In Silico Identification of Conserved MiRNAs from Physcomitrella patens ESTs and their Target Characterization

2018 ◽  
Vol 14 (1) ◽  
pp. 33-42 ◽  
Author(s):  
Behzad Hajieghrari ◽  
Naser Farrokhi ◽  
Bahram Goliaei ◽  
Kaveh Kavousi
Keyword(s):  
Plant Species ◽  
Physcomitrella Patens ◽  
Homology Search ◽  
Protein Coding ◽  
Reference Plant ◽  
Baseline Information ◽  
Target Characterization ◽  
In Silico Identification ◽  
Simple Sequence ◽  
Gene Index

Background: MicroRNAs (miRNAs) are groups of small non-protein-coding endogenous single stranded RNAs with approximately 18-24 nucleotides in length. High evolutionary sequence conservation of miRNAs among plant species and availability of powerful computational tools allow identification of new orthologs and paralogs. Methods: New conserved miRNAs in P. patens were found by EST-based homology search approaches. All candidates were screened according to a series of miRNA filtering criteria. Unigene, DFCI Gene Index (PpspGI) databases and psRNATarget algorithm were applied to identify target transcripts using P. patens putative conserved miRNA sequences. Results: Nineteen conserved P. patens miRNAs were identified. The sequences were homologous to known reference plant mature miRNA from 10 miRNA families. They could be folded into the typical miRNA secondary structures. RepeatMasker algorithm demonstrated that ppt-miR2919e and pptmiR1533 had simple sequence repeats in their sequences. Target sites (49 genes) were identified for 7 out of 19 miRNAs. GO and KEGG analysis of targets indicated the involvement of some in important multiple biological and metabolic processes. Conclusion: The majority of the registered miRNAs in databases were predicted by computational approaches while many more have remained unknown. Due to the conserved nature of miRNAs in plant species from closely to distantly related, homology search-based approaches between plants species could lead to the identification of novel miRNAs in other plant species providing baseline information for further search about the biological functions and evolution of miRNAs.

scholarly journals The Chloroplast Phylogenomics and Systematics of Zoysia (Poaceae)

Plants ◽  
2021 ◽  
Vol 10 (8) ◽  
pp. 1517
Author(s):  
Se-Hwan Cheon ◽  
Min-Ah Woo ◽  
Sangjin Jo ◽  
Young-Kee Kim ◽  
Ki-Joong Kim
Keyword(s):  
Northeast Asia ◽  
Single Copy ◽  
Rrna Genes ◽  
Bootstrap Support ◽  
Trna Genes ◽  
Protein Coding ◽  
Tropical Regions ◽  
Relationship Of ◽  
The Relationship ◽  
Simple Sequence

The genus Zoysia Willd. (Chloridoideae) is widely distributed from the temperate regions of Northeast Asia—including China, Japan, and Korea—to the tropical regions of Southeast Asia. Among these, four species—Zoysia japonica Steud., Zoysia sinica Hance, Zoysia tenuifolia Thiele, and Zoysia macrostachya Franch. & Sav.—are naturally distributed in the Korean Peninsula. In this study, we report the complete plastome sequences of these Korean Zoysia species (NCBI acc. nos. MF953592, MF967579~MF967581). The length of Zoysia plastomes ranges from 135,854 to 135,904 bp, and the plastomes have a typical quadripartite structure, which consists of a pair of inverted repeat regions (20,962~20,966 bp) separated by a large (81,348~81,392 bp) and a small (12,582~12,586 bp) single-copy region. In terms of gene order and structure, Zoysia plastomes are similar to the typical plastomes of Poaceae. The plastomes encode 110 genes, of which 76 are protein-coding genes, 30 are tRNA genes, and four are rRNA genes. Fourteen genes contain single introns and one gene has two introns. Three evolutionary hotspot spacer regions—atpB~rbcL, rps16~rps3, and rpl32~trnL-UAG—were recognized among six analyzed Zoysia species. The high divergences in the atpB~rbcL spacer and rpl16~rpl3 region are primarily due to the differences in base substitutions and indels. In contrast, the high divergence between rpl32~trnL-UAG spacers is due to a small inversion with a pair of 22 bp stem and an 11 bp loop. Simple sequence repeats (SSRs) were identified in 59 different locations in Z. japonica, 63 in Z. sinica, 62 in Z. macrostachya, and 63 in Z. tenuifolia plastomes. Phylogenetic analysis showed that the Zoysia (Zoysiinae) forms a monophyletic group, which is sister to Sporobolus (Sporobolinae), with 100% bootstrap support. Within the Zoysia clade, the relationship of (Z. sinica, Z japonica), (Z. tenuifolia, Z. matrella), (Z. macrostachya, Z. macrantha) was suggested.

