and linkage disequilibrium (LD) of this species is essential for the efficient organization and exploitation of genetic resources. Here, we obtained single-nucleotide polymorphisms (SNPs) using a genotyping-by-sequencing (GBS) approach and then employed the SNPs for the following objectives: (i) to identify the positions of SNPs on a genetic map of a segregating mapping population, (ii) to evaluate the population structure of a germplasm collection, and (iii) to detect patterns of LD decay among chromosomes for future genetic association studies in rubber tree. A total of 626 genotypes, including both germplasm accessions (368) and individuals from a genetic mapping population (254), were genotyped. A total of 77,660 and 21,283 SNPs were detected by GBS in the germplasm and mapping populations, respectively. The mapping population, which was previously mapped, was constructed with 1,062 markers, among which only 576 SNPs came from GBS, reducing the average interval between two adjacent markers to 4.4 cM. SNPs from GBS genotyping were used for the analysis of genetic structure and LD estimation in the germplasm accessions. Two groups, which largely corresponded to the cultivated and wild populations, were detected using STRUCTURE and via principal coordinate analysis. LD analysis, also using the mapped SNPs, revealed that non-random associations varied along chromosomes, with regions of high LD interspersed with regions of low LD. Considering the length of the genetic map (4,693 cM) and the mean LD (0.49 for cultivated and 0.02 for wild populations), a large number of evenly spaced SNPs would be needed to perform genome-wide association studies in rubber tree, and the wilder the genotypes used, the more difficult the mapping saturation.
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Affiliation(s)
- Livia M. de Souza
- Center of Molecular Biology and Genetic Engineering Center, University of Campinas, Campinas, Brazil
| | - Luciano H. B. dos Santos
- Center of Molecular Biology and Genetic Engineering Center, University of Campinas, Campinas, Brazil
| | - João R. B. F. Rosa
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz” Universidade de São Paulo, Piracicaba, Brazil
- FTS Sementes S.A., Research and Development Center, Ponta Grossa, Brazil
| | - Carla C. da Silva
- Center of Molecular Biology and Genetic Engineering Center, University of Campinas, Campinas, Brazil
| | - Camila C. Mantello
- Center of Molecular Biology and Genetic Engineering Center, University of Campinas, Campinas, Brazil
- The John Bingham Laboratory, National Institute of Agricultural Botany, Cambridge, United Kingdom
| | - André R. O. Conson
- Center of Molecular Biology and Genetic Engineering Center, University of Campinas, Campinas, Brazil
| | - Erivaldo J. Scaloppi
- Center of Rubber Tree and Agroforestry Systems, Agronomic Institute of Campinas, Votuporanga, Brazil
| | - Josefino de F. Fialho
- Centro de Pesquisa Agropecuária dos Cerrados (Cpac), Embrapa Cerrados, Empresa Brazileira de Pesquisa Agropecuária, Planaltina, Brazil
| | - Mario Luiz T. de Moraes
- Departamento de Fitotecnia, Faculdade de Engenharia de Ilha Solteira, Universidade Estadual Paulista, Ilha Solteira, Brazil
| | - Paulo de S. Gonçalves
- Center of Rubber Tree and Agroforestry Systems, Agronomic Institute of Campinas, Votuporanga, Brazil
| | - Gabriel R. A. Margarido
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz” Universidade de São Paulo, Piracicaba, Brazil
| | - Antonio A. F. Garcia
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz” Universidade de São Paulo, Piracicaba, Brazil
| | - Vincent Le Guen
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement, UMR AGAP, Montpellier, France
| | - Anete P. de Souza
- Center of Molecular Biology and Genetic Engineering Center, University of Campinas, Campinas, Brazil
- Department of Plant Biology, Biology Institute, University of Campinas, Campinas, Brazil
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11
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Onming S, Thongda W, Li C, Sawatdichaikul O, McMillan N, Klinbunga S, Peatman E, Poompuang S. Bioinformatics characterization of a cathepsin B transcript from the giant river prawn, Macrobrachium rosenbergii: Homology modeling and expression analysis after Aeromonas hydrophila infection. Comp Biochem Physiol B Biochem Mol Biol 2018; 221-222:18-28. [PMID: 29649577 DOI: 10.1016/j.cbpb.2018.04.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Cathepsin B is a lysosomal proteolytic enzyme that has been suggested to play a role in pathological processes of immune system. In this study, the full-length cDNA sequence of cathepsin B transcript in the giant river prawn Macrobrachium rosenbergii (MrCTSB) was obtained from 454 pyrosequencing of cDNAs from hepatopancreas and muscle. It was 1158 bp in length, containing an open reading frame (ORF) of 987 bp corresponding to 328 amino acids. The predicted molecular mass and pI of MrCTSB protein was 36.04 kDa and 4.73. The major characteristics of MrCTSB protein consisted of a propeptide of C1 peptidase family at the N-terminus and a cysteine protease (Pept_C1) domain at the C-terminus. The 3-dimentional structure of MrCTSB was constructed by computer-assisted homology modeling. The folding of MrCTSB was highly conserved to human CTSB structure and the modeled MrCTSB displayed characteristics of cysteine proteinases superfamily. The docking study was performed to investigate binding interactions between known inhibitors against MrCTSB. Known inhibitors were oriented in the groove of catalytic site cleft. They bound to subsites from S2, S1, S1', and S2', respectively, with key residues in each subsite. Challenge of juvenile prawns with Aeromonas hydrophila revealed that the MrCTSB transcript in hepatopancreas significantly increased at 60-96 h post injection (hpi). This suggested that MrCTSB may play roles in innate immunity of M. rosenbergii. Our results provide useful information for a more comprehensive study in immune-related functions of MrCTSB.
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Affiliation(s)
- Saowalak Onming
- Department of Aquaculture, Faculty of Fisheries, Kasetsart University, 50 Ngamwongwan Road, Bangkok 10900, Thailand
| | - Wilawan Thongda
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Chao Li
- Marine Science and Engineering College, Qingdao Agricultural University, Qingdao 266109, China
| | - Orathai Sawatdichaikul
- Department of Nutrition and Health, Institute of Food Research and Product Development, Kasetsart University, Bangkok 10900, Thailand
| | - Nichanun McMillan
- Department of Aquaculture, Faculty of Fisheries, Kasetsart University, 50 Ngamwongwan Road, Bangkok 10900, Thailand
| | - Sirawut Klinbunga
- Aquatic Molecular Genetics and Biotechnology Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Paholyothin Rd., Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand; Center of Excellence for Marine Biotechnology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Eric Peatman
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Supawadee Poompuang
- Department of Aquaculture, Faculty of Fisheries, Kasetsart University, 50 Ngamwongwan Road, Bangkok 10900, Thailand.
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12
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Taheri S, Lee Abdullah T, Yusop MR, Hanafi MM, Sahebi M, Azizi P, Shamshiri RR. Mining and Development of Novel SSR Markers Using Next Generation Sequencing (NGS) Data in Plants. Molecules 2018; 23:E399. [PMID: 29438290 PMCID: PMC6017569 DOI: 10.3390/molecules23020399] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 01/11/2018] [Accepted: 01/13/2018] [Indexed: 11/17/2022] Open
Abstract
Microsatellites, or simple sequence repeats (SSRs), are one of the most informative and multi-purpose genetic markers exploited in plant functional genomics. However, the discovery of SSRs and development using traditional methods are laborious, time-consuming, and costly. Recently, the availability of high-throughput sequencing technologies has enabled researchers to identify a substantial number of microsatellites at less cost and effort than traditional approaches. Illumina is a noteworthy transcriptome sequencing technology that is currently used in SSR marker development. Although 454 pyrosequencing datasets can be used for SSR development, this type of sequencing is no longer supported. This review aims to present an overview of the next generation sequencing, with a focus on the efficient use of de novo transcriptome sequencing (RNA-Seq) and related tools for mining and development of microsatellites in plants.
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Affiliation(s)
- Sima Taheri
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Thohirah Lee Abdullah
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Mohd Rafii Yusop
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Mohamed Musa Hanafi
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
- Laboratory of Plantation Science and Technology, Institute of Plantation Studies, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
- Department of Land Management, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Mahbod Sahebi
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Parisa Azizi
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Redmond Ramin Shamshiri
- Smart Farming Technology Research Center, Department of Biological and Agricultural Engineering, Faculty of Engineering, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
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13
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Makita Y, Kawashima M, Lau NS, Othman AS, Matsui M. Construction of Pará rubber tree genome and multi-transcriptome database accelerates rubber researches. BMC Genomics 2018; 19:922. [PMID: 29363422 PMCID: PMC5780850 DOI: 10.1186/s12864-017-4333-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Natural rubber is an economically important material. Currently the Pará rubber tree, Hevea brasiliensis is the main commercial source. Little is known about rubber biosynthesis at the molecular level. Next-generation sequencing (NGS) technologies brought draft genomes of three rubber cultivars and a variety of RNA sequencing (RNA-seq) data. However, no current genome or transcriptome databases (DB) are organized by gene. RESULTS A gene-oriented database is a valuable support for rubber research. Based on our original draft genome sequence of H. brasiliensis RRIM600, we constructed a rubber tree genome and transcriptome DB. Our DB provides genome information including gene functional annotations and multi-transcriptome data of RNA-seq, full-length cDNAs including PacBio Isoform sequencing (Iso-Seq), ESTs and genome wide transcription start sites (TSSs) derived from CAGE technology. Using our original and publically available RNA-seq data, we calculated co-expressed genes for identifying functionally related gene sets and/or genes regulated by the same transcription factor (TF). Users can access multi-transcriptome data through both a gene-oriented web page and a genome browser. For the gene searching system, we provide keyword search, sequence homology search and gene expression search; users can also select their expression threshold easily. CONCLUSION The rubber genome and transcriptome DB provides rubber tree genome sequence and multi-transcriptomics data. This DB is useful for comprehensive understanding of the rubber transcriptome. This will assist both industrial and academic researchers for rubber and economically important close relatives such as R. communis, M. esculenta and J. curcas. The Rubber Transcriptome DB release 2017.03 is accessible at http://matsui-lab.riken.jp/rubber/ .
