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Changyou Liu, Baojie Fan, Zhimin Cao, Qiuzhu Su, Yan Wang, Zhixiao Zhang, Jing Wu, Jing Tian
Mungbean (Vigna radiata L. Wilczek) is one of the most important leguminous food crops in Asia. We employed Illumina paired-end sequencing to analyse transcriptomes of three different mungbean genotypes. A total of 38.3-39.8 million pairedend reads with 73 bp lengths were generated. The pooled reads from the three libraries were assembled into 56,471 transcripts. Following a cluster analysis, 43,293 unigenes were obtained with an average length of 739 bp and N50 length of 1176 bp. Of the unigenes, 34,903 (80...
September 2016: Journal of Genetics
Zunzheng Wei, Zhenzhen Sun, Binbin Cui, Qixiang Zhang, Min Xiong, Xian Wang, Di Zhou
Colored calla lily is the short name for the species or hybrids in section Aestivae of genus Zantedeschia. It is currently one of the most popular flower plants in the world due to its beautiful flower spathe and long postharvest life. However, little genomic information and few molecular markers are available for its genetic improvement. Here, de novo transcriptome sequencing was performed to produce large transcript sequences for Z. rehmannii cv. 'Rehmannii' using an Illumina HiSeq 2000 instrument. More than 59...
2016: PeerJ
Taofeng Lu, Yujiao Sun, Qin Ma, Minghao Zhu, Dan Liu, Jianzhang Ma, Yuehui Ma, Hongyan Chen, Weijun Guan
The Siberian tiger, Panthera tigris altaica, is an endangered species, and much more work is needed to protect this species, which is still vulnerable to extinction. Conservation efforts may be supported by the genetic assessment of wild populations, for which highly specific microsatellite markers are required. However, only a limited amount of genetic sequence data is available for this species. To identify the genes involved in the lung transcriptome and to develop additional simple sequence repeat (SSR) markers for the Siberian tiger, we used high-throughput RNA-Seq to characterize the Siberian tiger transcriptome in lung tissue (designated 'PTA-lung') and a pooled tissue sample (designated 'PTA')...
September 8, 2016: Molecular Genetics and Genomics: MGG
Xin Yin, Yunqiang Yang, Yongping Yang
PREMISE OF THE STUDY: Expressed sequence tag-simple sequence repeat (EST-SSR) markers were developed using Illumina sequencing for further genetic diversity studies of Stipa purpurea (Poaceae). METHODS AND RESULTS: Twenty-nine polymorphic and eight monomorphic EST-SSR loci were developed and characterized in 90 individuals from nine S. purpurea populations. The number of alleles per locus ranged from two to 13, and heterozygosity within populations and total heterozygosity ranged from 0...
August 2016: Applications in Plant Sciences
Shanshan Zhu, Yanqian Ding, Zhaoyan Yap, Yingxiong Qiu
Lindera glauca (Lauraceae) is an economically important East Asian forest tree characterized by a dioecy in China and apomixis in Japan. However, patterns of population genetic diversity and structure of this species remain unknown for this species due to a lack of efficient molecular markers. In this study, we employed Illumina sequencing to analyze the transcriptomes of the female and male flower buds of L. glauca. We retrieved 59,753 and 75,075 unigenes for the female and male buds, respectively. Based on sequence similarity, 44,379 (74...
November 2016: Molecular Biology Reports
A W Gichira, Z C Long, Q F Wang, J M Chen, K Liao
Isoëtes sinensis is a critically endangered quillwort. To facilitate studies on the conservation genetics of this species, we developed expressed sequence tag-simple sequence repeat (EST-SSR) markers. A total of 50,063 unigenes were predicted by transcriptome sequencing, 5294 (10.6%) of which significantly matched 3011 Gene Ontology annotations and 2363 were assigned to Kyoto Encyclopedia of Genes and Genomes metabolic pathways. Most of these (2297) were involved in metabolism. A total of 1982 SSR motifs were identified, with trinucleotides being the dominant repeat motif, and 1438 (72...
2016: Genetics and Molecular Research: GMR
Marina Arias, Monica Hernandez, Naroa Remondegui, Koen Huvenaars, Peter van Dijk, Enrique Ritter
Taraxacum koksaghyz Rodin (TKS) has been studied in many occasions as a possible alternative source for natural rubber production of good quality and for inulin production. Some tire companies are already testing TKS tire prototypes. There are also many investigations on the production of bio-fuels from inulin and inulin applications for health improvement and in the food industry. A limited amount of genomic resources exist for TKS and particularly no genetic linkage map is available in this species. We have constructed the first TKS genetic linkage map based on AFLP, COS, SSR and EST-SSR markers...
