26s rdna
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2021 ◽  
Vol 913 (1) ◽  
pp. 012060
Author(s):  
A. Thontowi ◽  
A.P. Ramadhan ◽  
H. Saputra ◽  
L.N. Kholida ◽  
Fahrurrozi ◽  
...  

Abstract Corn and sugarcane-base bioethanol dominantly contributes to the 25 billion gallons of bioethanol worldwide. Recent researches focused on the potential microbes and biomasses for optimum production. This study is, therefore, aimed to screen the bioethanol generating yeast strains of Biotechnology Culture Collection (BTCC), isolated from chocolate fermentation in several medium containing various carbon sources. A total of 72 yeast strains were grown in the media containing sugarcane juice, sorghum juice, and molasses, which served as carbon sources. Based on 26S rDNA gene analysis, these species were included in 9 genera, encompassing Saccharomyces (63.9%), Hanseniaspora (9.7%), Candida (0.7%), Torulaspora (0.4%), Pichia (0.8%), Issatchenkia (0.1%), Wickerhamomyces (0.3%), Metschnikowia (0.1%), and Rhodotorula (0.1%). Therefore, spectrophotometer UV-Vis was used to analyze cell growth, while the fermentation products (sugars and ethanol) were evaluated using the HPLC, and about 70 strains produced bioethanol. The highest yields were obtained during fermentation, using sugarcane juice, molasses, molasses waste, and sorghum juice, at concentrations of 43, 50, and 7 g/L, respectively. Furthermore, the Saccharomyces cerevisiae strain were the most significant producers, as the genus was able to generate various concentrations from several carbon sources. However, the only genus without the ability to yield any related products during fermentation was Pichia (0.8%). Based on these results, it is necessary to further develop the yeast strains from chocolate fermentation, due to the potential for bioethanol production from biomasses.


Plants ◽  
2021 ◽  
Vol 10 (9) ◽  
pp. 1771
Author(s):  
Radka Vozárová ◽  
Eliška Macková ◽  
David Vlk ◽  
Jana Řepková

The genus Trifolium L. is characterized by basic chromosome numbers 8, 7, 6, and 5. We conducted a genus-wide study of ribosomal DNA (rDNA) structure variability in diploids and polyploids to gain insight into evolutionary history. We used fluorescent in situ hybridization to newly investigate rDNA variation by number and position in 30 Trifolium species. Evolutionary history among species was examined using 85 available sequences of internal transcribed spacer 1 (ITS1) of 35S rDNA. In diploid species with ancestral basic chromosome number (x = 8), one pair of 5S and 26S rDNA in separate or adjacent positions on a pair of chromosomes was prevalent. Genomes of species with reduced basic chromosome numbers were characterized by increased number of signals determined on one pair of chromosomes or all chromosomes. Increased number of signals was observed also in diploids Trifolium alpestre and Trifolium microcephalum and in polyploids. Sequence alignment revealed ITS1 sequences with mostly single nucleotide polymorphisms, and ITS1 diversity was greater in diploids with reduced basic chromosome numbers compared to diploids with ancestral basic chromosome number (x = 8) and polyploids. Our results suggest the presence of one 5S rDNA site and one 26S rDNA site as an ancestral state.


Plant Disease ◽  
2020 ◽  
Author(s):  
Hao Cheng ◽  
Wei Tang ◽  
Hanyang Wang ◽  
Qianwen Liu ◽  
Huan huan Li ◽  
...  

