scholarly journals Assembly of a Complete Mitogenome of Chrysanthemum nankingense Using Oxford Nanopore Long Reads and the Diversity and Evolution of Asteraceae Mitogenomes

Genes ◽  
2018 ◽  
Vol 9 (11) ◽  
pp. 547 ◽  
Author(s):  
Shuaibin Wang ◽  
Qingwei Song ◽  
Shanshan Li ◽  
Zhigang Hu ◽  
Gangqiang Dong ◽  
...  
Keyword(s):  
Structural Variation ◽  
Sequencing Data ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
The Core ◽  
Assembly Method ◽  
Long Reads ◽  
Oxford Nanopore ◽  
Complete Mitogenome ◽  
Rna Genes

Diversity in structure and organization is one of the main features of angiosperm mitochondrial genomes (mitogenomes). The ultra-long reads of Oxford Nanopore Technology (ONT) provide an opportunity to obtain a complete mitogenome and investigate the structural variation in unprecedented detail. In this study, we compared mitogenome assembly methods using Illumina and/or ONT sequencing data and obtained the complete mitogenome (208 kb) of Chrysanthemum nankingense based on the hybrid assembly method. The mitogenome encoded 19 transfer RNA genes, three ribosomal RNA genes, and 34 protein-coding genes with 21 group II introns disrupting eight intron-contained genes. A total of seven medium repeats were related to homologous recombination at different frequencies as supported by the long ONT reads. Subsequently, we investigated the variations in gene content and constitution of 28 near-complete mitogenomes from Asteraceae. A total of six protein-coding genes were missing in all Asteraceae mitogenomes, while four other genes were not detected in some lineages. The core fragments (~88 kb) of the Asteraceae mitogenomes had a higher GC content (~46.7%) than the variable and specific fragments. The phylogenetic topology based on the core fragments of the Asteraceae mitogenomes was highly consistent with the topologies obtained from the corresponding plastid datasets. Our results highlighted the advantages of the complete assembly of the C. nankingense mitogenome and the investigation of its structural variation based on ONT sequencing data. Moreover, the method based on local collinear blocks of the mitogenomes could achieve the alignment of highly rearrangeable and variable plant mitogenomes as well as construct a robust phylogenetic topology.

scholarly journals The genome of the American groundhog, Marmota monax

F1000Research ◽  
2020 ◽  
Vol 9 ◽  
pp. 1137
Author(s):  
Daniela Puiu ◽  
Aleksey Zimin ◽  
Alaina Shumate ◽  
Yuchen Ge ◽  
Jiabin Qiu ◽  
...  
Keyword(s):  
Protein Coding ◽  
Marmota Monax ◽  
Protein Coding Genes ◽  
The North ◽  
Long Reads ◽  
Oxford Nanopore ◽  
A Genome ◽  
Sequencing Strategy ◽  
Alpine Marmot ◽  
Combined Data

We sequenced the genome of the North American groundhog, Marmota monax, also known as the woodchuck. Our sequencing strategy included a combination of short, high-quality Illumina reads plus long reads generated by both Pacific Biosciences and Oxford Nanopore instruments. Assembly of the combined data produced a genome of 2.74 Gbp in total length, with an N50 contig size of 1,094,236 bp. To annotate the genome, we mapped the genes from another M. monax genome and from the closely related Alpine marmot, Marmota marmota, onto our assembly, resulting in 20,559 annotated protein-coding genes and 28,135 transcripts. The genome assembly and annotation are available in GenBank under BioProject PRJNA587092.

Complete mitogenome of Parum colligata (Lepidoptera: Sphingidae) and its phylogenetic position within the Sphingidae

Zootaxa ◽  
2019 ◽  
Vol 4652 (1) ◽  
pp. 126-134 ◽  
Author(s):  
JUN LI ◽  
KUNJIE HU ◽  
YAQI ZHAO ◽  
RUIRUI LIN ◽  
YAOYAO ZHANG ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Ribosomal Rna ◽  
Phylogenetic Analyses ◽  
Transfer Rna ◽  
Phylogenetic Position ◽  
Rich Region ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Complete Mitogenome ◽  
Rna Genes