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Affiliation(s)
- Yuko Makita
- Synthetic Genomics Research Group, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science (CSRS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Mika Kawashima
- Synthetic Genomics Research Group, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science (CSRS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Nyok Sean Lau
- Synthetic Genomics Research Group, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science (CSRS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.,Centre for Chemical Biology, Universiti Sains Malaysia, 11900 Bayan Lepas, Penang, Malaysia
| | - Ahmad Sofiman Othman
- Centre for Chemical Biology, Universiti Sains Malaysia, 11900 Bayan Lepas, Penang, Malaysia.,School of Biological Sciences, Universiti Sains Malaysia, 11800 Minden, Penang, Malaysia
| | - Minami Matsui
- Synthetic Genomics Research Group, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science (CSRS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
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14
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Zou Z, Xie G, Yang L. Papain-like cysteine protease encoding genes in rubber (Hevea brasiliensis): comparative genomics, phylogenetic, and transcriptional profiling analysis. PLANTA 2017; 246:999-1018. [PMID: 28752264 DOI: 10.1007/s00425-017-2739-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 06/29/2017] [Indexed: 05/22/2023]
Abstract
43 HbPLCPs representing nine subfamilies or 20 orthologous groups were found in rubber, where paralogs were resulted from the recent WGD and local duplication. Several senescence-associated genes were also identified. Papain-like cysteine proteases (PLCPs) comprise a large family of proteolytic enzymes involved in plant growth and development, seed germination, organ senescence, immunity, and stress response. Despite their importance and the extensive research in the model plant Arabidopsis thaliana, little information is available on rubber tree (Hevea brasiliensis), a rubber-producing plant of the Euphorbiaceae family. This study performed a genome-wide identification of PLCP family genes in rubber, resulting in a relatively high number of 43 members. The phylogenetic analysis assigned these genes into nine subfamilies, i.e., RD21 (6), CEP (4), XCP (4), XBCP3 (2), THI (1), SAG12 (18), RD19 (4), ALP (2), and CTB (2). Most of them were shown to have orthologs in Arabidopsis; however, several members in SAG12, CEP and XBCP3 subfamilies form new groups as observed in other core eudicots such as Manihot esculenta, Ricinus communis, Populus trichocarpa, and Vitis vinifera. Based on an expert sequence comparison, 20 orthologous groups (OGs) were proposed for core eudicots, and rubber paralogs were shown to be resulted from the recent whole-genome duplication (WGD) as well as local duplication. Transcriptional profiling showed distinct expression pattern of different members across various tissues, e.g., root, leaf, bark, laticifer, flower, and seed. By using the senescence-specific HbSAG12H1 as the indicator, the transcriptome of senescent rubber leaves was deeply sequenced and several senescence-associated PLCP genes were identified. Results obtained from this study provide valuable information for future functional analysis and utilization of PLCP genes in Hevea and other species.
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Affiliation(s)
- Zhi Zou
- Danzhou Investigation and Experiment Station of Tropical Crops, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, 571737, Hainan, People's Republic of China.
| | - Guishui Xie
- Danzhou Investigation and Experiment Station of Tropical Crops, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, 571737, Hainan, People's Republic of China
| | - Lifu Yang
- Danzhou Investigation and Experiment Station of Tropical Crops, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, 571737, Hainan, People's Republic of China
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15
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Wang J, Chen Z, Jin S, Hu Z, Huang Y, Diao Y. Development and characterization of simple sequence repeat (SSR) markers based on a full-length cDNA library of Napier Grass (Pennisetum purpureum Schum). Genes Genomics 2017. [DOI: 10.1007/s13258-017-0536-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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16
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Makita Y, Ng KK, Veera Singham G, Kawashima M, Hirakawa H, Sato S, Othman AS, Matsui M. Large-scale collection of full-length cDNA and transcriptome analysis in Hevea brasiliensis. DNA Res 2017; 24:159-167. [PMID: 28431015 PMCID: PMC5397604 DOI: 10.1093/dnares/dsw056] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 11/18/2016] [Indexed: 11/16/2022] Open
Abstract
Natural rubber has unique physical properties that cannot be replaced by products from other latex-producing plants or petrochemically produced synthetic rubbers. Rubber from Hevea brasiliensis is the main commercial source for this natural rubber that has a cis-polyisoprene configuration. For sustainable production of enough rubber to meet demand elucidation of the molecular mechanisms involved in the production of latex is vital. To this end, we firstly constructed rubber full-length cDNA libraries of RRIM 600 cultivar and sequenced around 20,000 clones by the Sanger method and over 15,000 contigs by Illumina sequencer. With these data, we updated around 5,500 gene structures and newly annotated around 9,500 transcription start sites. Second, to elucidate the rubber biosynthetic pathways and their transcriptional regulation, we carried out tissue- and cultivar-specific RNA-Seq analysis. By using our recently published genome sequence, we confirmed the expression patterns of the rubber biosynthetic genes. Our data suggest that the cytoplasmic mevalonate (MVA) pathway is the main route for isoprenoid biosynthesis in latex production. In addition to the well-studied polymerization factors, we suggest that rubber elongation factor 8 (REF8) is a candidate factor in cis-polyisoprene biosynthesis. We have also identified 39 transcription factors that may be key regulators in latex production. Expression profile analysis using two additional cultivars, RRIM 901 and PB 350, via an RNA-Seq approach revealed possible expression differences between a high latex-yielding cultivar and a disease-resistant cultivar.
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Affiliation(s)
- Yuko Makita
- Synthetic Genomics Research Group, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, Kanagawa 230-0045, Japan
| | - Kiaw Kiaw Ng
- Synthetic Genomics Research Group, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, Kanagawa 230-0045, Japan.,Molecular Ecology and Evolution Research Laboratory, School of Biological Sciences, Universiti Sains Malaysia, 11800 Minden, Pulau Pinang, Malaysia
| | - G Veera Singham
- Synthetic Genomics Research Group, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, Kanagawa 230-0045, Japan.,Centre for Chemical Biology, Universiti Sains Malaysia, 11900 Bayan Lepas, Pulau Pinang, Malaysia
| | - Mika Kawashima
- Synthetic Genomics Research Group, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, Kanagawa 230-0045, Japan
| | - Hideki Hirakawa
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu Chiba 292-0818, Japan
| | - Shusei Sato
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu Chiba 292-0818, Japan
| | - Ahmad Sofiman Othman
- Molecular Ecology and Evolution Research Laboratory, School of Biological Sciences, Universiti Sains Malaysia, 11800 Minden, Pulau Pinang, Malaysia.,Centre for Chemical Biology, Universiti Sains Malaysia, 11900 Bayan Lepas, Pulau Pinang, Malaysia
| | - Minami Matsui
- Synthetic Genomics Research Group, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, Kanagawa 230-0045, Japan
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17
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Zou Z, Liu J, Yang L, Xie G. Survey of the rubber tree genome reveals a high number of cysteine protease-encoding genes homologous to Arabidopsis SAG12. PLoS One 2017; 12:e0171725. [PMID: 28166280 PMCID: PMC5293227 DOI: 10.1371/journal.pone.0171725] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 01/23/2017] [Indexed: 11/18/2022] Open
Abstract
Arabidopsis thaliana SAG12, a senescence-specific gene encoding a cysteine protease, is widely used as a molecular marker for the study of leaf senescence. To date, its potential orthologues have been isolated from several plant species such as Brassica napus and Nicotiana tabacum. However, little information is available in rubber tree (Hevea brasiliensis), a rubber-producing plant of the Euphorbiaceae family. This study presents the identification of SAG12-like genes from the rubber tree genome. Results showed that an unexpected high number of 17 rubber orthologues with a single intron were found, contrasting the single copy with two introns in Arabidopsis. The gene expansion was also observed in another two Euphorbiaceae plants, castor bean (Ricinus communis) and physic nut (Jatropha curcas), both of which contain 8 orthologues. In accordance with no occurrence of recent whole-genome duplication (WGD) events, most duplicates in castor and physic nut were resulted from tandem duplications. In contrast, the duplicated HbSAG12H genes were derived from tandem duplications as well as the recent WGD. Expression analysis showed that most HbSAG12H genes were lowly expressed in examined tissues except for root and male flower. Furthermore, HbSAG12H1 exhibits a strictly senescence-associated expression pattern in rubber tree leaves, and thus can be used as a marker gene for the study of senescence mechanism in Hevea.
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Affiliation(s)
- Zhi Zou
- Danzhou Investigation & Experiment Station of Tropical Crops, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, Hainan, P. R. China
- * E-mail:
| | - Jianting Liu
- Danzhou Investigation & Experiment Station of Tropical Crops, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, Hainan, P. R. China
- Crops Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, P. R. China
| | - Lifu Yang
- Danzhou Investigation & Experiment Station of Tropical Crops, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, Hainan, P. R. China
| | - Guishui Xie
- Danzhou Investigation & Experiment Station of Tropical Crops, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, Hainan, P. R. China
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18
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De novo hybrid assembly of the rubber tree genome reveals evidence of paleotetraploidy in Hevea species. Sci Rep 2017; 7:41457. [PMID: 28150702 PMCID: PMC5288721 DOI: 10.1038/srep41457] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 12/19/2016] [Indexed: 12/11/2022] Open
Abstract
Para rubber tree (Hevea brasiliensis) is an important economic species as it is the sole commercial producer of high-quality natural rubber. Here, we report a de novo hybrid assembly of BPM24 accession, which exhibits resistance to major fungal pathogens in Southeast Asia. Deep-coverage 454/Illumina short-read and Pacific Biosciences (PacBio) long-read sequence data were acquired to generate a preliminary draft, which was subsequently scaffolded using a long-range "Chicago" technique to obtain a final assembly of 1.26 Gb (N50 = 96.8 kb). The assembled genome contains 69.2% repetitive sequences and has a GC content of 34.31%. Using a high-density SNP-based genetic map, we were able to anchor 28.9% of the genome assembly (363 Mb) associated with over two thirds of the predicted protein-coding genes into rubber tree's 18 linkage groups. These genetically anchored sequences allowed comparative analyses of the intragenomic homeologous synteny, providing the first concrete evidence to demonstrate the presence of paleotetraploidy in Hevea species. Additionally, the degree of macrosynteny conservation observed between rubber tree and cassava strongly supports the hypothesis that the paleotetraploidization event took place prior to the divergence of the Hevea and Manihot species.
