scholarly journals Transcriptome-wide Identification and Characterization of microRNAs and Their Targets in a Highly Adaptable Conifer Platycladus orientalis

2022 ◽  
Vol 147 (1) ◽  
pp. 7-17
Author(s):  
Ying Yang ◽  
Xian-Ge Hu ◽  
Bingsong Zheng ◽  
Yue Li ◽  
Tongli Wang ◽  
...  
Keyword(s):  
Stress Tolerance ◽  
Leucine Zipper ◽  
Class Iii ◽  
Conifer Species ◽  
Essential Information ◽  
Sequencing Platform ◽  
Platycladus Orientalis ◽  
Wide Range ◽  
Identification And Characterization

MicroRNAs (miRNAs) are short noncoding RNAs (20–25 nucleotides) that regulate gene expression posttranscriptionally. However, identification and characterization of miRNAs remain limited for conifer species. In this study, we applied transcriptome-wide miRNAs sequencing to a conifer species Platycladus orientalis, which is highly adaptable to a wide range of environmental adversities, including drought, barren soil, and mild salinity. A total of 17,181,542 raw reads were obtained from the Illumina sequencing platform; 31 conserved and 91 novel miRNAs were identified, and their unique characteristics were further analyzed. Ten randomly selected miRNAs were validated by quantificational real-time polymerase chain reaction. Through miRNA target predictions based on psRNATarget, 2331 unique mRNAs were predicted to be targets of P. orientalis miRNAs that involved in 187 metabolic pathways in KEGG database. These targets included not only important transcription factors (e.g., class III homeodomain leucine zipper targeted by por-miR166d) but also indispensable nontranscriptional factor proteins (i.e., por-miR482a-3p regulated nucleotide-binding site leucine-rich repeat protein). Interestingly, six miRNAs (por-miR16, -miR44, -miR60-5p, -miR69–3p, -miR166b-5p, and -miR395c) were found in adaptation-related pathways (e.g., drought), indicating their possible involved in this species’ stress-tolerance characteristics. The present study provided essential information for understanding the regulatory role of miRNAs in P. orientalis and sheds light on their possible use in tree improvement for stress tolerance.

Isolation and characterization of a class III homeodomain-leucine zipper-like gene fromGossypium barbadense

DNA Sequence ◽  
2006 ◽  
Vol 17 (5) ◽  
pp. 334-341 ◽  
Author(s):  
Chengxiang Qiu ◽  
Kaijing Zuo ◽  
Jie Qin ◽  
Jingya Zhao ◽  
Hua Ling ◽  
...  
Keyword(s):  
Leucine Zipper ◽  
Class Iii ◽  
Isolation And Characterization

scholarly journals Identification and characterization of two amylase producing bacteria Cellulosimicrobium sp. and Demequina sp. isolated from marine organisms

2015 ◽  
Vol 20 ◽  
pp. 8 ◽  
Author(s):  
Laila S.H. Al-Naamani ◽  
Sergey Dobretsov ◽  
Jamal Al-Sabahi ◽  
Bassam Soussi
Keyword(s):  
Cell Growth ◽  
Bacterial Species ◽  
Marine Organisms ◽  
Ulva Rigida ◽  
Wide Range ◽  
Amylase Production ◽  
Maximum Cell ◽  
Commercial Applications ◽  
Identification And Characterization

Marine sources have been known to yield novel compounds with a wide range of bioactivity with various commercial applications. In this study, the abilities of bacteria isolated from eight marine organisms to produce α-amylase were examined. All eight organisms were found to harbor amylase producing bacteria. Two bacterial species isolated from the green alga Ulva rigida and the sponge Mycale sp. were further identified and their α-amylases were purified and characterized. The bacterial species isolated from U. rigida and Mycale sp. were identified by DNA sequencing as Cellulosimicrobium sp. and Demequina sp., respectively. Cellulosimicrobium sp. obtained maximum cell growth and amylase production at 29.C and in the presence of lactose as a carbon source. Optimal cell growth and amylase production by Demequina sp. was observed at 35.C. While lactose enhanced cell growth of Demequina sp., maximum amylase production was found when fructose and glycerol were the available sources of carbon. Both strains grew better in the presence of tryptone, whilst peptone stimulated amylase production. Maximal cell growth and amylase production by both of the strains was found at a medium salinity of 3% NaCl. 