2016: Scientific Reports
Rakesh Singh, Rajesh Kumar, Ajay Kumar Mahato, Ritu Paliwal, Amit Kumar Singh, Sundeep Kumar, Soma S Marla, Ashok Kumar, Nagendra K Singh
Tinospora cordifolia is known for its medicinal properties owing to the presence of useful constituents such as terpenes, glycosides, steroids, alkaloids, and flavonoids belonging to secondary metabolism origin. However, there is little information available pertaining to critical genomic elements (ESTs, molecular markers) necessary for judicious exploitation of its germplasm. We employed 454 GS-FLX pyrosequencing of entire transcripts and altogether ∼25 K assembled transcripts or Expressed sequence tags (ESTs) were identified...
September 2016: Functional & Integrative Genomics
Haibin Wu, Xiaoli He, Hao Gong, Shaobo Luo, Mingzhu Li, Junqiu Chen, Changyuan Zhang, Ting Yu, Wangping Huang, Jianning Luo
The hybrids between Luffa acutangula (L.) Roxb. and L.cylindrica (L.) Roem. have strong heterosis effects. However, some reproductive isolation traits hindered their normal hybridization and fructification, which was mainly caused by the flowering time and hybrid pollen sterility. In order to study the genetic basis of two interspecific reproductive isolation traits, we constructed a genetic linkage map using an F2 population derived from a cross between S1174 [L. acutangula (L.) Roxb.] and 93075 [L. cylindrica (L...
2016: Frontiers in Plant Science
Landi Luo, Pin Zhang, Xiaokun Ou, Yupeng Geng
PREMISE OF THE STUDY: Tithonia diversifolia (Asteraceae) is an invasive plant species that can outcompete natives and thus poses a great threat to biodiversity in introduced areas. Here, expressed sequence tag-simple sequence repeat (EST-SSR) markers were developed and characterized. METHODS AND RESULTS: Sixteen polymorphic microsatellite loci were isolated from T. diversifolia using transcriptome sequencing and bioinformatic screening. The number of alleles per locus varied from two to four alleles in 48 individuals from three populations...
July 2016: Applications in Plant Sciences
Karim Sorkheh, Angela S Prudencio, Azim Ghebinejad, Mehrana Kohei Dehkordi, Deniz Erogul, Manuel Rubio, Pedro Martínez-Gómez
BACKGROUND: Simple sequence repeats (SSRs) are defined as sequence repeat units between 1 and 6 bp that occur in both coding and non-coding regions abundant in eukaryotic genomes, which may affect the expression of genes. In this study, expressed sequence tags (ESTs) of eight Prunus species were analyzed for in silico mining of EST-SSRs, protein annotation, and open reading frames (ORFs), and the identification of codon repetitions. RESULTS: A total of 316 SSRs were identified using MISA software...
2016: BMC Research Notes
Shangguo Feng, Renfeng He, Jiangjie Lu, Mengying Jiang, Xiaoxia Shen, Yan Jiang, Zhi'an Wang, Huizhong Wang
Chrysanthemum morifolium, is a well-known flowering plant worldwide, and has a high commercial, floricultural, and medicinal value. In this study, simple-sequence repeat (SSR) markers were generated from EST datasets and were applied to assess the genetic diversity among 32 cultivars. A total of 218 in silico SSR loci were identified from 7300 C. morifolium ESTs retrieved from GenBank. Of all SSR loci, 61.47% of them (134) were hexa-nucleotide repeats, followed by tri-nucleotide repeats (17.89%), di-nucleotide repeats (12...
2016: Frontiers in Genetics
Zongyu Zhang, Junchao Zhang, Xuhong Zhao, Wengang Xie, Yanrong Wang
Siberian wild rye (Elymus sibiricus L.) is an important native grass in the Qinghai-Tibet Plateau of China. It is difficult to grow for commercial seed production, since seed shattering causes yield losses during harvest. Assessing the genetic diversity and relationships among germplasm from its primary distribution area contributes to evaluating the potential for its utilization as a gene pool to improve the desired agronomic traits. In the study, 40 EST-SSR primers were used to assess the genetic diversity and population structure of 36 E...
2016: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Naoko Ishikawa, Shota Sakaguchi, Motomi Ito
PREMISE OF THE STUDY: Simple sequence repeat (SSR) markers were developed for Aster savatieri (Asteraceae) and the serpentine variety A. savatieri var. pygmaeus to re-evaluate their taxonomic status. METHODS AND RESULTS: Using RNA-Seq data, 22 expressed sequence tag (EST)-SSR markers were developed. Polymorphisms were assessed in A. savatieri and in A. savatieri var. pygmaeus. The average number of alleles ranged from four to 15, and expected heterozygosity ranged from 0...