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19
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Zhang Y, Zhang X, Wang YH, Shen SK. De Novo Assembly of Transcriptome and Development of Novel EST-SSR Markers in Rhododendron rex Lévl. through Illumina Sequencing. FRONTIERS IN PLANT SCIENCE 2017; 8:1664. [PMID: 29018469 PMCID: PMC5622969 DOI: 10.3389/fpls.2017.01664] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 09/11/2017] [Indexed: 05/18/2023]
Abstract
Transcriptome sequences generated by next-generation sequencing (NGS) technologies can be utilized to rapidly detect and characterize a large number of gene-based microsatellites from different plants. Rhododendron rex Lévl. is a perennial woody species from the family Ericaceae and an endangered plant with high ornamental value endemic to Southwestern China. Nevertheless, the genetic and genomic information of R. rex remain unknown. In this study, we performed transcriptome sequencing for R. rex leaf samples, and generated large transcript sequences for functional characterization and development gene-associated SSR markers. A total of 164,242 unigenes were assembled and 115,089 (70.07%) unigenes were successfully annotated in public databases. In addition, a total of 15,314 potential EST-SSRs were identified, and the frequency of SSRs in the R. rex unigenes was 9.32%, with an average of one EST-SSR per 5.65 kb. The most abundant type was repeated di-nucleotide (54.63%), followed by mono- (26.03%) and tri-nucleotide (18.51%) repeats. Based on the SSR-containing sequence, 100 primer pairs were randomly selected and synthesized and used for assessment of the polymorphism. Thirty-six primer pairs were polymorphic and revealed polymorphism among 20 individuals from four R. rex populations. A total of 197 alleles were identified, with an average of 5.472 alleles per locus. The Polymorphism Information Content ranged from 0.154 to 0.870, with a mean of 0.482. The newly developed EST-SSR markers exhibited high transferability (58.33-83.33%) among the six subgenera. Thus, these novel EST-SSR markers developed would provide valuable sequence resources for population structure, genetic diversity analysis, and genetic resource assessments of R. rex and its related species.
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20
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Male Parent Identification of Triploid Rubber Trees (Hevea brasiliensis) and the Mechanism of 2n Gametes Formation. FORESTS 2016. [DOI: 10.3390/f7120301] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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21
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Transcriptome Analysis of the Signalling Networks in Coronatine-Induced Secondary Laticifer Differentiation from Vascular Cambia in Rubber Trees. Sci Rep 2016; 6:36384. [PMID: 27808245 PMCID: PMC5093416 DOI: 10.1038/srep36384] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 10/14/2016] [Indexed: 11/09/2022] Open
Abstract
The secondary laticifer in rubber tree (Hevea brasiliensis Muell. Arg.) is a specific tissue within the secondary phloem. This tissue differentiates from the vascular cambia, and its function is natural rubber biosynthesis and storage. Given that jasmonates play a pivotal role in secondary laticifer differentiation, we established an experimental system with jasmonate (JA) mimic coronatine (COR) for studying the secondary laticifer differentiation: in this system, differentiation occurs within five days of the treatment of epicormic shoots with COR. In the present study, the experimental system was used to perform transcriptome sequencing and gene expression analysis. A total of 67,873 unigenes were assembled, and 50,548 unigenes were mapped at least in one public database. Of these being annotated unigenes, 15,780 unigenes were differentially expressed early after COR treatment, and 19,824 unigenes were differentially expressed late after COR treatment. At the early stage, 8,646 unigenes were up-regulated, while 7,134 unigenes were down-regulated. At the late stage, the numbers of up- and down-regulated unigenes were 7,711 and 12,113, respectively. The annotation data and gene expression analysis of the differentially expressed unigenes suggest that JA-mediated signalling, Ca2+ signal transduction and the CLAVATA-MAPK-WOX signalling pathway may be involved in regulating secondary laticifer differentiation in rubber trees.
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De novo assembly and characterization of leaf transcriptome for the development of EST-SSR markers of the non-model species Indigofera szechuensis. BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2016.06.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Liu H, Fu J, Du H, Hu J, Wuyun T. De novo sequencing of Eucommia ulmoides flower bud transcriptomes for identification of genes related to floral development. GENOMICS DATA 2016; 9:105-10. [PMID: 27486566 PMCID: PMC4957572 DOI: 10.1016/j.gdata.2016.07.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 06/28/2016] [Accepted: 07/06/2016] [Indexed: 12/18/2022]
Abstract
Eucommia ulmoides Oliver is a woody perennial dioecious species native to China and has great economic value. However, little is known about flower bud development in this species. In this study, the transcriptomes of female and male flower buds were sequenced using the Illumina platform, a next-generation sequencing technology that provides cost-effective, highly efficient transcriptome profiling. In total, 11,558,188,080 clean reads were assembled into 75,065 unigenes with an average length of 1011 bp by de novo assembly using Trinity software. Through similarity comparisons with known protein databases, 47,071 unigenes were annotated, 146 of which were putatively related to the floral development of E. ulmoides. Fifteen of the 146 unigenes had significantly different expression levels between the two samples. Additionally, 24,346 simple sequence repeats were identified in 18,565 unigenes with 12,793 sequences suitable for the designed primers. In total, 67,447 and 58,236 single nucleotide polymorphisms were identified in male and female buds, respectively. This study provides a valuable resource for further conservation genetics and functional genomics research on E. ulmoides.
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Affiliation(s)
- Huimin Liu
- Non-timber Forestry Research and Development Center of Chinese Academy of Forestry, Zhengzhou 450003, Henan, China; The Eucommia Engineering Research Center of State Forestry Administration, Zhengzhou 450003, Henan, China
| | - JianMin Fu
- Non-timber Forestry Research and Development Center of Chinese Academy of Forestry, Zhengzhou 450003, Henan, China
| | - Hongyan Du
- Non-timber Forestry Research and Development Center of Chinese Academy of Forestry, Zhengzhou 450003, Henan, China; The Eucommia Engineering Research Center of State Forestry Administration, Zhengzhou 450003, Henan, China
| | - Jingjing Hu
- Total Genomics Solution Limited, Shenzhen 518081, China
| | - Tana Wuyun
- Non-timber Forestry Research and Development Center of Chinese Academy of Forestry, Zhengzhou 450003, Henan, China; The Eucommia Engineering Research Center of State Forestry Administration, Zhengzhou 450003, Henan, China
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Lau NS, Makita Y, Kawashima M, Taylor TD, Kondo S, Othman AS, Shu-Chien AC, Matsui M. The rubber tree genome shows expansion of gene family associated with rubber biosynthesis. Sci Rep 2016; 6:28594. [PMID: 27339202 PMCID: PMC5008842 DOI: 10.1038/srep28594] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 06/06/2016] [Indexed: 11/14/2022] Open
Abstract
Hevea brasiliensis Muell. Arg, a member of the family Euphorbiaceae, is the sole natural resource exploited for commercial production of high-quality natural rubber. The properties of natural rubber latex are almost irreplaceable by synthetic counterparts for many industrial applications. A paucity of knowledge on the molecular mechanisms of rubber biosynthesis in high yield traits still persists. Here we report the comprehensive genome-wide analysis of the widely planted H. brasiliensis clone, RRIM 600. The genome was assembled based on ~155-fold combined coverage with Illumina and PacBio sequence data and has a total length of 1.55 Gb with 72.5% comprising repetitive DNA sequences. A total of 84,440 high-confidence protein-coding genes were predicted. Comparative genomic analysis revealed strong synteny between H. brasiliensis and other Euphorbiaceae genomes. Our data suggest that H. brasiliensis's capacity to produce high levels of latex can be attributed to the expansion of rubber biosynthesis-related genes in its genome and the high expression of these genes in latex. Using cap analysis gene expression data, we illustrate the tissue-specific transcription profiles of rubber biosynthesis-related genes, revealing alternative means of transcriptional regulation. Our study adds to the understanding of H. brasiliensis biology and provides valuable genomic resources for future agronomic-related improvement of the rubber tree.
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Affiliation(s)
- Nyok-Sean Lau
- Centre for Chemical Biology, Universiti Sains Malaysia, 11900 Bayan Lepas, Penang, Malaysia
- Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, Biomass Engineering Research Division, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Yuko Makita
- Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, Biomass Engineering Research Division, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Mika Kawashima
- Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, Biomass Engineering Research Division, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Todd D. Taylor
- Laboratory for Integrated Bioinformatics, RIKEN Center for Integrative Medical Sciences, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Shinji Kondo
- Transdisciplinary Research Integration Center, National Institute of Polar Research, Tachikawa, Tokyo 190-8518, Japan
| | - Ahmad Sofiman Othman
- Centre for Chemical Biology, Universiti Sains Malaysia, 11900 Bayan Lepas, Penang, Malaysia
- School of Biological Sciences, Universiti Sains Malaysia, 11800 Minden, Penang, Malaysia
| | - Alexander Chong Shu-Chien
- Centre for Chemical Biology, Universiti Sains Malaysia, 11900 Bayan Lepas, Penang, Malaysia
- School of Biological Sciences, Universiti Sains Malaysia, 11800 Minden, Penang, Malaysia
| | - Minami Matsui
- Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, Biomass Engineering Research Division, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
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25
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Hodel RGJ, Gitzendanner MA, Germain-Aubrey CC, Liu X, Crowl AA, Sun M, Landis JB, Segovia-Salcedo MC, Douglas NA, Chen S, Soltis DE, Soltis PS. A new resource for the development of SSR markers: Millions of loci from a thousand plant transcriptomes. APPLICATIONS IN PLANT SCIENCES 2016; 4:apps1600024. [PMID: 27347455 PMCID: PMC4915922 DOI: 10.3732/apps.1600024] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 05/09/2016] [Indexed: 05/29/2023]
Abstract
PREMISE OF THE STUDY The One Thousand Plant Transcriptomes Project (1KP, 1000+ assembled plant transcriptomes) provides an enormous resource for developing microsatellite loci across the plant tree of life. We developed loci from these transcriptomes and tested their utility. METHODS AND RESULTS Using software packages and custom scripts, we identified microsatellite loci in 1KP transcriptomes. We assessed the potential for cross-amplification and whether loci were biased toward exons, as compared to markers derived from genomic DNA. We characterized over 5.7 million simple sequence repeat (SSR) loci from 1334 plant transcriptomes. Eighteen percent of loci substantially overlapped with open reading frames (ORFs), and electronic PCR revealed that over half the loci would amplify successfully in conspecific taxa. Transcriptomic SSRs were approximately three times more likely to map to translated regions than genomic SSRs. CONCLUSIONS We believe microsatellites still have a place in the genomic age-they remain effective and cost-efficient markers. The loci presented here are a valuable resource for researchers.
