Transcriptome analysis of two contrasting genotypes of pearl millet to gain insight into heat stress responses

Abstract Background Pennisetum glaucum (L.) R. Br. is mainly grown in arid and semi-arid regions. Being naturally tolerant to various adverse condtitions, it is a good biological resource for deciphering the molecular basis of abiotic stresses such as heat stress in plants but limited studies have been carried out till date to this effect. Here, we performed RNA-sequencing from the leaf of two contrasting genotypes of pearl millet (841-B and PPMI-69) subjected to heat stress (42 °C for 6 h). Results Over 274 million high quality reads with an average length of 150 nt were generated. Assembly was carried out using trinity, obtaining 47,310 unigenes having an average length of 1254 nucleotides, N50 length of 1853 nucleotides and GC content of 53.11%. Blastx resulted in annotation of 35,628 unigenes and functional classification showed 15,950 unigenes designated to 51 Gene Ontology terms, 13,786 unigenes allocated to 23 Clusters of Orthologous Groups and 4,255 unigenes distributed into 132 functional KEGG pathways. 12,976 simple sequence repeats were identified from 10,294 unigenes for the development of functional markers. A total of 3,05,759 SNPs were observed in the transcriptome data. Out of 2,301 differentially expressed genes, 10 potential candidates genes were selected based on log2 fold change and adjusted p-value parameters for their differential gene expression by qRT-PCR. Conclusions The dynamic expression changes in two genotypes of P. glaucum reflect transcriptome regulation of signaling pathways in heat stress response. In order to develop genetic markers, 12,976 simple sequence repeats (SSRs) were identified. The sequencing data generated in this study shall serve as an important resource for further research in the area of crop biotechnology.

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Detection of simple sequence repeats in the chloroplast genome of Tetraphis pellucida Hedw.

Plant Science Today ◽

10.14719/pst.2016.3.2.206 ◽

2016 ◽

Vol 3 (2) ◽

pp. 207 ◽

Cited By ~ 1

Author(s):

Asheesh Shanker

Keyword(s):

Chloroplast Genome ◽

Simple Sequence Repeats ◽

Average Length ◽

Accession Number ◽

Repeat Type ◽

Perl Script ◽

Repeat Units ◽

Short Repeat ◽

Diversity Studies ◽

Simple Sequence

Simple sequence repeats (SSRs) consist of short repeat motifs of 1-6 nucleotides and are found in DNA sequences.The present study was conducted to detect SSRs in chloroplast genome of Tetraphis pellucida (Accession number: NC_024291), downloaded from the National Center for Biotechnology Information (NCBI). The sequence was mined with the help of MISA, a Perl script, to detect SSRs. The length of SSRs defined as ≥12 for mono, di, tri and tetranucleotide, ≥15 for pentanucleotide and ≥18 for hexanucleotide repeats. In total, 41 perfect microsatellites were identified in 127.489 kb sequence mined. An average length of 13.56 bp was calculated for mined SSRs with a density of 1 SSR/3.04 kb. Depending on the repeat units, the length of SSRs ranged from 12 to 20 nt. Dinucleotides (14, 34.15%) were the most frequent repeat type, followed by tetranucleotides (10, 24.39%), trinucleotides (7, 17.07%), mononucleotides (6, 14.63%) and pentanucleotide (4, 9.76%) repeats. Hexanucleotide repeats were completely absent in chloroplast genome of Tetraphis pellucida. The mined SSRs can be used to develop molecular markers and genetic diversity studies in Tetraphis species.

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Transcriptome analysis of two contrasting genotypes of pearl millet to gain insight into heat stress responses

10.21203/rs.3.rs-23605/v2 ◽

2020 ◽

Author(s):

Albert Maibam ◽

Sunil Nigombam ◽

Harinder Vishwakarma ◽

Showkat Ahmad Lone ◽

Kishor Gaikwad ◽

...

Keyword(s):

Heat Stress ◽

Pearl Millet ◽

Transcriptome Analysis ◽

Stress Responses ◽

Insight Into

Abstract The authors have withdrawn this preprint due to erroneous posting.

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The Cipher Code of Simple Sequence Repeats in “Vampire Pathogens”

Scientific Reports ◽

10.1038/srep12441 ◽

2015 ◽

Vol 5 (1) ◽

Author(s):

Geng Zou ◽

Bernardo Bello-Orti ◽

Virginia Aragon ◽

Alexander W. Tucker ◽

Rui Luo ◽

...