Kiwifruit (Actinidia spp.) has been extensively cultivated (about 165728 hm2 recorded in 2017) and postharvest rot diseases have caused severe losses to the industry in China. In October 2019, fruit (n=60) of cv. Xuxiang (A. deliciosa) were obtained from a farm (120.62°E, 28.92°N) in Pan’an county, Zhejiang province, China. After the fruit were stored at 24 °C and 70% relative humidity (RH) for 10 days, soft lesions (20 to 45 mm in diameter) with sour odor and white mycelium were observed on ~20% of fruits (Fig. 1a). Irregular lesions were produced on the mesocarp were off-white to pale yellow (Fig. 1b). Small pieces (4×4 mm) from the lesion margins were excised, surface disinfested in 70% ethanol for 1 min and 10% NaOCl for 5 min, washed, dried, plated on PDA and incubated at 25°C for 7 days. A total of seven pure fungal colonies were obtained, and included two isolates of Nigrospora sphaerica (Li et al. 2018) and five unknown isolates. The remaining five isolates produced thin, flat, white to cream and feathery (Fig.1c & d) mycelium. Hyphae were hyaline, septate, dichotomously branched and break into chains of subglobose to cylindrical arthrospores (Fig. 1e, f & g). The dimension of arthrospores varies from 4.11 to 12.55 × 2.54 to 5.84 µm (n=100) (Fig. 1h). To identify these isolates to species, the internal transcribed spacer (ITS), 26S rDNA, translation elongation factor-1 alpha regions (TEF-1α) were amplified and sequenced (Ma et al. 2018). Sequence analysis indicated no differences in 26S rDNA and TEF-1α, but the ITS that placed the isolates into two phylogenetic groups. Isolates gx2-2 and gx3-1 representing group one (gx2-1, gx2-2, and gx5-1) and group two (gx3-1 and gx4-1) respectively, were employed for further studies. Based on BLASTn analysis, ITS sequences for gx2-2 (MT946912) and gx3-1(MT946913) isolates had 100% and 98.40% identity respectively, with G. candidum accessions KY103452 and KY103455. Nevertheless, 26S rDNA sequences (MT981194; MT981195) showed 99.82% identity with G. candidum accessions JN974268 and KF112070. Consistently, the TEF-1α (MT981184; MT981185) had 100% identity with G. candidum accession MT346370. Phylogenetic trees were constructed using the Neighbor-Joining method with a dataset of ITS (Fig. 2a) and 26S rDNA sequences (Fig. 2b), respectively. Based on morphology and phylogenetic analysis, the pathogens gx2-2 and gx3-1 were identified as Geotrichum candidum (De Hoog et al. 1986). To determine pathogenicity, healthy and mature kiwis cv. Xuxiang were surface sterilized. Wounded and unwounded fruits were inoculated with each conidial suspension derived from the two isolates (107 conidia/mL, 30 μL for each fruit) and stored at 24 °C under 90% RH. Control fruit were treated with sterile distilled water. Each treatment consisted of 20 fruit was evaluated daily for 10 days and repeated once. The symptom was mimic the naturally infected fruits (Fig.1i, m & n). The pathogen could develop into inner pericarp after 7 days while cv. Jinyan (A. chinensis) was used as host (Fig. 1k & l). However, control group remained disease-free (Fig. 1j, o & p). The fungus could penetrate into fruit peel and produce spores that were visualized by scanning electron microscope (Fig.1q & r). For both isolates, the incidence of wounded fruit were 100%, and the incidence of unwounded fruit was 80%. The fungi were re-isolated from diseased tissues and re-identified as G. candidum based on morphology and sequences analyses. G. candidum causes sour rot on many hosts and similar symptom have been previously reported in other regions(Pennycook et al.1989; Horita et al. 2016; Ma, et al. 2018; Zhang et al. 2018; Khan et al. 2019; Halfeld-Vieira et al. 2020), but this is the first report of G. candidum on kiwifruit in China.


2020 ◽  
Vol 127 (1) ◽  
pp. 63-73
Author(s):  
Min Zhang ◽  
Yi-Wei Tang ◽  
Ying Xu ◽  
Takahiro Yonezawa ◽  
Yang Shao ◽  
...  