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Affiliation(s)
- Richard G. J. Hodel
- Department of Biology, University of Florida, Gainesville, Florida 32611 USA
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA
| | | | | | - Xiaoxian Liu
- Department of Biology, University of Florida, Gainesville, Florida 32611 USA
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA
| | - Andrew A. Crowl
- Department of Biology, University of Florida, Gainesville, Florida 32611 USA
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA
| | - Miao Sun
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA
| | - Jacob B. Landis
- Department of Biology, University of Florida, Gainesville, Florida 32611 USA
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA
| | | | - Norman A. Douglas
- Department of Biology, University of Florida, Gainesville, Florida 32611 USA
| | - Shichao Chen
- College of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Douglas E. Soltis
- Department of Biology, University of Florida, Gainesville, Florida 32611 USA
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA
- The Genetics Institute, University of Florida, Gainesville, Florida 32611 USA
| | - Pamela S. Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA
- The Genetics Institute, University of Florida, Gainesville, Florida 32611 USA
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26
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Hodel RGJ, Gitzendanner MA, Germain-Aubrey CC, Liu X, Crowl AA, Sun M, Landis JB, Segovia-Salcedo MC, Douglas NA, Chen S, Soltis DE, Soltis PS. A new resource for the development of SSR markers: Millions of loci from a thousand plant transcriptomes. APPLICATIONS IN PLANT SCIENCES 2016. [PMID: 27347455 DOI: 10.5061/dryad.rb7h0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
PREMISE OF THE STUDY The One Thousand Plant Transcriptomes Project (1KP, 1000+ assembled plant transcriptomes) provides an enormous resource for developing microsatellite loci across the plant tree of life. We developed loci from these transcriptomes and tested their utility. METHODS AND RESULTS Using software packages and custom scripts, we identified microsatellite loci in 1KP transcriptomes. We assessed the potential for cross-amplification and whether loci were biased toward exons, as compared to markers derived from genomic DNA. We characterized over 5.7 million simple sequence repeat (SSR) loci from 1334 plant transcriptomes. Eighteen percent of loci substantially overlapped with open reading frames (ORFs), and electronic PCR revealed that over half the loci would amplify successfully in conspecific taxa. Transcriptomic SSRs were approximately three times more likely to map to translated regions than genomic SSRs. CONCLUSIONS We believe microsatellites still have a place in the genomic age-they remain effective and cost-efficient markers. The loci presented here are a valuable resource for researchers.
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Affiliation(s)
- Richard G J Hodel
- Department of Biology, University of Florida, Gainesville, Florida 32611 USA; Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA
| | | | | | - Xiaoxian Liu
- Department of Biology, University of Florida, Gainesville, Florida 32611 USA; Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA
| | - Andrew A Crowl
- Department of Biology, University of Florida, Gainesville, Florida 32611 USA; Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA
| | - Miao Sun
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA
| | - Jacob B Landis
- Department of Biology, University of Florida, Gainesville, Florida 32611 USA; Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA
| | | | - Norman A Douglas
- Department of Biology, University of Florida, Gainesville, Florida 32611 USA
| | - Shichao Chen
- College of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Douglas E Soltis
- Department of Biology, University of Florida, Gainesville, Florida 32611 USA; Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA; The Genetics Institute, University of Florida, Gainesville, Florida 32611 USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA; The Genetics Institute, University of Florida, Gainesville, Florida 32611 USA
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27
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Li D, Zeng R, Li Y, Zhao M, Chao J, Li Y, Wang K, Zhu L, Tian WM, Liang C. Gene expression analysis and SNP/InDel discovery to investigate yield heterosis of two rubber tree F1 hybrids. Sci Rep 2016; 6:24984. [PMID: 27108962 PMCID: PMC4842955 DOI: 10.1038/srep24984] [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: 08/26/2015] [Accepted: 04/06/2016] [Indexed: 01/06/2023] Open
Abstract
As an important industrial material, natural rubber is mainly harvested from the rubber tree. Rubber tree breeding is inefficient, expensive and time-consuming, whereas marker-assisted selection is a feasible method for early selection of high-yield hybrids. We thus sequenced and analyzed the transcriptomes of two parent rubber trees (RRIM 600 and PR 107) and their most productive hybrids (RY 7-33-97 and RY 7-20-59) to understand their gene expression patterns and genetic variations including single nucleotide polymorphisms (SNPs) and small insertions/deletions (InDels). We discovered >31,000 genetic variations in 112,702 assembled unigenes. Our results showed that the higher yield in F1 hybrids was positively associated with their higher genome heterozygosity, which was further confirmed by genotyping 10 SNPs in 20 other varieties. We also showed that RY 7-33-97 and RY 7-20-59 were genetically closer to RRIM 600 and PR 107, respectively, in agreement with both their phenotypic similarities and gene expression profiles. After identifying ethylene- and jasmonic acid–responsive genes at the transcription level, we compared and analyzed the genetic variations underlying rubber biosynthesis and the jasmonic acid and ethylene pathways in detail. Our results suggest that genome-wide genetic variations play a substantive role in maintaining rubber tree heterosis.
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Affiliation(s)
- Dejun Li
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, Hainan, China
| | - Rizhong Zeng
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, Hainan, China
| | - Yan Li
- State Key Laboratory of Plant Genomics and National Plant Gene Research Centre (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 5 Datun Road, Chaoyang District, 100101 Beijing, China
| | - Manman Zhao
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, Hainan, China.,College of Horticulture &Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 China
| | - Jinquan Chao
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, Hainan, China
| | - Yu Li
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, Hainan, China
| | - Kai Wang
- State Key Laboratory of Plant Genomics and National Plant Gene Research Centre (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 5 Datun Road, Chaoyang District, 100101 Beijing, China
| | - Lihuang Zhu
- State Key Laboratory of Plant Genomics and National Plant Gene Research Centre (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 5 Datun Road, Chaoyang District, 100101 Beijing, China
| | - Wei-Min Tian
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, Hainan, China
| | - Chengzhi Liang
- State Key Laboratory of Plant Genomics and National Plant Gene Research Centre (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 5 Datun Road, Chaoyang District, 100101 Beijing, China
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28
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Liu JP, Zhuang YF, Guo XL, Li YJ. Molecular mechanism of ethylene stimulation of latex yield in rubber tree (Hevea brasiliensis) revealed by de novo sequencing and transcriptome analysis. BMC Genomics 2016; 17:257. [PMID: 27008913 PMCID: PMC4806457 DOI: 10.1186/s12864-016-2587-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 03/14/2016] [Indexed: 12/29/2022] Open
Abstract
Background Rubber tree (Hevea brasiliensis) is an important industrial crop cultivated in tropical areas for natural rubber production. Treatment of the bark of rubber trees with ehephon (an ethylene releaser) has been a routine measure to increase latex yield, but the molecular mechanism behind the stimulation of rubber production by ethylene still remains a puzzle. Deciphering the enigma is of great importance for improvement of rubber tree for high yield. Results De novo sequencing and assembly of the bark transciptomes of Hevea brasiliensis induced with ethephon for 8 h (E8) and 24 h (E24) were performed. 51,965,770, 52,303,714 and 53,177,976 high-quality clean reads from E8, E24 and C (control) samples were assembled into 81,335, 80,048 and 80,800 unigenes respectively, with a total of 84,425 unigenes and an average length of 1,101 bp generated. 10,216 and 9,374 differentially expressed genes (DEGs) in E8 and E24 compared with C were respectively detected. The expression of several enzymes in crucial points of regulation in glycolysis were up-regulated and DEGs were not significantly enriched in isopentenyl diphosphate (IPP) biosynthesis pathway. In addition, up-regulated genes of great regulatory importance in carbon fixation (Calvin cycle) were identified. Conclusions The rapid acceleration of glycolytic pathway supplying precursors for the biosynthesis of IPP and natural rubber, instead of rubber biosynthesis per se, may be responsible for ethylene stimulation of latex yield in rubber tree. The elevated rate of flux throughout the Calvin cycle may account for some durability of ethylene-induced stimulation. Our finding lays the foundations for molecular diagnostic and genetic engineering for high-yielding improvement of rubber tree. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2587-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jin-Ping Liu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Agronomy, Hainan University, Haikou, Hainan Province, 570228, P. R. China.
| | - Yu-Fen Zhuang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Agronomy, Hainan University, Haikou, Hainan Province, 570228, P. R. China
| | - Xiu-Li Guo
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Agronomy, Hainan University, Haikou, Hainan Province, 570228, P. R. China
| | - Yi-Jian Li
- Service Center of Science and Technology, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, Hainan Province, 571737, P. R. China
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29
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Li D, Wang X, Deng Z, Liu H, Yang H, He G. Transcriptome analyses reveal molecular mechanism underlying tapping panel dryness of rubber tree (Hevea brasiliensis). Sci Rep 2016; 6:23540. [PMID: 27005401 PMCID: PMC4804210 DOI: 10.1038/srep23540] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 03/04/2016] [Indexed: 11/22/2022] Open
Abstract
Tapping panel dryness (TPD) is a serious threat to natural rubber yields from rubber trees, but the molecular mechanisms underlying TPD remain poorly understood. To identify TPD-related genes and reveal these molecular mechanisms, we sequenced and compared the transcriptomes of bark between healthy and TPD trees. In total, 57,760 assembled genes were obtained and analyzed in details. In contrast to healthy rubber trees, 5652 and 2485 genes were up- or downregulated, respectively, in TPD trees. The TPD-related genes were significantly enriched in eight GO terms and five KEGG pathways and were closely associated with ROS metabolism, programmed cell death and rubber biosynthesis. Our results suggest that rubber tree TPD is a complex process involving many genes. The observed lower rubber yield from TPD trees might result from lower isopentenyl diphosphate (IPP) available for rubber biosynthesis and from downregulation of the genes in post-IPP steps of rubber biosynthesis pathway. Our results not only extend our understanding of the complex molecular events involved in TPD but also will be useful for developing effective measures to control TPD of rubber trees.