June 2016: Applications in Plant Sciences
Shamshad Ul Haq, Pradeep Kumar, R K Singh, Kumar Sambhav Verma, Ritika Bhatt, Meenakshi Sharma, Sumita Kachhwaha, S L Kothari
Expressed sequence tags (ESTs) are important resource for gene discovery, gene expression and its regulation, molecular marker development, and comparative genomics. We procured 10000 ESTs and analyzed 267 EST-SSRs markers through computational approach. The average density was one SSR/10.45 kb or 6.4% frequency, wherein trinucleotide repeats (66.74%) were the most abundant followed by di- (26.10%), tetra- (4.67%), penta- (1.5%), and hexanucleotide (1.2%) repeats. Functional annotations were done and after-effect newly developed 63 EST-SSRs were used for cross transferability, genetic diversity, and bulk segregation analysis (BSA)...
2016: Genetics Research International
Q Z Wang, M Huang, S R Downie, Z X Chen
Invasive plants tend to spread aggressively in new habitats and an understanding of their genetic diversity and population structure is useful for their management. In this study, expressed sequence tag-simple sequence repeat (EST-SSR) markers were developed for the invasive plant species Praxelis clematidea (Asteraceae) from 5548 Stevia rebaudiana (Asteraceae) expressed sequence tags (ESTs). A total of 133 microsatellite-containing ESTs (2.4%) were identified, of which 56 (42.1%) were hexanucleotide repeat motifs and 50 (37...
2016: Genetics and Molecular Research: GMR
Li Huang, Bei Wu, Jiaojiao Zhao, Haitao Li, Weigang Chen, Yanli Zheng, Xiaoping Ren, Yuning Chen, Xiaojing Zhou, Yong Lei, Boshou Liao, Huifang Jiang
Microsatellite or simple sequence repeat (SSR) is one of the most widely distributed molecular markers that have been widely utilized to assess genetic diversity and genetic mapping for important traits in plants. However, the understanding of microsatellite characteristics in Arachis species and the currently available amount of high-quality SSR markers remain limited. In this study, we identified 16,435 genome survey sequences SSRs (GSS-SSRs) and 40,199 expressed sequence tag SSRs (EST-SSRs) in Arachis hypogaea and its wild relative species using the publicly available sequence data...
2016: PloS One
Sathaporn Chotechung, Prakit Somta, Jinbing Chen, Tarika Yimram, Xin Chen, Peerasak Srinives
The Br locus confers bruchid resistance in mungbean; VrPGIP2 (encoding a polygalacturonase inhibitor) is a strong candidate gene for this resistance. The VrPGIP2 sequence differs between resistant and susceptible lines. Azuki bean weevil (Callosobruchus chinensis) and cowpea weevil (Callosobruchus maculatus) are serious insect pests of mungbean during storage. Bruchid resistance in mungbean is controlled by a single dominant locus, Br. Although the Br locus has been located on a genetic map, molecular basis and function of the gene remain unknown...
September 2016: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
Yong-Ping Fu, Yuan Liang, Yue-Ting Dai, Chen-Tao Yang, Ming-Zheng Duan, Zhuo Zhang, Song-Nian Hu, Zhi-Wu Zhang, Yu Li
Cold stimulation of Bailinggu's mycelia is the main factor that triggers primordia initiation for successful production of fruiting bodies under commercial cultivation. Yet, the molecular-level mechanisms involved in mycelia response to cold stimulation are still unclear. Here, we performed comparative transcriptomic analysis using RNA-Seq technology to better understand the gene expression regulation during different temporal stages of cold stimulation in Bailinggu. A total of 21,558 Bailinggu mycelia unigenes were de novo assembled and annotated from four libraries (control at 25 °C, plus cold stimulation treatments at -3 °C for a duration of 1-2 days, 5-6 days, and 9-10 days)...
2016: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Peng Wang, Yuzhu Ma, Lingling Ma, Ya Li, Shu'an Wang, Linfang Li, Rutong Yang, Qing Wang
PREMISE OF THE STUDY: Catalpa bungei (Bignoniaceae) is a deciduous tree native to China. We developed microsatellite markers for C. bungei to investigate its population genetics. METHODS AND RESULTS: One hundred seventy-seven expressed sequence tag (EST)-simple sequence repeat (SSR) primer pairs were isolated and characterized using next-generation sequencing. Thirty of these primer pairs were polymorphic loci in 52 individuals of C. bungei. The number of alleles ranged from two to 18 with observed and expected heterozygosity values of 0...
April 2016: Applications in Plant Sciences
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