scholarly journals Genome-Wide Analysis and Expression Profiling of HD-ZIP III Genes in Three Brassica Species

Diversity ◽  
2021 ◽  
Vol 13 (12) ◽  
pp. 684
Author(s):  
Han Wang ◽  
Wenna Shao ◽  
Min Yan ◽  
Ye Xu ◽  
Shaohua Liu ◽  
...  
Keyword(s):  
Leucine Zipper ◽  
Brassica Species ◽  
Class Iii ◽  
Transcription Profiling ◽  
Promoter Regions ◽  
Single Nucleotide ◽  
Response Diversity ◽  
Genome Wide ◽  
Gene Expression Levels

Class III homeodomain-leucine zipper (HD-ZIP III) genes encode plant-specific transcription factors that play pivotal roles in plant growth and development. There is no systematic report on HD-ZIP III members in Brassica plants and their responses to stress are largely unknown. In this study, a total of 10, 9 and 16 HD-ZIP III genes were identified from B. rapa, B. oleracea and B. napus, respectively. The phylogenetic analysis showed that HD-ZIP III proteins were grouped into three clades: PHB/PHV, REV and CNA/HB8. Genes in the same group tended to have similar exon–intron structures. Various phytohormone-responsive elements and stress-responsive elements were detected in the promoter regions of HD-ZIP III genes. Gene expression levels in different tissues, as well as under different stress conditions, were investigated using public transcription profiling data. The HD-ZIP III genes were constitutively expressed among all the tested tissues and were highly accumulated in root and stem. In B. rapa, only one BrREV gene especially responded to heat stress, BrPHB and BrREV members were downregulated upon cold stress and most HD-ZIP III genes exhibited divergent responses to drought stress. In addition, we investigated the genetic variation at known miR165/166 complementary sites of the identified HD-ZIP III genes and found one single nucleotide polymorphism (SNP) in PHB members and two SNPs in REV members, which were further confirmed using Sanger sequencing. Taken together, these results provide information for the genome-wide characterization of HD-ZIP III genes and their stress response diversity in Brassica species.

Identification and characterization of a class III chitin synthase gene of Moniliophthora perniciosa, the fungus that causes witches’ broom disease of cacao

2009 ◽  
Vol 47 (4) ◽  
pp. 431-440 ◽  
Author(s):  
Catiane S. Souza ◽  
Bruno M. Oliveira ◽  
Gustavo G. L. Costa ◽  
Albert Schriefer ◽  
Alessandra Selbach-Schnadelbach ◽  
...  
Keyword(s):  
Chitin Synthase ◽  
Class Iii ◽  
Moniliophthora Perniciosa ◽  
Broom Disease ◽  
Identification And Characterization

scholarly journals Identification and Characterization of Andalusicin – N-terminally Dimethylated Class III Lantibiotic from Bacillus thuringiensis sv. andalousiensis

iScience ◽  
2021 ◽  
pp. 102480
Author(s):  
Anastasiia Grigoreva ◽  
Julia Andreeva ◽  
Dmitry Bikmetov ◽  
Anastasiia Rusanova ◽  
Marina Serebryakova ◽  
...  
Keyword(s):  
Bacillus Thuringiensis ◽  
Class Iii ◽  
Identification And Characterization

scholarly journals Recent amplification of microsatellite-associated miniature inverted-repeat transposable elements in the pineapple genome

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Lianyu Lin ◽  
Anupma Sharma ◽  
Qingyi Yu
Keyword(s):  
Transposable Elements ◽  
Inverted Repeat ◽  
Sequence Similarity ◽  
Genome Structure ◽  
Terminal Inverted Repeat ◽  
Essential Information ◽  
Dna Transposon ◽  
Genome Wide ◽  
Identification And Characterization