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Affiliation(s)
- Dejun Li
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Baodao Xincun, Danzhou, Hainan 571737, China
| | - Xuncheng Wang
- Tsinghua-Peking Center for Life Sciences, Center for Plant Biology, School of Life Sciences, Tsinghua University, Tsinghua Park No. 1, Haidian District, Beijing 100084, China.,State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, No. 5 Yiheyuan Road, Haidian District, Beijing 100871, China
| | - Zhi Deng
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Baodao Xincun, Danzhou, Hainan 571737, China
| | - Hui Liu
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Baodao Xincun, Danzhou, Hainan 571737, China
| | - Hong Yang
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Baodao Xincun, Danzhou, Hainan 571737, China
| | - Guangming He
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, No. 5 Yiheyuan Road, Haidian District, Beijing 100871, China
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30
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Zhou T, Li ZH, Bai GQ, Feng L, Chen C, Wei Y, Chang YX, Zhao GF. Transcriptome Sequencing and Development of Genic SSR Markers of an Endangered Chinese Endemic Genus Dipteronia Oliver (Aceraceae). Molecules 2016; 21:166. [PMID: 26907245 PMCID: PMC6272838 DOI: 10.3390/molecules21030166] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 01/25/2016] [Accepted: 01/26/2016] [Indexed: 11/16/2022] Open
Abstract
Dipteronia Oliver (Aceraceae) is an endangered Chinese endemic genus consisting of two living species, Dipteronia sinensis and Dipteronia dyeriana. However, studies on the population genetics and evolutionary analyses of Dipteronia have been hindered by limited genomic resources and genetic markers. Here, the generation, de novo assembly and annotation of transcriptome datasets, and a large set of microsatellite or simple sequence repeat (SSR) markers derived from Dipteronia have been described. After Illumina pair-end sequencing, approximately 93.2 million reads were generated and assembled to yield a total of 99,358 unigenes. A majority of these unigenes (53%, 52,789) had at least one blast hit against the public protein databases. Further, 12,377 SSR loci were detected and 4179 primer pairs were designed for experimental validation. Of these 4179 primer pairs, 435 primer pairs were randomly selected to test polymorphism. Our results show that products from 132 primer pairs were polymorphic, in which 97 polymorphic SSR markers were further selected to analyze the genetic diversity of 10 natural populations of Dipteronia. The identification of SSR markers during our research will provide the much valuable data for population genetic analyses and evolutionary studies in Dipteronia.
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Affiliation(s)
- Tao Zhou
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an 710069, China.
| | - Zhong-Hu Li
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an 710069, China.
| | - Guo-Qing Bai
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an 710069, China.
- Xi'an Botanical Garden of Shaanxi Province, Xi'an 710061, China.
| | - Li Feng
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an 710069, China.
| | - Chen Chen
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an 710069, China.
| | - Yue Wei
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an 710069, China.
| | - Yong-Xia Chang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an 710069, China.
| | - Gui-Fang Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an 710069, China.
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31
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Thottathil GP, Jayasekaran K, Othman AS. Sequencing Crop Genomes: A Gateway to Improve Tropical Agriculture. Trop Life Sci Res 2016; 27:93-114. [PMID: 27019684 PMCID: PMC4807965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023] Open
Abstract
Agricultural development in the tropics lags behind development in the temperate latitudes due to the lack of advanced technology, and various biotic and abiotic factors. To cope with the increasing demand for food and other plant-based products, improved crop varieties have to be developed. To breed improved varieties, a better understanding of crop genetics is necessary. With the advent of next-generation DNA sequencing technologies, many important crop genomes have been sequenced. Primary importance has been given to food crops, including cereals, tuber crops, vegetables, and fruits. The DNA sequence information is extremely valuable for identifying key genes controlling important agronomic traits and for identifying genetic variability among the cultivars. However, massive DNA re-sequencing and gene expression studies have to be performed to substantially improve our understanding of crop genetics. Application of the knowledge obtained from the genomes, transcriptomes, expression studies, and epigenetic studies would enable the development of improved varieties and may lead to a second green revolution. The applications of next generation DNA sequencing technologies in crop improvement, its limitations, future prospects, and the features of important crop genome projects are reviewed herein.
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Affiliation(s)
- Gincy Paily Thottathil
- Centre for Chemical Biology, Universiti Sains Malaysia, 11800 USM, Pulau Pinang, Malaysia
| | - Kandakumar Jayasekaran
- Centre for Chemical Biology, Universiti Sains Malaysia, 11800 USM, Pulau Pinang, Malaysia
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117543
| | - Ahmad Sofiman Othman
- Centre for Chemical Biology, Universiti Sains Malaysia, 11800 USM, Pulau Pinang, Malaysia
- School of Biological Sciences, Universiti Sains Malaysia, 11800 USM, Pulau Pinang, Malaysia
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32
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Zou Z, Gong J, An F, Xie G, Wang J, Mo Y, Yang L. Genome-wide identification of rubber tree (Hevea brasiliensis Muell. Arg.) aquaporin genes and their response to ethephon stimulation in the laticifer, a rubber-producing tissue. BMC Genomics 2015; 16:1001. [PMID: 26606923 PMCID: PMC4658816 DOI: 10.1186/s12864-015-2152-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Accepted: 10/27/2015] [Indexed: 03/25/2024] Open
Abstract
BACKGROUND Natural rubber, an important industrial raw material, is specifically synthesized in laticifers located inside the rubber tree (Hevea brasiliensis Muell. Arg.) trunk. Due to the absence of plasmodesmata, the laticifer water balance is mediated by aquaporins (AQPs). However, to date, the characterization of H. brasiliensis AQPs (HbAQPs) is still in its infancy. RESULTS In this study, 51 full-length AQP genes were identified from the rubber tree genome. The phylogenetic analysis assigned these AQPs to five subfamilies, including 15 plasma membrane intrinsic proteins (PIPs), 17 tonoplast intrinsic proteins (TIPs), 9 NOD26-like intrinsic proteins (NIPs), 4 small basic intrinsic proteins (SIPs) and 6 X intrinsic proteins (XIPs). Functional prediction based on the analysis of the aromatic/arginine (ar/R) selectivity filter, Froger's positions and specificity-determining positions (SDPs) showed a remarkable difference in substrate specificity among subfamilies. Homology analysis supported the expression of 44 HbAQP genes in at least one of the examined tissues. Furthermore, deep sequencing of the laticifer transcriptome in the form of latex revealed a key role of several PIP subfamily members in the laticifer water balance, and qRT-PCR analysis showed diverse expression patterns of laticifer-expressed HbAQP genes upon ethephon treatment, a widely-used practice for the stimulation of latex yield. CONCLUSIONS This study provides an important genetic resource of HbAQP genes, which will be useful to improve the water use efficiency and latex yield of Hevea.
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Affiliation(s)
- Zhi Zou
- Danzhou Investigation & Experiment Station of Tropical Crops, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, 571737, P. R. China.
| | - Jun Gong
- Danzhou Investigation & Experiment Station of Tropical Crops, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, 571737, P. R. China.
| | - Feng An
- Danzhou Investigation & Experiment Station of Tropical Crops, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, 571737, P. R. China.
| | - Guishui Xie
- Danzhou Investigation & Experiment Station of Tropical Crops, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, 571737, P. R. China.
| | - Jikun Wang
- Danzhou Investigation & Experiment Station of Tropical Crops, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, 571737, P. R. China.
| | - Yeyong Mo
- Danzhou Investigation & Experiment Station of Tropical Crops, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, 571737, P. R. China.
| | - Lifu Yang
- Danzhou Investigation & Experiment Station of Tropical Crops, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, 571737, P. R. China.
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Development of Polymorphic Genic SSR Markers by Transcriptome Sequencing in the Welsh Onion (Allium fistulosum L.). APPLIED SCIENCES-BASEL 2015. [DOI: 10.3390/app5041050] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Zhou XJ, Wang YY, Xu YN, Yan RS, Zhao P, Liu WZ. De Novo Characterization of Flower Bud Transcriptomes and the Development of EST-SSR Markers for the Endangered Tree Tapiscia sinensis. Int J Mol Sci 2015; 16:12855-70. [PMID: 26057749 PMCID: PMC4490475 DOI: 10.3390/ijms160612855] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Revised: 05/12/2015] [Accepted: 05/27/2015] [Indexed: 11/16/2022] Open
Abstract
Tapiscia sinensis Oliv (Tapisciaceae) is an endangered species native to China famous for its androdioecious breeding system. However, there is a lack of genomic and transcriptome data on this species. In this study, the Tapiscia sinensis transcriptomes from two types of sex flower buds were sequenced. A total of 97,431,176 clean reads were assembled into 52,169 unigenes with an average length of 1116 bp. Through similarity comparison with known protein databases, 36,662 unigenes (70.27%) were annotated. A total of 10,002 (19.17%) unigenes were assigned to 124 pathways using the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database. Additionally, 10,371 simple sequence repeats (SSRs) were identified in 8608 unigenes, with 16,317 pairs of primers designed for applications. 150 pairs of primers were chosen for further validation, and the 68 pairs (45.5%) were able to produce clear polymorphic bands. Six polymorphic SSR markers were used to Bayesian clustering analysis of 51 T. sinensis individuals. This is the first report to provide transcriptome information and to develop large-scale SSR molecular markers for T. sinensis. This study provides a valuable resource for conservation genetics and functional genomics research on T. sinensis for future work.
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Affiliation(s)
- Xiao-Jun Zhou
- School of Life Sciences, Northwest University, 229 Taibai Bei Road, Xi'an 710069, China.
- School of Life Sciences, Luoyang Normal University, 71 Longmen Road, Luoyang 471022, China.
| | - Yue-Yue Wang
- School of Life Sciences, Northwest University, 229 Taibai Bei Road, Xi'an 710069, China.
| | - Ya-Nan Xu
- School of Life Sciences, Northwest University, 229 Taibai Bei Road, Xi'an 710069, China.
| | - Rong-Shan Yan
- School of Life Sciences, Northwest University, 229 Taibai Bei Road, Xi'an 710069, China.
| | - Peng Zhao
- School of Life Sciences, Northwest University, 229 Taibai Bei Road, Xi'an 710069, China.
| | - Wen-Zhe Liu
- School of Life Sciences, Northwest University, 229 Taibai Bei Road, Xi'an 710069, China.