scholarly journals Draft Genome Sequence of the Lactococcus lactis 11/19-B1 Strain, Isolated from Kiwifruit

2020 ◽  
Vol 9 (36) ◽  
Author(s):  
Ken Ishioka ◽  
Kyoko Nishiyama ◽  
Tatsuo Suzutani
Keyword(s):  
Lactococcus Lactis ◽  
Genome Sequence ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Homology Search ◽  
Protein Coding ◽  
Coding Sequences ◽  
Content Type

ABSTRACT We report here the draft genome sequence of Lactococcus lactis strain 11/19-B1, isolated from kiwifruit. The 11/19-B1 strain possesses one chromosome and five plasmids and has a predicted 2,429 protein-coding sequences. DFAST annotation and a BLASTp homology search estimated that 11/19-B1 possesses three bacteriocin immunity proteins and four bacteriocin proteins.

scholarly journals Computational Mining and Genome Wide Distribution of Microsatellite in Fusarium oxysporum f. sp. lycopersici

2012 ◽  
Vol 4 (4) ◽  
pp. 127-131 ◽  
Author(s):  
Sudheer KUMAR ◽  
Deepak MAURYA ◽  
Shalini RAI ◽  
Prem Lal KASHYAP ◽  
Alok Kumar SRIVASTAVA
Keyword(s):  
Fusarium Oxysporum ◽  
Genomic Analysis ◽  
Wide Distribution ◽  
Chromosome 1 ◽  
Coding Region ◽  
Chromosome 11 ◽  
High Throughput Analysis ◽  
Genome Wide ◽  
Baseline Information ◽  
Simple Sequence

Simple sequence repeat (SSR) is currently the most preferred molecular marker system owing to their highly desirable properties viz., abundance, hyper-variability, and suitability for high-throughput analysis. Hence, in present study an attempt was made to mine and analyze microsatellite dynamics in whole genome of Fusarium oxysporum f. sp. lycopersici. The distribution pattern of different SSR motifs provides the evidence of greater accumulation of tetra-nucleotide (3837) repeats followed by tri-nucleotide (3367) repeats. Maximum frequency distribution in coding region was shown by mono-nucleotide SSR motifs (34.8%), where as minimum frequency is observed for penta-nucleotide SSR (0.87%). Highest relative abundance (1023 SSR/Mb) and density of SSRs (114.46 bp/Mb) were observed on chromosome 1, while least density of SSR motifs was recorded on chromosome 11 (7.40 bp/Mb) and 12 (7.41 bp/Mb), respectively. Maximum trinucleotide (34.24%) motifs code for glutamic acid (GAA) while GT/CT were the most frequent repeat of dinucleotide SSRs. Most common and highly repeated SSR motifs were identified as (A)64, (T)48, (GT)24, (GAA)31, (TTTC)24, (TTTCT)28 and (AACCAG)27. Overall, the generated information may serve as baseline information for developing SSR markers that could find applications in genomic analysis of F. oxysporum f. sp. lycopersici for better understanding of evolution, diversity analysis, population genetics, race identification and acquisition of new virulence.

Highly informative nature of inter simple sequence repeat (ISSR) sequences amplified using tri- and tetra-nucleotide primers from DNA of cauliflower (Brassica oleracea var. botrytis L.)

Genome ◽  
2002 ◽  
Vol 45 (5) ◽  
pp. 890-896 ◽  
Author(s):  
B Bornet ◽  
C Muller ◽  
F Paulus ◽  
M Branchard
Keyword(s):  
Arabidopsis Thaliana ◽  
Brassica Oleracea ◽  
Simple Sequence Repeat ◽  
Dna Interaction ◽  
Inter Simple Sequence Repeat ◽  
Homology Search ◽  
Sequence Repeat ◽  
Pcr Products ◽  
Or Gene ◽  
Simple Sequence