In this study, the complete mitochondrial DNA sequence of Parum colligata (Lepidoptera: Sphingidae: Smerinthinae) was sequenced firstly. The mitogenome is 15,288 bp in size, containing 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and an A+T-rich region. In the mitogenome, Ile, Leu2, and Phe are the most frequently used codon families, while codons GCG, TGC, GGC, CTG, AGG, and ACG are absent. The A+T-rich region is 358 bp in length including a motif ‘ATAGA’, an 18 bp poly-T stretch, three copies of a 12 bp ‘TATATATATATA’, and a short poly-A element. The nucleotides sequence of A+T-rich region is closer to Sphinginae than Macroglossinae. Phylogenetic analyses, based on the PCGs by using Maximum Likelihood (ML) and Bayesian Inference (BI) methods, generated consistent results that Smerinthinae was clustered together with Sphinginae to be the sister groups rather than Macroglossinae. 

scholarly journals The complete mitogenome of  Lysmata vittata (Crustacea: Decapoda: Hippolytidae) and its phylogenetic position in Decapoda

2021 ◽  
Author(s):  
Longqiang Zhu ◽  
Zhihuang Zhu ◽  
Leiyu Zhu ◽  
Dingquan Wang ◽  
Jianxin Wang ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
Stop Codon ◽  
Nucleotide Composition ◽  
Start Codon ◽  
Phylogenetic Position ◽  
Base Pairs ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Complete Mitogenome ◽  
Rna Genes

In this study, the complete mitogenome of Lysmata vittata (Crustacea: Decapoda: Hippolytidae) has been determined. The genome sequence was 22003 base pairs (bp) and it included thirteen protein-coding genes (PCGs), twenty-two transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and three putative control regions (CRs). The nucleotide composition of AT was 71.50%, with a slightly negative AT skewness (-0.04). Usually the standard start codon of the PCGs was ATN, while cox1, nad4L and cox3 began with TTG, TTG and GTG. The canonical termination codon was TAA, while nad5 and nad4 ended with incomplete stop codon T, and cox1 ended with TAG. We compared the order of genes of Decapoda ancestor and found that the positions of the two tRNAs genes ( trnA and trnR ) of the L. vittata were translocated. The phylogenetic tree showed that L. vittata was an independent clade, namely Hippolytidae.

scholarly journals Genome of the Single Human Chromosome 18 as a “Gold Standard” for Its Transcriptome

2021 ◽  
Vol 12 ◽  
Author(s):  
Ekaterina Ilgisonis ◽  
Nikita Vavilov ◽  
Elena Ponomarenko ◽  
Andrey Lisitsa ◽  
Ekaterina Poverennaya ◽  
...  
Keyword(s):  
Human Chromosome ◽  
Quantitative Polymerase Chain Reaction ◽  
Sequencing Analysis ◽  
Sample Type ◽  
Sequencing Data ◽  
Chromosome 18 ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Oxford Nanopore ◽  
Long Read

The cutoff level applied in sequencing analysis varies according to the sequencing technology, sample type, and study purpose, which can largely affect the coverage and reliability of the data obtained. In this study, we aimed to determine the optimal combination of parameters for reliable RNA transcriptome data analysis. Toward this end, we compared the results obtained from different transcriptome analysis platforms (quantitative polymerase chain reaction, Illumina RNASeq, and Oxford Nanopore Technologies MinION) for the transcriptome encoded by human chromosome 18 (Chr 18) using the same sample types (HepG2 cells and liver tissue). A total of 275 protein-coding genes encoded by Chr 18 was taken as the gene set for evaluation. The combination of Illumina RNASeq and MinION nanopore technologies enabled the detection of at least one transcript for each protein-coding gene encoded by Chr 18. This combination also reduced the probability of false-positive detection of low-copy transcripts due to the simultaneous confirmation of the presence of a transcript by the two fundamentally different technologies: short reads essential for reliable detection (Illumina RNASeq) and long-read sequencing data (MinION). The combination of these technologies achieved complete coverage of all 275 protein-coding genes on Chr 18, identifying transcripts with non-zero expression levels. This approach can improve distinguishing the biological and technical reasons for the absence of mRNA detection for a given gene in transcriptomics.

scholarly journals Chromosomal assembly of the nuclear genome of the endosymbiont-bearing trypanosomatid Angomonas deanei

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
John W Davey ◽  
Carolina M C Catta-Preta ◽  
Sally James ◽  
Sarah Forrester ◽  
Maria Cristina M Motta ◽  
...  
Keyword(s):  
Chromosome Number ◽  
Noncoding Rnas ◽  
Nuclear Genome ◽  
Supernumerary Chromosome ◽  
Ribosomal Rnas ◽  
Protein Coding ◽  
Transfer Rnas ◽  
Protein Coding Genes ◽  
Oxford Nanopore ◽  
Genome Assemblies