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Liu JP, Xia ZQ, Tian XY, Li YJ. Transcriptome sequencing and analysis of rubber tree (Hevea brasiliensis Muell.) to discover putative genes associated with tapping panel dryness (TPD). BMC Genomics 2015; 16:398. [PMID: 25994052 PMCID: PMC4438507 DOI: 10.1186/s12864-015-1562-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 04/21/2015] [Indexed: 01/13/2023] Open
Abstract
Background Tapping panel dryness (TPD) involves in the partial or complete cessation of latex flow thus seriously affect latex production in rubber tree (Hevea brasiliensis). Numerous studies have been conducted to define its origin and nature, but the molecular nature and mechanism of TPD occurrence remains unknown. This study is committed to de novo sequencing and comparative analysis of the transcriptomes of healthy (H) and TPD-affected (T) rubber trees to identify the genes and pathways related to the TPD. Results Total raw reads of 34,632,012 and 35,913,020 bp were obtained from H and T library, respectively using Illumina Hiseq 2000 sequencing technology. De novo assemblies yielded 141,456 and 169,285 contigs, and 96,070 and 112,243 unigenes from H and T library, respectively. Among 73597 genes, 22577 genes were identified as differential expressed genes between H and T library via comparative transcript profiling. A majority of genes involved in natural rubber biosynthesis and jasmonate synthesis with most potential relevance in TPD occurrence were found to be differentially expressed. Conclusions In TPD-affected trees, the expression of most genes related to the latex biosynthesis and jasmonate synthesis was severely inhibited and is probably the direct cause of the TPD. These new de novo transcriptome data sets provide a significant resource for the discovery of genes related to TPD and improve our understanding of the occurrence and maintainace of TPD. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1562-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jin-Ping Liu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Agronomy, Hainan University, Haikou, Hainan Province, 570228, P. R China.
| | - Zhi-Qiang Xia
- The Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan Province, 571101, P. R China.
| | - Xiao-Yan Tian
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Agronomy, Hainan University, Haikou, Hainan Province, 570228, P. R China.
| | - Yi-Jian Li
- Service Center of Science and Technology, Rubber Research Institute Chinese Academy of Tropical Agricultural Sciences, Danzhou, Hainan Province, 571737, P. R China.
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Chao J, Chen Y, Wu S, Tian WM. Comparative transcriptome analysis of latex from rubber tree clone CATAS8-79 and PR107 reveals new cues for the regulation of latex regeneration and duration of latex flow. BMC PLANT BIOLOGY 2015; 15:104. [PMID: 25928745 PMCID: PMC4410575 DOI: 10.1186/s12870-015-0488-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Accepted: 04/02/2015] [Indexed: 05/29/2023]
Abstract
BACKGROUND Rubber tree (Hevea brasiliensis Muell. Arg.) is the primarily commercial source of natural rubber in the world. Latex regeneration and duration of latex flow after tapping are the two factors that determine rubber yield of rubber tree, and exhibit a huge variation between rubber tree clones CATAS8-79 and PR107. RESULTS To dissect the molecular mechanism for the regulation of latex regeneration and duration of latex flow, we sequenced and comparatively analyzed latex of rubber tree clone CATAS8-79 and PR107 at transriptome level. More than 26 million clean reads were generated in each pool and 51,829 all-unigenes were totally assembled. A total of 6,726 unigenes with differential expression patterns were detected between CATAS8-79 and PR107. Functional analysis showed that genes related to mass of categories were differentially enriched between the two clones. Expression pattern of genes which were involved in latex regeneration and duration of latex flow upon successive tapping was analyzed by quantitative PCR. Several genes related to rubber biosynthesis, cellulose and lignin biosynthesis and rubber particle aggregation were differentially expressed between CATAS8-79 and PR107. CONCLUSIONS This is the first report about probing latex regeneration and duration of latex flow by comparative transcriptome analysis. Among all the suggested factors, it is more important that the level of endogenous jasmonates, carbohydrate metabolism, hydroxymethylglutaryl-CoA reductase (HMGR) and Hevea rubber transferase (HRT) in mevalonate (MVA) parthway for latex regeneration while the level of endogenous ethylene (ETH), lignin content of laticifer cell wall, antioxidants and glucanases for the duration of latex flow. These data will provide new cues for understanding the molecular mechanism for the regulation of latex regeneration and duration of latex flow in rubber tree.
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Affiliation(s)
- Jinquan Chao
- Ministry of Agriculture Key Laboratory of Biology and Genetic Resources of Rubber Tree/ State Key Laboratory Breeding Base of Cultivation and Physiology for Tropical Crops, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, Hainan, 571737, PR China.
| | - Yueyi Chen
- Ministry of Agriculture Key Laboratory of Biology and Genetic Resources of Rubber Tree/ State Key Laboratory Breeding Base of Cultivation and Physiology for Tropical Crops, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, Hainan, 571737, PR China.
| | - Shaohua Wu
- Ministry of Agriculture Key Laboratory of Biology and Genetic Resources of Rubber Tree/ State Key Laboratory Breeding Base of Cultivation and Physiology for Tropical Crops, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, Hainan, 571737, PR China.
| | - Wei-Min Tian
- Ministry of Agriculture Key Laboratory of Biology and Genetic Resources of Rubber Tree/ State Key Laboratory Breeding Base of Cultivation and Physiology for Tropical Crops, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, Hainan, 571737, PR China.
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Isolation and molecular characterization of 1-aminocyclopropane-1-carboxylic acid synthase genes in Hevea brasiliensis. Int J Mol Sci 2015; 16:4136-49. [PMID: 25690030 PMCID: PMC4346948 DOI: 10.3390/ijms16024136] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 02/06/2015] [Indexed: 12/22/2022] Open
Abstract
Ethylene is an important factor that stimulates Hevea brasiliensis to produce natural rubber. 1-Aminocyclopropane-1-carboxylic acid synthase (ACS) is a rate-limiting enzyme in ethylene biosynthesis. However, knowledge of the ACS gene family of H. brasiliensis is limited. In this study, nine ACS-like genes were identified in H. brasiliensis. Sequence and phylogenetic analysis results confirmed that seven isozymes (HbACS1–7) of these nine ACS-like genes were similar to ACS isozymes with ACS activity in other plants. Expression analysis results showed that seven ACS genes were differentially expressed in roots, barks, flowers, and leaves of H. brasiliensis. However, no or low ACS gene expression was detected in the latex of H. brasiliensis. Moreover, seven genes were differentially up-regulated by ethylene treatment.These results provided relevant information to help determine the functions of the ACS gene in H. brasiliensis, particularly the functions in regulating ethylene stimulation of latex production.
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Long Y, Wang Y, Wu S, Wang J, Tian X, Pei X. De novo assembly of transcriptome sequencing in Caragana korshinskii Kom. and characterization of EST-SSR markers. PLoS One 2015; 10:e0115805. [PMID: 25629164 PMCID: PMC4309406 DOI: 10.1371/journal.pone.0115805] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 11/27/2014] [Indexed: 01/05/2023] Open
Abstract
Caragana korshinskii Kom. is widely distributed in various habitats, including gravel desert, clay desert, fixed and semi-fixed sand, and saline land in the Asian and African deserts. To date, no previous genomic information or EST-SSR marker has been reported in Caragana Fabr. genus. In this study, more than two billion bases of high-quality sequence of C. korshinskii were generated by using illumina sequencing technology and demonstrated the de novo assembly and annotation of genes without prior genome information. These reads were assembled into 86,265 unigenes (mean length = 709 bp). The similarity search indicated that 33,955 and 21,978 unigenes showed significant similarities to known proteins from NCBI non-redundant and Swissprot protein databases, respectively. Among these annotated unigenes, 26,232 a unigenes were separately assigned to Gene Ontology (GO) database. When 22,756 unigenes searched against the Kyoto Encyclopedia of Genes and Genomes Pathway (KEGG) database, 5,598 unigenes were assigned to 5 main categories including 32 KEGG pathways. Among the main KEGG categories, metabolism was the biggest category (2,862, 43.7%), suggesting the active metabolic processes in the desert tree. In addition, a total of 19,150 EST-SSRs were identified from 15,484 unigenes, and the characterizations of EST-SSRs were further compared with other four species in Fabraceae. 126 potential marker sites were randomly selected to validate the assembly quality and develop EST-SSR markers. Among the 9 germplasms in Caranaga Fabr. genus, PCR success rate were 93.7% and the phylogenic tree was constructed based on the genotypic data. This research generated a substantial fraction of transcriptome sequences, which were very useful resources for gene annotation and discovery, molecular markers development, genome assembly and annotation. The EST-SSR markers identified and developed in this study will facilitate marker-assisted selection breeding.
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Affiliation(s)
- Yan Long
- Institute of Biotechnology, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yanyan Wang
- College of Plant science and technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shanshan Wu
- College of Plant science and technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jiao Wang
- Institute of Biotechnology, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xinjie Tian
- Institute of Biotechnology, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xinwu Pei
- Institute of Biotechnology, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- * E-mail:
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Pootakham W, Ruang-Areerate P, Jomchai N, Sonthirod C, Sangsrakru D, Yoocha T, Theerawattanasuk K, Nirapathpongporn K, Romruensukharom P, Tragoonrung S, Tangphatsornruang S. Construction of a high-density integrated genetic linkage map of rubber tree (Hevea brasiliensis) using genotyping-by-sequencing (GBS). FRONTIERS IN PLANT SCIENCE 2015; 6:367. [PMID: 26074933 PMCID: PMC4444744 DOI: 10.3389/fpls.2015.00367] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 05/09/2015] [Indexed: 05/18/2023]
Abstract
Construction of linkage maps is crucial for genetic studies and marker-assisted breeding programs. Recent advances in next generation sequencing technologies allow for the generation of high-density linkage maps, especially in non-model species lacking extensive genomic resources. Here, we constructed a high-density integrated genetic linkage map of rubber tree (Hevea brasiliensis), the sole commercial producer of high-quality natural rubber. We applied a genotyping-by-sequencing (GBS) technique to simultaneously discover and genotype single nucleotide polymorphism (SNP) markers in two rubber tree populations. A total of 21,353 single nucleotide substitutions were identified, 55% of which represented transition events. GBS-based genetic maps of populations P and C comprised 1704 and 1719 markers and encompassed 2041 cM and 1874 cM, respectively. The average marker densities of these two maps were one SNP in 1.23-1.25 cM. A total of 1114 shared SNP markers were used to merge the two component maps. An integrated linkage map consisted of 2321 markers and spanned the cumulative length of 2052 cM. The composite map showed a substantial improvement in marker density, with one SNP marker in every 0.89 cM. To our knowledge, this is the most saturated genetic map in rubber tree to date. This integrated map allowed us to anchor 28,965 contigs, covering 135 Mb or 12% of the published rubber tree genome. We demonstrated that GBS is a robust and cost-effective approach for generating a common set of genome-wide SNP data suitable for constructing integrated linkage maps from multiple populations in a highly heterozygous agricultural species.