Keyword(s):

Amino Acids ◽

Simple Sequence Repeats ◽

Potential Role ◽

Gc Content ◽

Nucleotide Metabolism ◽

Coding Regions ◽

Purine Nucleotide Metabolism ◽

Go Terms ◽

Simple Sequence

Abstract Blood inside mammals is a forbidden area for the majority of prokaryotic microbes; however, red blood cells tropism microbes, like “vampire pathogens” (VP), succeed in matching scarce nutrients and surviving strong immunity reactions. Here, we found VP of Mycoplasma, Rhizobiales and Rickettsiales showed significantly higher counts of (AG)n dimeric simple sequence repeats (Di-SSRs) in the genomes, coding and non-coding regions than non Vampire Pathogens (N_VP). Regression analysis indicated a significant correlation between GC content and the span of (AG)n-Di-SSR variation. Gene Ontology (GO) terms with abundance of (AG)3-Di-SSRs shared by the VP strains were associated with purine nucleotide metabolism (FDR < 0.01), indicating an adaptation to the limited availability of purine and nucleotide precursors in blood. Di-amino acids coded by (AG)n-Di-SSRs included all three six-fold code amino acids (Arg, Leu and Ser) and significantly higher counts of Di-amino acids coded by (AG)3, (GA)3 and (TC)3 in VP than N_VP. Furthermore, significant differences (P < 0.001) on the numbers of triplexes formed from (AG)n-Di-SSRs between VP and N_VP in Mycoplasma suggested the potential role of (AG)n-Di-SSRs in gene regulation.

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Genome-Wide Characterization and Comparative Analyses of Simple Sequence Repeats among Four Miniature Pig Breeds

Animals ◽

10.3390/ani10101792 ◽

2020 ◽

Vol 10 (10) ◽

pp. 1792

Author(s):

Hongyang Wang ◽

Yang Fu ◽

Peng Gu ◽

Yingying Zhang ◽

Weilong Tu ◽

...

Keyword(s):

Simple Sequence Repeats ◽

Growth And Development ◽

Miniature Pig ◽

Sequencing Data ◽

Pig Breeds ◽

Polymorphic Ssrs ◽

Repeat Units ◽

Genome Wide ◽

Polymerase Chain ◽

Simple Sequence

Simple sequence repeats (SSRs) are commonly used as molecular markers in research on genetic diversity and discrimination among taxa or breeds because polymorphisms in these regions contribute to gene function and phenotypically important traits. In this study, we investigated genome-wide characteristics, repeat units, and polymorphisms of SSRs using sequencing data from SSR-enriched libraries created from Wuzhishan (WZS), Bama (BM), inbred Luchuan (LC) and Zangxiang (ZX) miniature pig breeds. The numbers and types of SSRs, distributions of repeat units and polymorphic SSRs varied among the four breeds. Compared to the Duroc pig reference genome, 2518 polymorphic SSRs were unique and common to all four breeds and functional annotation revealed that they may affect the coding and regulatory regions of genes. Several examples, such as FGF23, MYF6, IGF1R, and LEPROT, are associated with growth and development in pigs. Three of the polymorphic SSRs were selected to confirm the polymorphism and the corresponding alleles through fluorescence polymerase chain reaction (PCR) and capillary electrophoresis. Together, this study provides useful insights into the discovery, characteristics and distribution of SSRs in four pig breeds. The polymorphic SSRs, especially those common and unique to all four pig breeds, might affect associated genes and play important roles in growth and development.

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Development of a program for in silico optimized selection of oligonucleotide-based molecular barcodes

PLoS ONE ◽

10.1371/journal.pone.0246354 ◽

2021 ◽

Vol 16 (2) ◽

pp. e0246354

Author(s):

In Seok Yang ◽

Sang Won Bae ◽

BeumJin Park ◽

Sangwoo Kim

Keyword(s):