Inter simple sequence repeat (ISSR) sequences as molecular markers can lead to the detection of polymorphism and also be a new approach to the study of SSR distribution and frequency. In this study, ISSR amplification with nonanchored primer was performed in closely related cauliflower lines. Fourty-four different amplified fragments were sequenced. Sequences of PCR products are delimited by the expected motifs and number of repeats, which validates the ISSR nonanchored primer amplification technique. DNA and amino acids homology search between internal sequences and databases (i) show that the majority of the internal regions of ISSR had homologies with known sequences, mainly with genes coding for proteins implicated in DNA interaction or gene expression, which reflected the significance of amplified ISSR sequences and (ii) display long and numerous homologies with the Arabidopsis thaliana genome. ISSR amplifications revealed a high conservation of these sequences between Arabidopsis thaliana and Brassica oleracea var. botrytis. Thirty-four of the 44 ISSRs had one or several perfect or imperfect internal microsatellites. Such distribution indicates the presence in genomes of highly concentrated regions of SSR, or "SSR hot spots." Among the four nonanchored primers used in this study, trinucleotide repeats, and especially (CAA)5, were the most powerful primers for ISSR amplifications regarding the number of amplified bands, level of polymorphism, and their nature. Key words: inter simple sequence repeat (ISSR), nonanchored primer, DNA marker sequence, SSR, cluster of SSRs.

scholarly journals The complete mitochondrial genome sequence of Scolopendra mutilans L. Koch, 1878 (Scolopendromorpha, Scolopendridae), with a comparative analysis of other centipede genomes

ZooKeys ◽  
2020 ◽  
Vol 925 ◽  
pp. 73-88
Author(s):  
Chaoyi Hu ◽  
Shuaibin Wang ◽  
Bisheng Huang ◽  
Hegang Liu ◽  
Lei Xu ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Complete Mitochondrial Genome ◽  
Gc Content ◽  
Sister Group ◽  
Rrna Genes ◽  
Sister Group Relationship ◽  
Trna Genes ◽  
Protein Coding ◽  
Generation Sequencing ◽  
Simple Sequence

Scolopendra mutilans L. Koch, 1878 is an important Chinese animal with thousands of years of medicinal history. However, the genomic information of this species is limited, which hinders its further application. Here, the complete mitochondrial genome (mitogenome) of S. mutilans was sequenced and assembled by next-generation sequencing. The genome is 15,011 bp in length, consisting of 13 protein-coding genes (PCGs), 14 tRNA genes, and two rRNA genes. Most PCGs start with the ATN initiation codon, and all PCGs have the conventional stop codons TAA and TAG. The S. mutilans mitogenome revealed nine simple sequence repeats (SSRs), and an obviously lower GC content compared with other seven centipede mitogenomes previously sequenced. After analysis of homologous regions between the eight centipede mitogenomes, the S. mutilans mitogenome further showed clear genomic rearrangements. The phylogenetic analysis of eight centipedes using 13 conserved PCG genes was finally performed. The phylogenetic reconstructions showed Scutigeromorpha as a separate group, and Scolopendromorpha in a sister-group relationship with Lithobiomorpha and Geophilomorpha. Collectively, the S. mutilans mitogenome provided new genomic resources, which will improve its medicinal research and applications in the future.

scholarly journals Transcriptome analysis of developmental stages of cocoa pod borer, Conopomorpha cramerella: A polyphagous insect pest of economic importance in Southeast Asia.

2021 ◽  
Author(s):  
Chia Lock Tan ◽  
Rosmin Kasran ◽  
Wei Wei Lee ◽  
Wai Mun Leong
Keyword(s):  
Southeast Asia ◽  
Developmental Stages ◽  
Transcriptome Assembly ◽  
Insect Pest ◽  
Homology Search ◽  
General Function ◽  
Protein Coding ◽  
Pod Borer ◽  
Three Stages ◽  
Polyphagous Insect