Abstract Background and Aims The ribosomal DNA (rDNA) gene family, encoding ribosomal RNA (rRNA), has long been regarded as an archetypal example illustrating the model of concerted evolution. However, controversy is arising, as rDNA in many eukaryotic species has been proved to be polymorphic. Here, a metagenomic strategy was applied to detect the intragenomic polymorphism as well as the evolutionary patterns of 26S rDNA across the genus Camellia. Methods Degenerate primer pairs were designed to amplify the 26S rDNA fragments from different Camellia species. The amplicons were then paired-end sequenced on the Illumina MiSeq platform. Key Results An extremely high level of rDNA polymorphism existed universally in Camellia. However, functional rDNA was still the major component of the family, and was relatively conserved among different Camellia species. Sequence variations mainly came from rRNA pseudogenes and favoured regions that are rich in GC. Specifically, some rRNA pseudogenes have existed in the genome for a long time, and have even experienced several expansion events, which has greatly enriched the abundance of rDNA polymorphism. Conclusions Camellia represents a group in which rDNA is subjected to a mixture of concerted and birth-and-death evolution. Some rRNA pseudogenes may still have potential functions. Conversely, when released from selection constraint, they can evolve in the direction of decreasing GC content and structural stability through a methylation-induced process, and finally be eliminated from the genome.


2020 ◽  
Vol 306 (4) ◽  
Author(s):  
Deniz Aygoren Uluer ◽  
Julie A. Hawkins ◽  
Félix Forest
Keyword(s):  
26S Rdna ◽  

2018 ◽  
Vol 55 (1A) ◽  
pp. 99
Author(s):  
Dao Thi Luong

During the study on yeast diversity from natural samples in Viet Nam, we have collected 38 samples of flowers, fruits, leaves, litter and soils in Con Dao Island and isolated 54 yeast strains. They were identified based on morphology observation and sequences of D1/D2 domain of 26S rDNA. The results showed that they belonged to 13 genera, 28 species, of which 15 strains were suspected as 13 new species. Thirty-nine strains were identified as Ascomycetes belonging 7 genera, 11 species, and the fifteen remaining strains belonged to Basidomycetes, 6 genera and 13 species. The results also showed that four Ascomycetous and nine Basidomycetous isolated were suspected to be new species. The results also showed that Candida was the genus with highest number isolates- 26 strains, and half of these were Candida rugosa. The most diverse species in this study was found in Cryptococcus genus with 7 species from 8 isolates only, and all of them were suspected to be new species. This study also proved that the samples had differences in yeast diversity and species composition among them. Therefore, Con Dao Island is multi potential to discover and publish new yeast species in Vietnam. 


Genome ◽  
2017 ◽  
Vol 60 (8) ◽  
pp. 679-685 ◽  
Author(s):  
Ruijuan Liu ◽  
Richard R.-C. Wang ◽  
Feng Yu ◽  
Xingwang Lu ◽  
Quanwen Dou

Genomes of ten species of Elymus, either presumed or known as tetraploid StY, were characterized using fluorescence in situ hybridization (FISH) and genomic in situ hybridization (GISH). These tetraploid species could be grouped into three categories. Type I included StY genome reported species—Roegneria pendulina, R. nutans, R. glaberrima, R. ciliaris, and Elymus nevskii, and StY genome presumed species—R. sinica, R. breviglumis, and R. dura, whose genome could be separated into two sets based on different GISH intensities. Type I genome constitution was deemed as putative StY. The St genome were mainly characterized with intense hybridization with pAs1, fewer AAG sites, and linked distribution of 5S rDNA and 18S-26S rDNA, while the Y genome with less intense hybridization with pAs1, more varied AAG sites, and isolated distribution of 5S rDNA and 18S-26S rDNA. Nevertheless, further genomic variations were detected among the different StY species. Type II included E. alashanicus, whose genome could be easily separated based on GISH pattern. FISH and GISH patterns suggested that E. alashanicus comprised a modified St genome and an unknown genome. Type III included E. longearistatus, whose genome could not be separated by GISH and was designated as StlYl. Notably, a close relationship between Sl and Yl genomes was observed.


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