Abstract Background Miniature inverted-repeat transposable elements (MITEs) are non-autonomous DNA transposable elements that play important roles in genome organization and evolution. Genome-wide identification and characterization of MITEs provide essential information for understanding genome structure and evolution. Results We performed genome-wide identification and characterization of MITEs in the pineapple genome. The top two MITE families, accounting for 29.39% of the total MITEs and 3.86% of the pineapple genome, have insertion preference in (TA) n dinucleotide microsatellite regions. We therefore named these MITEs A. comosus microsatellite-associated MITEs (Ac-mMITEs). The two Ac-mMITE families, Ac-mMITE-1 and Ac-mMITE-2, shared sequence similarity in the terminal inverted repeat (TIR) regions, suggesting that these two Ac-mMITE families might be derived from a common or closely related autonomous elements. The Ac-mMITEs are frequently clustered via adjacent insertions. Among the 21,994 full-length Ac-mMITEs, 46.1% of them were present in clusters. By analyzing the Ac-mMITEs without (TA) n microsatellite flanking sequences, we found that Ac-mMITEs were likely derived from Mutator-like DNA transposon. Ac-MITEs showed highly polymorphic insertion sites between cultivated pineapples and their wild relatives. To better understand the evolutionary history of Ac-mMITEs, we filtered and performed comparative analysis on the two distinct groups of Ac-mMITEs, microsatellite-targeting MITEs (mt-MITEs) that are flanked by dinucleotide microsatellites on both sides and mutator-like MITEs (ml-MITEs) that contain 9/10 bp TSDs. Epigenetic analysis revealed a lower level of host-induced silencing on the mt-MITEs in comparison to the ml-MITEs, which partially explained the significantly higher abundance of mt-MITEs in pineapple genome. The mt-MITEs and ml-MITEs exhibited differential insertion preference to gene-related regions and RNA-seq analysis revealed their differential influences on expression regulation of nearby genes. Conclusions Ac-mMITEs are the most abundant MITEs in the pineapple genome and they were likely derived from Mutator-like DNA transposon. Preferential insertion in (TA) n microsatellite regions of Ac-mMITEs occurred recently and is likely the result of damage-limiting strategy adapted by Ac-mMITEs during co-evolution with their host. Insertion in (TA) n microsatellite regions might also have promoted the amplification of mt-MITEs. In addition, mt-MITEs showed no or negligible impact on nearby gene expression, which may help them escape genome control and lead to their amplification.

scholarly journals Identifikasi dan Karakterisasi Sumber Daya Genetik Buah-buahan di Kabupaten Buleleng

2019 ◽  
Vol 8 (2) ◽  
pp. 137
Author(s):  
I GUSTI AGUNG BAGUS SURADARMA ◽  
GEDE WIJANA ◽  
I NYOMAN SUTEDJA
Keyword(s):  
Genetic Resources ◽  
Economic Value ◽  
Secondary Data ◽  
Agronomic Characters ◽  
Prospective Development ◽  
Wide Range ◽  
Fruit Genetic Resources ◽  
Growing Environment ◽  
Identification And Characterization

Identification and Characterization of Fruit Genetic Resources in Buleleng Regency. Fruits have great potential to be developed both to meet the needs of domestic and foreign demand, because the fruits is a source of supply of vitamins, minerals, and fiber needed in the daily menu. Several types of fruit are also required as spa, medicines, and as a means of upakara. One of the prospective development of fruits in Bali is Buleleng. Types of fruit in Buleleng are grape, mango, durian, rambutan and banana. Until now there has been generally identified genetic resources fruits in Buleleng. This study aims to identify, profile and draw up a map of the geographic distribution of genetic resources of fruits in Buleleng. Implementation of the study consists of four activities, namely: secondary data collection, survey of the types of genetic resources and distribution, identification of morphological and agronomic characters of each type of genetic resources and the growing environment and the benefits of fruits. The seeded fruit is determined by Location Quotion (LQ). Based on the observations in the field, Buleleng has a wide range of genetic resources. In a direct observation to the field there are 32 kinds of fruit and 31 sub-types of fruit. Fruits are grouped based on the economic value and their role, including: commercial fruit, rare fruit, fruit for upakara and fruit for medicine. Based on the calculation of LQ method, Buleleng has four featured i.e. avocado, grape, mango and rambutan (LQ>1).

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