Simple Sequence Repeats ◽

Hamming Distance ◽

Gc Content ◽

Computation Time ◽

High Tech ◽

Molecular Barcoding ◽

Dna Oligonucleotides ◽

Comparable Performance ◽

Simple Sequence ◽

Molecular Barcodes

Short DNA oligonucleotides (~4 mer) have been used to index samples from different sources, such as in multiplex sequencing. Presently, longer oligonucleotides (8–12 mer) are being used as molecular barcodes with which to distinguish among raw DNA molecules in many high-tech sequence analyses, including low-frequent mutation detection, quantitative transcriptome analysis, and single-cell sequencing. Despite some advantages of using molecular barcodes with random sequences, such an approach, however, makes it impossible to know the exact sequences used in an experiment and can lead to inaccurate interpretation due to misclustering of barcodes arising from the occurrence of unexpected mutations in the barcodes. The present study introduces a tool developed for selecting an optimal barcode subset during molecular barcoding. The program considers five barcode factors: GC content, homopolymers, simple sequence repeats with repeated units of dinucleotides, Hamming distance, and complementarity between barcodes. To evaluate a selected barcode set, penalty scores for the factors are defined based on their distributions observed in random barcodes. The algorithm employed in the program comprises two steps: i) random generation of an initial set and ii) optimal barcode selection via iterative replacement. Users can execute the program by inputting barcode length and the number of barcodes to be generated. Furthermore, the program accepts a user’s own values for other parameters, including penalty scores, for advanced use, allowing it to be applied in various conditions. In many test runs to obtain 100000 barcodes with lengths of 12 nucleotides, the program showed fast performance, efficient enough to generate optimal barcode sequences with merely the use of a desktop PC. We also showed that VFOS has comparable performance, flexibility in program running, consideration of simple sequence repeats, and fast computation time in comparison with other two tools (DNABarcodes and FreeBarcodes). Owing to the versatility and fast performance of the program, we expect that many researchers will opt to apply it for selecting optimal barcode sets during their experiments, including next-generation sequencing.

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Transcriptome analysis of heat stress and drought stress in pearl millet based on Pacbio full-length transcriptome sequencing

10.21203/rs.3.rs-16719/v1 ◽

2020 ◽

Author(s):

Min Sun ◽

Ailing Zhang ◽

Dejun Huang ◽

Imran Khan ◽

Haidong Yan ◽

...

Keyword(s):

Heat Stress ◽

Drought Stress ◽

Stress Tolerance ◽

Pearl Millet ◽

Plant Stress ◽

Differentially Expressed ◽

Reference Sequence ◽

Sequencing Data ◽

New Genes ◽

Protein Response

Abstract Background: Heat and drought are the serious threats to crop growth and development. As the sixth cereal crop in the world, pearl millet can be used not only for food and forage but also as bioenergy. Pearl millet has high tolerance under heat and drought. Given this, it is considered as an ideal crop for plant stress tolerance studying and can be used to excavate heat-resistant genes. Results: In this study, we used Pacbio sequencing data as a reference sequence to analyze the Illumina data of pearl millet for 48 hours under heat and drought stress. By taking an overview of previous studies, we found 26,299 new genes and 63,090 new transcripts, and the number of gene annotations increased by 20.18%. We identified 2,792 transcription factors (TFs) and 1,223 transcriptional regulators (TRs). There were 318 TFs and 149 TRs differentially expressed under heat stress, and 315 TFs and 128 TRs were differentially expressed under drought stress. By RNA sequencing, we identified 6,920 genes and 6,484 genes differentially expressed under heat stress and drought stress, respectively. Comparing DEGs under heat tolerance with DEGs under drought stress, we found that even in the same pathway, pearl millet would choose a different protein response. Conclusions: This information will provide new insights to study pearl millet at molecular and genetic level to understand the mechanisms involved in drought and heat stress tolerance.

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Molecular cloning and characterization of genes encoding Pennisetum glaucum ascorbate peroxidase and heat-shock factor: Interlinking oxidative and heat-stress responses

Journal of Plant Physiology ◽

10.1016/j.jplph.2009.04.007 ◽

2009 ◽

Vol 166 (15) ◽

pp. 1646-1659 ◽

Cited By ~ 17

Author(s):

Ramesha A. Reddy ◽

Bhumesh Kumar ◽

Palakolanu Sudhakar Reddy ◽

Rabi N. Mishra ◽

Srikrishna Mahanty ◽

...

Keyword(s):

Heat Stress ◽

Heat Shock ◽

Molecular Cloning ◽

Ascorbate Peroxidase ◽

Stress Responses ◽

Pennisetum Glaucum ◽

Heat Shock Factor ◽

Genes Encoding

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Pacific Biosciences long reads-based genome sequencing data from a widespread bee fungal parasite, Nosema ceranae

10.1101/2020.04.05.026849 ◽

2020 ◽

Author(s):

Huazhi Chen ◽

Wende Zhang ◽

Yu Du ◽

Xiaoxue Fan ◽

Jie Wang ◽

...

