scholarly journals De novo Assembly and Characterization of the Testis Transcriptome and Development of EST-SSR Markers in the Cockroach Periplaneta americana

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Wan Chen ◽  
Yu-Xiang Liu ◽  
Guo-Fang Jiang
Keyword(s):  
Ssr Markers ◽  
Illumina Sequencing ◽  
Periplaneta Americana ◽  
De Novo ◽  
Average Length ◽  
Sequencing Technology ◽  
Reproductive Ability ◽  
Clusters Of Orthologous Groups ◽  
Similarity Searches

Abstract The cockroach Periplaneta americana is a notorious pest and threat to health worldwide, with a high reproductive ability. However, a limited amount of data is available on the developmental stage-specific transcriptomes of P. americana. To identify genes involved in developmental processes and to develop additional SSR markers in P. americana, we carried out de novo assembly of the P. americana transcriptome using Illumina sequencing. After removing low-quality sequences, we obtained 64,954,709 contigs, which were further assembled into 125,390 unigenes with an average length of 711 bp. Based on similarity searches against known proteins, we identified 48,300 unigenes based on a cut-off E-value of 10−5. The assembled sequences were annotated according to gene descriptions, gene ontology and clusters of orthologous groups. A total of 14,195 potential SSRs were identified and 41 of 63 randomly chosen primer pairs successfully amplified the predicted SSR markers, seven of which were polymorphic in size in P. americana. Furthermore, the Spag6 gene was confirmed to be testes specific and the fru and RPSA genes were related to the development of the testis. This is the special report of a P. americana transcriptome obtained using Illumina sequencing technology and a large number of molecular markers were developed.

scholarly journals De novo Characterization of the Platycladus orientalis Transcriptome and Analysis of Photosynthesis-Related Genes during Aging

Forests ◽  
2019 ◽  
Vol 10 (5) ◽  
pp. 393
Author(s):  
Ermei Chang ◽  
Jin Zhang ◽  
Xiamei Yao ◽  
Shuo Tang ◽  
Xiulian Zhao ◽  
...  
Keyword(s):  
De Novo ◽  
Average Length ◽  
Transcriptome Assembly ◽  
Expression Patterns ◽  
Age And Growth ◽  
Potential Candidate ◽  
Platycladus Orientalis ◽  
Oxidation Reduction ◽  
Old Trees

In China, Platycladus orientalis has a lifespan of thousands of years. The long lifespan of these trees may be relevant for the characterization of plant aging at the molecular level. However, the molecular mechanism of the aging process of P. orientalis is still unknown. To explore the relationship between age and growth of P. orientalis, we analyzed physiological changes during P. orientalis senescence. The malondialdehyde content was greater in 200-, 700-, and 1100-year-old ancient trees than in 20-year-old trees, whereas the peroxidase and superoxide dismutase activities, as well as the soluble protein content, exhibited the opposite trend. Furthermore, we performed a de novo transcriptome assembly using RNA-Seq and obtained 48,044 unigenes with an average length of 896 bp. A total of 418 differentially expressed genes were identified in different stages of aging of P. orientalis. Clustering analysis revealed distinct timepoints at which the oxidation–reduction and photosynthesis pathways changed. Eight clusters with distinct expression patterns were identified. The expression levels of photosynthesis-, oxidation–reduction-, and transporter-related genes were down-regulated, whereas those of transcription-, signaling-, and senescence-related genes were up-regulated during aging. In addition, consistent with the most obviously down-regulated genes of photosynthesis-related genes, the photosynthetic indexes including chlorophyll a and b levels decreased steadily during P. orientalis aging. This study combined transcriptome with physiological and biochemical data, revealing potential candidate genes influencing senescence during P. orientalis aging.

scholarly journals Isolation and characterization of polymorphic microsatellite markers in Toxicodendron vernicifluum

2018 ◽  
Vol 54 (No. 1) ◽  
pp. 17-25 ◽  
Author(s):  
D.-D. Vu ◽  
T.T.-X. Bui ◽  
T.H.-N. Nguyen ◽  
S.N.M. Shah ◽  
N.-H. Vu ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Expressed Sequence Tag ◽  
De Novo ◽  
Average Length ◽  
Polymorphic Information Content ◽  
Shaanxi Province ◽  
Illumina Hiseq ◽  
Tissue Samples ◽  
Isolation And Characterization ◽  
Toxicodendron Vernicifluum

A total 20 074 230 sequencing reads were generated by Illumina HiSeq<sup>™ </sup>2500 from three different Toxicodendron vernicifluum tissue samples. In total, 48 693 unigenes with an average length of 703.34 bp were obtained by de novo assembly. 3392 potential EST-SSRs (expressed sequence tag-simple sequence repeat) were identified as potential molecular markers from unigenes with lengths exceeding 1 kb. A total of 80 pairs of PCR primers were randomly selected to validate the assembly quality and develop EST-SSR markers from genomic DNA. Of these primer pairs, 14 primer pairs successfully amplified DNA fragments and detected significant amounts of polymorphism within the lacquer tree population in Langao, Shaanxi province, China. There were high genetic diversities (number of alleles per locus (A) = 2.93, polymorphic information content (PIC) = 0.53, observed heterozygosity (Ho) = 0.62 and expected heterozygosity (He) = 0.85) in the lacquer tree natural population. The four loci were significantly deviated from Hardy-Weinberg equilibrium. These results suggested high homozygosity in the population and low or deficiency in heterozygosity (inbreeding coefficient (Fis) = 0.27). These polymorphic EST-SSR markers will provide the base for further studies of genetic structure and breeding in T. vernicifluum.

scholarly journals Development and Characterization of SSR Markers in the Gossypium Barbadense Genome

2021 ◽  
Author(s):  
Wenjuan ZHONG ◽  
Can YUAN ◽  
Zhengjie CHEN ◽  
Yonghang ZHOU ◽  
Siwei Chen ◽  
...  
Keyword(s):  
Ssr Markers ◽  
De Novo ◽  
Low Cost ◽  
Fiber Quality ◽  
Gossypium Barbadense ◽  
Pcr Analysis ◽  
Genetic Studies ◽  
Genome Wide ◽  
User Friendly

Abstract BackgroundThe fiber quality and resistance traits of Gossypium barbadense are considerably better than that of other Gossypium species. Simple sequence repeats (SSRs) are user friendly, low cost markers widely used in genetic studies. However, most SSRs have been developed from G. hirsutum, G. arboreum, and G. raimondii; no genome-wide SSRs have been developed from G. barbadense.The de novo sequences of G. barbadense cv. Xinhai21 were utilized to develop SSR markers and scanned to detect SSRs using the MIcroSAtellite (http://pgrc.ipk-gatersleben.de/misa/) identification tool. And then in silico PCR analysis was conducted to evaluate these primers polymorphism in five Gossypium species.ResultsIn total, 85,582 SSRs were identified with different motifs. 153,560 primer pairs were successfully designed for 73,419 SSRs. In silico analysis, we found that 8,466 primer pairs of 3,288 SSRs yielded one product (monomorphic) simultaneously in five Gossypium species. two Gossypium species (30 G. hirsutum and 27 G. barbadense accessions) were successfully separated by 300 primer pairs with the polymorphism information content (PIC) ranging from 0.00 to 0.93. ConclusionThese newly developed SSR markers will be helpful for the construction of genetic linkage maps, genetic diversity analyses, QTL mapping, and molecular breeding of Gossypium species.

Sign in / Sign up

Export Citation Format

Share Document