Abstract Angomonas deanei is an endosymbiont-bearing trypanosomatid with several highly fragmented genome assemblies and unknown chromosome number. We present an assembly of the A. deanei nuclear genome based on Oxford Nanopore sequence that resolves into 29 complete or close-to-complete chromosomes. The assembly has several previously unknown special features; it has a supernumerary chromosome, a chromosome with a 340-kb inversion, and there is a translocation between two chromosomes. We also present an updated annotation of the chromosomal genome with 10,365 protein-coding genes, 59 transfer RNAs, 26 ribosomal RNAs, and 62 noncoding RNAs.

scholarly journals Novel gene rearrangement in the mitochondrial genome of Muraenesox cinereus and the phylogenetic relationship of Anguilliformes

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kun Zhang ◽  
Kehua Zhu ◽  
Yifan Liu ◽  
Hua Zhang ◽  
Li Gong ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Gene Rearrangement ◽  
Tandem Duplication ◽  
Mitochondrial Gene ◽  
Gene Arrangement ◽  
Protein Coding ◽  
Muraenesox Cinereus ◽  
Complete Mitogenome ◽  
Relationship Of ◽  
Rna Genes

AbstractThe structure and gene sequence of the fish mitochondrial genome are generally considered to be conservative. However, two types of gene arrangements are found in the mitochondrial genome of Anguilliformes. In this paper, we report a complete mitogenome of Muraenesox cinereus (Anguilliformes: Muraenesocidae) with rearrangement phenomenon. The total length of the M. cinereus mitogenome was 17,673 bp, and it contained 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNA genes, and two identical control regions (CRs). The mitochondrial genome of M. cinereus was obviously rearranged compared with the mitochondria of typical vertebrates. The genes ND6 and the conjoint trnE were translocated to the location between trnT and trnP, and one of the duplicated CR was translocated to the upstream of the ND6. The tandem duplication and random loss is most suitable for explaining this mitochondrial gene rearrangement. The Anguilliformes phylogenetic tree constructed based on the whole mitochondrial genome well supports Congridae non-monophyly. These results provide a basis for the future Anguilliformes mitochondrial gene arrangement characteristics and further phylogenetic research.

Screening and survival analysis of melanoma immunodrug response-related genes and the function of magnetic nanoparticles in gene extraction

2021 ◽  
Vol 11 (8) ◽  
pp. 1306-1312
Author(s):  
Li Song ◽  
Ningchao Du ◽  
Haitao Luo ◽  
Furong Li
Keyword(s):  
Survival Analysis ◽  
Magnetic Nanoparticles ◽  
Drug Response ◽  
High Throughput Sequencing ◽  
Cox Proportional Hazards ◽  
Sequencing Data ◽  
Protein Coding ◽  
Non Coding Rna ◽  
Long Non Coding Rna ◽  
Rna Genes

This study aimed to identify the association of protein coding and long non coding RNA genes with immunotherapy response in melanoma. Based on RNA sequencing data of melanoma specimens, the expression levels of protein coding and long non coding RNA genes were calculated using the Kallisto RNA-seq quantification method, and differently expressed genes were detected using the DESeq2 method. Cox proportional hazards regression was used to evaluate the effects of gene expression on survival. According to the clinical data of 14 patients with drug response and 11 patients without drug response, 18 protein coding genes and 14 long non coding RNAs showed differential expressions (multiple of difference > 2 and P < 0.01 after correction), among which the coding genes of differential expression were significantly enriched through the process of cell adhesion (P < 0.01). The results of survival analysis showed that 18 coding genes and 14 long non coding RNA genes had significant effects on patient survival (P < 0.01). In this study, magnetic nanoparticles can be used to extract genomic DNA and total RNA due to their paramagnetism and biocompatibility, then transcriptome high-throughput sequencing was performed. The method has the advantages of removing dangerous reagents such as phenol and chloroform, replacing inorganic coating such as silica with organic oil, and shortening reaction time. Protein coding and long non coding RNA genes as well as magnetic nanoparticles may serve as potential cancer immune biomarker targets for developing future oncological treatments.

scholarly journals Identification and characterization of cis-regulatory elements for photoreceptor type-specific transcription in zebrafish

2019 ◽  
Author(s):  
Wei Fang ◽  
Yi Wen ◽  
Xiangyun Wei
Keyword(s):  
Core Promoter ◽  
Regulatory Elements ◽  
Specific Gene ◽  
Protein Coding ◽  
Core Promoters ◽  
Protein Coding Genes ◽  
The Core ◽  
Cell Type Specific ◽  
Identification And Characterization