Keyword(s):

Genome Sequencing ◽

Average Length ◽

Length Distribution ◽

Gc Content ◽

Nosema Ceranae ◽

Sequencing Data ◽

Smrt Sequencing ◽

Fungal Parasite ◽

Total Length ◽

Pacific Biosciences

ABSTRACTNosema ceranae is a widespread fungal parasite that infects both adult honeybee and honeybee larvae, leading to microsporidiosis, which seriously affects bee health and apicultural industry. In this article, genome sequencing of clean spores of N. ceranae was conducted using third-generation Pacific Biosciences (PacBio) single molecule real time (SMRT) sequencing technology. In total, 152671 subreads were obtained after quality control of raw reads from PacBio SMRT sequencing, with a N50 and average length of 14422 bp and 11310 bp, respectively. Additionally, the length distribution of subreads was from 10000 bp to more than 50000 bp. Nineteen scaffords with a total length of 7354221 bp were assembled, and the N50, N90 and maximum scafford length were 728543 bp, 198795 bp and 1917792 bp, respectively. The GC content was 25.97%. Furthermore, by integration of genes predicted from de novo and homology-based methods, 3112 N. ceranae genes were finally assembled, with a total length of 2730179 bp and mean length of 877.31 bp. In addition, the total length and mean length of exons were 2657637 bp and 854 bp, respectively; and the total length and mean length of introns were 72542 bp and 23.31 bp, respectively. The genome sequencing data documented here will give deep insights into the molecular biology of N. ceranae, facilitate exploration of genes and pathways associated with toxin factors and infection-related factors, and benefit research on comparative genomics and phylogenetic diversity of Nosema species.

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Genome-wide identification and expression analysis of WRKY transcription factors in pearl millet (Pennisetum glaucum) under dehydration and salinity stress.

10.21203/rs.2.24672/v1 ◽

2020 ◽

Author(s):

Jeky Chanwala ◽

Suresh Satpati ◽

Anshuman Dixit ◽

Ajay Parida ◽

Mrunmay Kumar Giri ◽

...

Keyword(s):

Transcription Factors ◽

Expression Pattern ◽

Pearl Millet ◽

Salinity Stress ◽

Stress Responses ◽

Pennisetum Glaucum ◽

Regulatory Elements ◽

Stress Conditions ◽

Wrky Transcription Factors ◽

Genome Wide

Abstract Background: Plants have developed various sophisticated mechanisms to cope up with climate extremes and different stress conditions, especially by involving specific transcription factors (TFs). The members of the WRKY TF family are well known for their role in plant development, phytohormone signaling and developing resistance against biotic or abiotic stresses. In this study, we performed a genome-wide screening to identify and analyze the WRKY TFs in pearl millet ( Pennisetum glaucum; PgWRKY ) , which is one of the most widely grown cereal crop in the semi-arid regions. Results: A total number of 97 putative PgWRKY proteins were identified and classified into three major Groups (I-III) based on the presence of WRKY DNA binding domain and zinc-finger motif structures. Members of Group II have been further subdivided into five subgroups (IIa-IIe) based on the phylogenetic analysis. In-silico analysis of PgWRKYs revealed the presence of various cis-regulatory elements in their promoter region like ABRE, DRE, ERE, EIRE, Dof, AUXRR, G-box, etc., suggesting their probable involvement in growth, development and stress responses of pearl millet. Chromosomal mapping evidenced uneven distribution of identified 97 PgWRKY genes across all the seven chromosomes of pearl millet. Synteny analysis of PgWRKYs established their orthologous and paralogous relationship among the WRKY gene family of Arabidopsis thaliana, Oryza sativa and Setaria italica . Gene ontology (GO) annotation functionally categorized these PgWRKYs under cellular components, molecular functions and biological processes. Further, the differential expression pattern of PgWRKY s was noticed in different tissues (leaf, stem, root) and under both drought and salt stress conditions. The expression pattern of PgWRKY33 , PgWRKY62 and PgWRKY65 indicates their probable involvement in both dehydration and salinity stress responses in pearl millet. Conclusion: Functional characterization of identified PgWRKY s can be useful in delineating their role behind the natural stress tolerance of pearl millet against harsh environmental conditions. Further, these PgWRKY s can be employed in genome editing for millet crop improvement. Keywords : Pearl millet, WRKY Transcription Factors , cis-regulatory elements, Synteny, Abiotic stress

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