The cocoa pod borer, Conopomorpha cramerella (Snellen) is a serious pest in cocoa plantations in Southeast Asia.  It causes significant losses in the crop.  Unfortunately, genetic resources for this insect is extremely scarce.  To improve these resources, we sequenced the transcriptome of C. cramerella representing the three stages of development, larva, pupa and adult moth using Illumina NovaSeq6000.  Transcriptome assembly was performed by Trinity for all the samples.  A total number of 147,356,088 high quality reads were obtained.  Of these, 285,882 contigs were assembled.  The mean contig size was 374 bp.  Protein coding sequence (CDS) was extracted from the reconstructed transcripts by TransDecoder.  Subsequently, BlastX and InterProScan were applied for homology search to make a prediction of the function of CDS in unigene.  Additionally, we identified a number of genes that are involved in reproduction and development such as genes involved in general function processes in the insect.  Genes found to be involved in reproduction such as porin, dsx, bol and fruitless were associated with sex determination, spermatogenesis and pheromone binding.  Furthermore, transcriptome changes during development were analysed.  There were 2,843 differentially expressed genes (DEG) detected between the larva and pupa samples.  A total of 2,861 DEG were detected between adult and larva stage whereas between adult and pupa stage, 1,953 DEG were found.  In conclusion, the transcriptomes could be a valuable genetic resource for identification of genes in C. cramerella and the study will provide putative targets for RNAi pest control.

scholarly journals Wild edible plant species used in the Ağrı province, eastern Turkey

2020 ◽  
Vol 77 (2) ◽  
pp. e098
Author(s):  
Zakine Kadioglu ◽  
Kemal Cukadar ◽  
Nalan Nazan Kalkan ◽  
Huseyin Vurgun ◽  
Ozkan Kaya
Keyword(s):  
Plant Species ◽  
Amaranthus Retroflexus ◽  
Natural Food ◽  
Edible Plants ◽  
Wild Edible Plant ◽  
Edible Plant ◽  
Important Species ◽  
Baseline Information ◽  
Plant Families ◽  
Increasing Demand

Wild edible plant species found in Ağrı are nutritionally and economically relevant. Plants are collected by the villagers and brought to the market for sale in the spring. Interest in these plants responds to the increasing demand for organic and natural food. In this study, 350 in-depth face-to-face interviews with villagers about the edible plants used in Ağrı (7 districts, 35 villages) were conducted in the region from April 2016 to October 2017. The species, parts used and their consumption and preservation techniques were analyzed and documented. Some of the wild edible plant species are consumed cured or canned, raw or cooked, dried, and some are frozen. The collected 100 wild edible species belong to 25 different plant families. Species are consumed as vegetables (91), spices (19), beverages (16), subterranean parts (5), fruits (3), seeds (3) and exudates (2). The most important species according to their cultural importance were: Amaranthus retroflexus, Beta trigyna, Gundelia tournefortii, Mentha longifolia, Polygonum persicaria, Rumex scutatus, Tragopogon porrifolius subsp. longirostris, and Urtica dioica. Leaves and young shoots were the most frequently used parts. Our study shows that wild edible plants are still well known and used by the local people of Ağrı as a food source. The documented data on these plants herein could be used as baseline information for further investigations on nutritional contents, as they could have the potential to become valuable nutrition sources.

scholarly journals Extending MapMan Ontology to Tobacco for Visualization of Gene Expression

2013 ◽  
Vol 2013 ◽  
pp. 1-7 ◽  
Author(s):  
Maurice H. T. Ling ◽  
Roel C. Rabara ◽  
Prateek Tripathi ◽  
Paul J. Rushton ◽  
Xijin Ge
Keyword(s):  
Plant Species ◽  
Microarray Data ◽  
Large Scale ◽  
Ontology Mapping ◽  
Manual Inspection ◽  
Custom Made ◽  
Genome Level ◽  
The Many ◽  
Mapping File ◽  
Gene Index

Microarrays are a large-scale expression profiling method which has been used to study the transcriptome of plants under various environmental conditions. However, manual inspection of microarray data is difficult at the genome level because of the large number of genes (normally at least 30 000) and the many different processes that occur within any given plant. MapMan software, which was initially developed to visualize microarray data for Arabidopsis, has been adapted to other plant species by mapping other species onto MapMan ontology. This paper provides a detailed procedure and the relevant computing codes to generate a MapMan ontology mapping file for tobacco (Nicotiana tabacum L.) using potato and Arabidopsis as intermediates. The mapping file can be used directly with our custom-made NimbleGen oligoarray, which contains gene sequences from both the tobacco gene space sequence and the tobacco gene index 4 (NTGI4) collection of ESTs. The generated dataset will be informative for scientists working on tobacco as their model plant by providing a MapMan ontology mapping file to tobacco, homology between tobacco coding sequences and that of potato and Arabidopsis, as well as adapting our procedure and codes for other plant species where the complete genome is not yet available.

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