AbstractTissue-specific or cell type-specific transcription of protein-coding genes is controlled by both trans-regulatory elements (TREs) and cis-regulatory elements (CREs). However, it is challenging to identify TREs and CREs, which are unknown for most genes. Here, we describe a protocol for identifying two types of transcription-activating CREs—core promoters and enhancers—of zebrafish photoreceptor type-specific genes. This protocol is composed of three phases: bioinformatic prediction, experimental validation, and characterization of the CREs. To better illustrate the principles and logic of this protocol, we exemplify it with the discovery of the core promoter and enhancer of the mpp5b apical polarity gene (also known as ponli), whose red, green, and blue (RGB) cone-specific transcription requires its enhancer, a member of the rainbow enhancer family. While exemplified with an RGB cone-specific gene, this protocol is general and can be used to identify the core promoters and enhancers of other protein-coding genes.

scholarly journals Chromosome-scale assembly of the Sparassis latifolia genome obtained using long-read and Hi-C sequencing

2021 ◽  
Author(s):  
Chi yang ◽  
Lu Ma ◽  
Donglai Xiao ◽  
Xiaoyu Liu ◽  
Xiaoling Jiang ◽  
...  
Keyword(s):  
Repetitive Sequences ◽  
Draft Genome ◽  
Edible Mushroom ◽  
Illumina Hiseq ◽  
Protein Coding ◽  
Long Reads ◽  
Oxford Nanopore ◽  
Genome Features ◽  
Long Read ◽  
Genomic Studies

Sparassis latifolia is a valuable edible mushroom cultivated in China. In 2018, our research group reported an incomplete and low quality genome of S. latifolia was obtained by Illumina HiSeq 2500 sequencing. These limitations in the available genome have constrained genetic and genomic studies in this mushroom resource. Herein, an updated draft genome sequence of S. latifolia was generated by Oxford Nanopore sequencing and the Hi-C technique. A total of 8.24 Gb of Oxford Nanopore long reads representing ~198.08X coverage of the S. latifolia genome were generated. Subsequently, a high-quality genome of 41.41 Mb, with scaffold and contig N50 sizes of 3.31 Mb and 1.51 Mb, respectively, was assembled. Hi-C scaffolding of the genome resulted in 12 pseudochromosomes containing 93.56% of the bases in the assembled genome. Genome annotation further revealed that 17.47% of the genome was composed of repetitive sequences. In addition, 13,103 protein-coding genes were predicted, among which 98.72% were functionally annotated. BUSCO assay results further revealed that there were 92.07% complete BUSCOs. The improved chromosome-scale assembly and genome features described here will aid further molecular elucidation of various traits, breeding of S. latifolia, and evolutionary studies with related taxa.

scholarly journals The complete mitochondrial genome of Microphysogobio elongatus (Teleostei, Cyprinidae) and its phylogenetic implications

ZooKeys ◽  
2021 ◽  
Vol 1061 ◽  
pp. 57-73
Author(s):  
Renyi Zhang ◽  
Qian Tang ◽  
Lei Deng
Keyword(s):  
Complete Mitochondrial Genome ◽  
Genetic Material ◽  
Start Codon ◽  
Trna Genes ◽  
Protein Coding ◽  
Simple Loop ◽  
Stop Codons ◽  
Phylogenetic Implications ◽  
Complete Mitogenome ◽  
Rna Genes

Mitochondria are important organelles with independent genetic material of eukaryotic organisms. In this study, we sequenced and analyzed the complete mitogenome of a small cyprinid fish, Microphysogobio elongatus (Yao &amp; Yang, 1977). The mitogenome of M. elongatus is a typical circular molecule of 16,612 bp in length containing 13 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes, and a 930 bp control region. The base composition of the M. elongatus mitogenome is 30.8% A, 26.1% T, 16.7% G, and 26.4% C. All PCGs used the standard ATG start codon with the exception of COI. Six PCGs terminate with complete stop codons, whereas seven PCGs (ND2, COII, ATPase 6, COIII, ND3, ND4, and Cyt b) terminate with incomplete (T or TA) stop codons. All tRNA genes exhibited typical cloverleaf secondary structures with the exception of tRNASer(AGY), for which the dihydrouridine arm forms a simple loop. The phylogenetic analysis divided the subfamily Gobioninae in three clades with relatively robust support, and that Microphysogobio is not a monophyletic group. The complete mitogenome of M. elongatus provides a valuable resource for future studies about molecular phylogeny and/or population genetics of Microphysogobio.

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