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Affiliation(s)
- Wirulda Pootakham
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development AgencyPathum Thani, Thailand
| | - Panthita Ruang-Areerate
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development AgencyPathum Thani, Thailand
| | - Nukoon Jomchai
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development AgencyPathum Thani, Thailand
| | - Chutima Sonthirod
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development AgencyPathum Thani, Thailand
| | - Duangjai Sangsrakru
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development AgencyPathum Thani, Thailand
| | - Thippawan Yoocha
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development AgencyPathum Thani, Thailand
| | - Kanikar Theerawattanasuk
- Department of Agriculture, Rubber Research Institute of Thailand, Ministry of Agriculture and CooperativesBangkok, Thailand
| | - Kanlaya Nirapathpongporn
- Department of Agriculture, Rubber Research Institute of Thailand, Ministry of Agriculture and CooperativesBangkok, Thailand
| | - Phayao Romruensukharom
- Department of Agriculture, Rubber Research Institute of Thailand, Ministry of Agriculture and CooperativesBangkok, Thailand
| | - Somvong Tragoonrung
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development AgencyPathum Thani, Thailand
| | - Sithichoke Tangphatsornruang
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development AgencyPathum Thani, Thailand
- *Correspondence: Sithichoke Tangphatsornruang, National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
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Long Y, Zhang J, Tian X, Wu S, Zhang Q, Zhang J, Dang Z, Pei XW. De novo assembly of the desert tree Haloxylon ammodendron (C. A. Mey.) based on RNA-Seq data provides insight into drought response, gene discovery and marker identification. BMC Genomics 2014; 15:1111. [PMID: 25511667 PMCID: PMC4377846 DOI: 10.1186/1471-2164-15-1111] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 12/11/2014] [Indexed: 11/17/2022] Open
Abstract
Background Haloxylon ammodendron (C. A. Mey.) is widely distributed across a range of habitats, including gravel desert, clay desert, fixed and semi-fixed sand, and saline land in Asian and African deserts. To date, no genomic information or expressed sequence tag-simple sequence repeat (EST-SSR) marker has been reported for H. ammodendron plants. Results Using Illumina sequencing technology, we generated over two billion bases of high-quality sequence data on H. ammodendron and conducted de novo assembly and annotation of genes without prior genome information. These reads were assembled into 79,918 unigenes (mean length = 728 bp). Based on similarity searches comparing these unigenes with known proteins in the non-redundant (nr) protein database, 25,619 unigenes were functionally annotated with a cut-off E-value of 10-5. In addition, DGE reads were mapped to the assembled transcriptome for gene expression analysis under drought stress. In total, 1,060 differentially expressed genes were identified. Among these genes, 356 genes were upregulated after drought treatment, and 704 genes were downregulated. We used the KEGG database to annotate these drought-induced genes; 207 unigenes were identified in the KEGG pathway annotation, and approximately 12.1% of the unigenes with known function fell into categories related to fatty acid metabolism, starch and sucrose metabolism, and nitrogen metabolism, suggesting that these pathways or processes may be involved in the drought response. Together, a total of 35 drought-inducible transcription factors were identified, including WRKY, MYB and bZIP family members. Conclusions Our study is the first to provide a transcriptome sequence resource for H. ammodendron plants and to determine its digital gene expression profile under drought conditions using the assembled transcriptome data for reference. These data provide a valuable resource for genetic and genomic studies of desert plants under abiotic conditions. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1111) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | - Zhanhai Dang
- Institute of Biotechnology, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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Pirrello J, Leclercq J, Dessailly F, Rio M, Piyatrakul P, Kuswanhadi K, Tang C, Montoro P. Transcriptional and post-transcriptional regulation of the jasmonate signalling pathway in response to abiotic and harvesting stress in Hevea brasiliensis. BMC PLANT BIOLOGY 2014; 14:341. [PMID: 25443311 PMCID: PMC4274682 DOI: 10.1186/s12870-014-0341-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 11/19/2014] [Indexed: 05/12/2023]
Abstract
BACKGROUND Latex harvesting in Hevea brasiliensis amounts to strong abiotic stress that can cause a halt in production in the most susceptible clones. Although the role of jasmonic acid has been suggested in laticifer differentiation, its role in latex production and in the response to harvesting stress has received very little attention. Only a few key genes acting in the COI-JAZ-MYC module have been isolated and studied at transcriptional level. RESULTS Use of a reference transcriptome obtained on rubber clone PB 260 covering a large number of tissues under different environmental conditions enabled us to identify 24 contigs implicated in the jasmonate signalling pathway in the rubber tree. An analysis of their expression profile by qPCR, combined with hierarchical clustering, suggested that the jasmonate signalling pathway is highly activated in laticifer cells and, more particularly, in the response to harvesting stress. By comparison with their genomic sequences, the existence of regulation by alternative splicing was discovered for JAZ transcripts in response to harvesting stress. Lastly, positive transcriptional regulation of the HbJAZ_1405 gene by MYC was demonstrated. CONCLUSION This study led to the identification of all actors of jasmonate signalling pathway and revealed a specific gene expression pattern in latex cells. In-depth analysis of this regulation showed alternative splicing that has been previously shown in Arabidopsis. Interestingly, genotypic variation was observed in Hevea clones with contrasting latex metabolism. This result suggests an involvement of jasmonate signalling pathway in latex production. The data suggest that specific variability of the JA pathway may have some major consequences for resistance to stress. The data support the hypothesis that a better understanding of transcriptional regulations of jasmonate pathway during harvesting stress, along with the use of genotypic diversity in response to such stress, can be used to improve resistance to stress and rubber production in Hevea.
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Affiliation(s)
| | | | | | | | - Piyanuch Piyatrakul
- />CIRAD, UMR AGAP, F-34398 Montpellier, France
- />Rubber Research Institute, Chatuchak, Bangkok 10900 Thailand
| | - Kuswanhadi Kuswanhadi
- />Sembawa Research Centre, Indonesian Rubber Research Institute, P.O 1127, Palembang, 30001 Indonesia
| | - Chaorong Tang
- />Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, 571737 Hainan China
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Wei F, Luo S, Zheng Q, Qiu J, Yang W, Wu M, Xiao X. Transcriptome sequencing and comparative analysis reveal long-term flowing mechanisms in Hevea brasiliensis latex. Gene 2014; 556:153-62. [PMID: 25431836 DOI: 10.1016/j.gene.2014.11.048] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 11/18/2014] [Accepted: 11/21/2014] [Indexed: 12/27/2022]
Abstract
BACKGROUND The rubber tree, Hevea brasiliensis, is a major commercial source of natural rubber. Increasing the rubber yield of rubber trees is a very serious problem since the demands for high quality rubber materials are great. Establishment of a tapping system is based on an estimate of tapping intensity from the rubber tree. Latex flowing time is one of the most critical factors that determine the rubber yield. Long-term flow is a type of phenomenon of the rubber tree latex with longer flowing time than normal latex flow, and is always caused by intensive tapping. Thus, transcriptome and expression profiling data for long-term flowing latex (LFL) are needed as an important resource to identify genes and to better understand the biological mechanisms of latex flow in rubber trees. RESULTS The transcripts were sequenced using the Illumina sequencing platform. After cleaning, quality checks and sequencing, 98,697 transcripts and 38,584 unigenes were assembled with the mean size of 1437.31bp and 923.86bp, respectively. In BLAST searches of our database against public databases, 65.17% (25,147) of the unigenes were annotated with gene descriptions, conserved protein domains, or gene ontology terms. Functional categorization further revealed 853 individual unigenes related to long-term flow. According to KEGG classification, the clusters for "cysteine and methionine metabolism", "energy", "oxidative phosphorylation", "terpenoid backbone biosynthesis", "plant hormone signal transduction" and "copper, potassium transporter" were significantly enriched metabolic pathways. CONCLUSIONS We conducted high-resolution transcriptome profiling related to LFL in H. brasiliensis. The research facilitates further studies on gene discovery and on the molecular mechanisms related to the estimation of tapping intensity and prolonging latex flowing time. We concluded that it was necessary to improve energy supplies for intensive tapping and the copper ion content of rubber tree latex could be considered as a standard to estimate tapping intensity.
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Affiliation(s)
- Fang Wei
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, Hainan 571737, China.
| | - Shiqiao Luo
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, Hainan 571737, China.
| | - Qiankun Zheng
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, Hainan 571737, China.
| | - Jian Qiu
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, Hainan 571737, China.
| | - Wenfeng Yang
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, Hainan 571737, China.
| | - Ming Wu
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, Hainan 571737, China.
| | - Xianzhou Xiao
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, Hainan 571737, China.
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Jia X, Deng Y, Sun X, Liang L, Ye X. Characterization of the global transcriptome using Illumina sequencing and novel microsatellite marker information in seashore paspalum. Genes Genomics 2014. [DOI: 10.1007/s13258-014-0231-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Developing conversed microsatellite markers and their implications in evolutionary analysis of the Bemisia tabaci complex. Sci Rep 2014; 4:6351. [PMID: 25220501 PMCID: PMC4163675 DOI: 10.1038/srep06351] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Accepted: 08/22/2014] [Indexed: 12/27/2022] Open
Abstract
The study of population genetics among the Bemisia tabaci complex is limited due to the lack of conserved molecular markers. In this study, 358, 433 and 322 new polynucleotide microsatellites are separately identified from the transcriptome sequences of three cryptic species of the B. tabaci complex. The cross species transferability of 57 microsatellites was then experimentally validated. The results indicate that these markers are conserved and have high inter-taxon transferability. Thirteen markers were employed to assess the genetic relationships among six cryptic species of the B. tabaci complex. To our surprise, the inferred phylogeny was consistent with that of mitochondrial COI sequences, indicating that microsatellites have the potential to distinguish species of the B. tabaci complex. Our results demonstrate that development of microsatellites from transcriptome data is a fast and cost-effective approach. These markers can be used to analyze the population genetics and evolutionary patterns of the B. tabaci complex.
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Mantello CC, Cardoso-Silva CB, da Silva CC, de Souza LM, Scaloppi Junior EJ, de Souza Gonçalves P, Vicentini R, de Souza AP. De novo assembly and transcriptome analysis of the rubber tree (Hevea brasiliensis) and SNP markers development for rubber biosynthesis pathways. PLoS One 2014; 9:e102665. [PMID: 25048025 PMCID: PMC4105465 DOI: 10.1371/journal.pone.0102665] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 06/22/2014] [Indexed: 01/26/2023] Open
Abstract
Hevea brasiliensis (Willd. Ex Adr. Juss.) Muell.-Arg. is the primary source of natural rubber that is native to the Amazon rainforest. The singular properties of natural rubber make it superior to and competitive with synthetic rubber for use in several applications. Here, we performed RNA sequencing (RNA-seq) of H. brasiliensis bark on the Illumina GAIIx platform, which generated 179,326,804 raw reads on the Illumina GAIIx platform. A total of 50,384 contigs that were over 400 bp in size were obtained and subjected to further analyses. A similarity search against the non-redundant (nr) protein database returned 32,018 (63%) positive BLASTx hits. The transcriptome analysis was annotated using the clusters of orthologous groups (COG), gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Pfam databases. A search for putative molecular marker was performed to identify simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs). In total, 17,927 SSRs and 404,114 SNPs were detected. Finally, we selected sequences that were identified as belonging to the mevalonate (MVA) and 2-C-methyl-D-erythritol 4-phosphate (MEP) pathways, which are involved in rubber biosynthesis, to validate the SNP markers. A total of 78 SNPs were validated in 36 genotypes of H. brasiliensis. This new dataset represents a powerful information source for rubber tree bark genes and will be an important tool for the development of microsatellites and SNP markers for use in future genetic analyses such as genetic linkage mapping, quantitative trait loci identification, investigations of linkage disequilibrium and marker-assisted selection.
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Affiliation(s)
- Camila Campos Mantello
- Centro de Biologia Molecular e Engenharia Genética (CBMEG) - Universidade Estadual de Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, Campinas, São Paulo, Brazil
- * E-mail: (APS); (CCM)
| | - Claudio Benicio Cardoso-Silva
- Centro de Biologia Molecular e Engenharia Genética (CBMEG) - Universidade Estadual de Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, Campinas, São Paulo, Brazil
| | - Carla Cristina da Silva
- Centro de Biologia Molecular e Engenharia Genética (CBMEG) - Universidade Estadual de Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, Campinas, São Paulo, Brazil
| | - Livia Moura de Souza
- Centro de Biologia Molecular e Engenharia Genética (CBMEG) - Universidade Estadual de Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, Campinas, São Paulo, Brazil
| | | | | | - Renato Vicentini
- Centro de Biologia Molecular e Engenharia Genética (CBMEG) - Universidade Estadual de Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, Campinas, São Paulo, Brazil
| | - Anete Pereira de Souza
- Centro de Biologia Molecular e Engenharia Genética (CBMEG) - Universidade Estadual de Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, Campinas, São Paulo, Brazil
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, Campinas, São Paulo, Brazil
- * E-mail: (APS); (CCM)
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Vukosavljev M, Esselink GD, van ’t Westende WPC, Cox P, Visser RGF, Arens P, Smulders MJM. Efficient development of highly polymorphic microsatellite markers based on polymorphic repeats in transcriptome sequences of multiple individuals. Mol Ecol Resour 2014; 15:17-27. [DOI: 10.1111/1755-0998.12289] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 05/29/2014] [Accepted: 05/30/2014] [Indexed: 11/26/2022]
Affiliation(s)
- M. Vukosavljev
- Wageningen UR Plant Breeding; Wageningen University & Research Centre; P.O. Box 386 NL-6700AJ Wageningen the Netherlands
- C.T. de Wit Graduate School for Production Ecology and Resource Conservation (PE&RC); Wageningen the Netherlands
| | - G. D. Esselink
- Wageningen UR Plant Breeding; Wageningen University & Research Centre; P.O. Box 386 NL-6700AJ Wageningen the Netherlands
| | - W. P. C. van ’t Westende
- Wageningen UR Plant Breeding; Wageningen University & Research Centre; P.O. Box 386 NL-6700AJ Wageningen the Netherlands
| | - P. Cox
- Roath BV; Eindhoven the Netherlands
| | - R. G. F. Visser
- Wageningen UR Plant Breeding; Wageningen University & Research Centre; P.O. Box 386 NL-6700AJ Wageningen the Netherlands
| | - P. Arens
- Wageningen UR Plant Breeding; Wageningen University & Research Centre; P.O. Box 386 NL-6700AJ Wageningen the Netherlands
| | - M. J. M. Smulders
- Wageningen UR Plant Breeding; Wageningen University & Research Centre; P.O. Box 386 NL-6700AJ Wageningen the Netherlands
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Sequence and expression analyses of ethylene response factors highly expressed in latex cells from Hevea brasiliensis. PLoS One 2014; 9:e99367. [PMID: 24971876 PMCID: PMC4074046 DOI: 10.1371/journal.pone.0099367] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Accepted: 05/05/2014] [Indexed: 11/21/2022] Open
Abstract
The AP2/ERF superfamily encodes transcription factors that play a key role in plant development and responses to abiotic and biotic stress. In Hevea brasiliensis, ERF genes have been identified by RNA sequencing. This study set out to validate the number of HbERF genes, and identify ERF genes involved in the regulation of latex cell metabolism. A comprehensive Hevea transcriptome was improved using additional RNA reads from reproductive tissues. Newly assembled contigs were annotated in the Gene Ontology database and were assigned to 3 main categories. The AP2/ERF superfamily is the third most represented compared with other transcription factor families. A comparison with genomic scaffolds led to an estimation of 114 AP2/ERF genes and 1 soloist in Hevea brasiliensis. Based on a phylogenetic analysis, functions were predicted for 26 HbERF genes. A relative transcript abundance analysis was performed by real-time RT-PCR in various tissues. Transcripts of ERFs from group I and VIII were very abundant in all tissues while those of group VII were highly accumulated in latex cells. Seven of the thirty-five ERF expression marker genes were highly expressed in latex. Subcellular localization and transactivation analyses suggested that HbERF-VII candidate genes encoded functional transcription factors.
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Kumar S, Shah N, Garg V, Bhatia S. Large scale in-silico identification and characterization of simple sequence repeats (SSRs) from de novo assembled transcriptome of Catharanthus roseus (L.) G. Don. PLANT CELL REPORTS 2014; 33:905-918. [PMID: 24482265 DOI: 10.1007/s00299-014-1569-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Revised: 12/17/2013] [Accepted: 01/09/2014] [Indexed: 06/03/2023]
Abstract
Transcriptomic data of C. roseus offering ample sequence resources for providing better insights into gene diversity: large resource of genic SSR markers to accelerate genomic studies and breeding in Catharanthus . Next-generation sequencing is an efficient system for generating high-throughput complete transcripts/genes and developing molecular markers. We present here the transcriptome sequencing of a 26-day-old Catharanthus roseus seedling tissue using Illumina GAIIX platform that resulted in a total of 3.37 Gb of nucleotide sequence data comprising 29,964,104 reads which were de novo assembled into 26,581 unigenes. Based on similarity searches 58 % of the unigenes were annotated of which 13,580 unique transcripts were assigned 5016 gene ontology terms. Further, 7,687 of the unigenes were found to have Cluster of Orthologous Group classifications, and 4,006 were assigned to 289 Kyoto Encyclopedia of Genes and Genome pathways. Also, 5,221 (19.64 %) of transcripts were distributed to 81 known transcription factor (TF) families. In-silico analysis of the transcriptome resulted in identification of 11,004 SSRs in 26.62 % transcripts from which 2,520 SSR markers were designed which exhibited a non-random pattern of distribution. The most abundant was the trinucleotide repeats (AAG/CTT) followed by the dinucleotide repeats (AG/CT). Location specific analysis of SSRs revealed that SSRs were preferentially associated with the 5'-UTRs with a predicted role in regulation of gene expression. A PCR validation of a set of 48 primers revealed 97.9 % successful amplification, and 76.6 % of them showed polymorphism across different Catharanthus species as well as accessions of C. roseus. In summary, this study will provide an insight into understanding the seedling development and resources for novel gene discovery and SSR development for utilization in marker-assisted selective breeding in C. roseus.
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Affiliation(s)
- Santosh Kumar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, PO Box 10531, New Delhi, 110067, India
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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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Salgado LR, Koop DM, Pinheiro DG, Rivallan R, Le Guen V, Nicolás MF, de Almeida LGP, Rocha VR, Magalhães M, Gerber AL, Figueira A, Cascardo JCDM, de Vasconcelos AR, Silva WA, Coutinho LL, Garcia D. De novo transcriptome analysis of Hevea brasiliensis tissues by RNA-seq and screening for molecular markers. BMC Genomics 2014; 15:236. [PMID: 24670056 PMCID: PMC4051172 DOI: 10.1186/1471-2164-15-236] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Accepted: 03/24/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The rubber tree, Hevea brasiliensis, is a species native to the Brazilian Amazon region and it supplies almost all the world's natural rubber, a strategic raw material for a variety of products. One of the major challenges for developing rubber tree plantations is adapting the plant to biotic and abiotic stress. Transcriptome analysis is one of the main approaches for identifying the complete set of active genes in a cell or tissue for a specific developmental stage or physiological condition. RESULTS Here, we report on the sequencing, assembling, annotation and screening for molecular markers from a pool of H. brasiliensis tissues. A total of 17,166 contigs were successfully annotated. Then, 2,191 Single Nucleotide Variation (SNV) and 1.397 Simple Sequence Repeat (SSR) loci were discriminated from the sequences. From 306 putative, mainly non-synonymous SNVs located in CDS sequences, 191 were checked for their ability to characterize 23 Hevea genotypes by an allele-specific amplification technology. For 172 (90%), the nucleotide variation at the predicted genomic location was confirmed, thus validating the different steps from sequencing to the in silico detection of the SNVs. CONCLUSIONS This is the first study of the H. brasiliensis transcriptome, covering a wide range of tissues and organs, leading to the production of the first developed SNP markers. This process could be amplified to a larger set of in silico detected SNVs in expressed genes in order to increase the marker density in available and future genetic maps. The results obtained in this study will contribute to the H. brasiliensis genetic breeding program focused on improving of disease resistance and latex yield.
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Affiliation(s)
- Leonardo Rippel Salgado
- Departamento de Genética/FMRP/USP, Laboratório de Genética Molecular e Bioinformática, Rua Tenente Catão Roxo, 2501, CEP 14,051- 140 Ribeirão Preto, São Paulo, Brazil.
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