A Comparative Analyses of the Complete Mitochondrial Genomes of Fungal Endosymbionts in Sogatella furcifera, White-Backed Planthoppers

Sogatella furcifera Horvath, commonly known as the white-backed planthoppers (WBPH), is an important pest in East Asian rice fields. Fungal endosymbiosis is widespread among planthoppers in the infraorder Fulgoromorpha and suborder Auchenorrhyncha. We successfully obtained complete mitogenome of five WBPH fungal endosymbionts, belonging to the Ophiocordycipitaceae family, from next-generation sequencing (NGS) reads obtained from S. furcifera samples. These five mitogenomes range in length from 55,390 bp to 55,406 bp, which is shorter than the mitogenome of the fungal endosymbiont found in Ricania speculum, black planthoppers. Twenty-eight protein-coding genes (PCGs), 12 tRNAs, and 2 rRNAs were found in the mitogenomes. Two single-nucleotide polymorphisms, two insertions, and three deletions were identified among the five mitogenomes, which were fewer in number than those of four species of Ophiocordycipitaceae, Ophiocordyceps sinensis, Hirsutella thompsonii, Hirsutella rhossiliensis, and Tolypocladium inflatum. Noticeably short lengths (up to 18 bp) of simple sequence repeats were identified in the five WBPH fungal endosymbiont mitogenomes. Phylogenetic analysis based on conserved PCGs across 25 Ophiocordycipitaceae mitogenomes revealed that the five mitogenomes were clustered with that of R. speculum, forming an independent clade. In addition to providing the full mitogenome sequences, obtaining complete mitogenomes of WBPH endosymbionts can provide insights into their phylogenetic positions without needing to isolate the mtDNA from the host. This advantage is of value to future studies involving fungal endosymbiont mitogenomes.

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Analysis of Inter-Chromosomal Distribution of Disease-Related Genes in Human Genome

Current Protein and Peptide Science ◽

10.2174/1389203721666200426233158 ◽

2020 ◽

Vol 21 (11) ◽

pp. 1068-1077

Author(s):

Xiaochao Sun ◽

Bin Yang ◽

Qunye Zhang

Keyword(s):

Spatial Distribution ◽

Model Organisms ◽

Nucleotide Polymorphisms ◽

Chromosomal Distribution ◽

Single Nucleotide ◽

Protein Coding ◽

Single Chromosome ◽

Deletion Mutations ◽

Protein Coding Genes ◽

Disease Related Genes

: Many studies have shown that the spatial distribution of genes within a single chromosome exhibits distinct patterns. However, little is known about the characteristics of inter-chromosomal distribution of genes (including protein-coding genes, processed transcripts and pseudogenes) in different genomes. In this study, we explored these issues using the available genomic data of both human and model organisms. Moreover, we also analyzed the distribution pattern of protein-coding genes that have been associated with 14 common diseases and the insert/deletion mutations and single nucleotide polymorphisms detected by whole genome sequencing in an acute promyelocyte leukemia patient. We obtained the following novel findings. Firstly, inter-chromosomal distribution of genes displays a nonstochastic pattern and the gene densities in different chromosomes are heterogeneous. This kind of heterogeneity is observed in genomes of both lower and higher species. Secondly, protein-coding genes involved in certain biological processes tend to be enriched in one or a few chromosomes. Our findings have added new insights into our understanding of the spatial distribution of genome and disease- related genes across chromosomes. These results could be useful in improving the efficiency of disease-associated gene screening studies by targeting specific chromosomes.

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PSI-40 Two mitochondrial lineages revealed in North American yak

Journal of Animal Science ◽

10.1093/jas/skaa278.833 ◽

2020 ◽

Vol 98 (Supplement_4) ◽

pp. 477-477

Author(s):

Leah K Treffer ◽

Edward S Rice ◽

Anna M Fuller ◽

Samuel Cutler ◽

Jessica L Petersen

Keyword(s):

Sequence Data ◽

Haplotype Network ◽

Ovis Aries ◽

Similar Species ◽

Nucleotide Polymorphisms ◽

Mt Dna ◽

Protein Coding ◽

Sister Clade ◽

Mtdna Sequence ◽

The Impact

Abstract Domestic yak (Bos grunniens) are bovids native to the Asian Qinghai-Tibetan Plateau. Studies of Asian yak have revealed that introgression with domestic cattle has contributed to the evolution of the species. When imported to North America (NA), some hybridization with B. taurus did occur. The objective of this study was to use mitochondrial (mt) DNA sequence data to better understand the mtDNA origin of NA yak and their relationship to Asian yak and related species. The complete mtDNA sequence of 14 individuals (12 NA yak, 1 Tibetan yak, 1 Tibetan B. indicus) was generated and compared with sequences of similar species from GeneBank (B. indicus, B. grunniens (Chinese), B. taurus, B. gaurus, B. primigenius, B. frontalis, Bison bison, and Ovis aries). Individuals were aligned to the B. grunniens reference genome (ARS_UNL_BGru_maternal_1.0), which was also included in the analyses. The mtDNA genes were annotated using the ARS-UCD1.2 cattle sequence as a reference. Ten unique NA yak haplotypes were identified, which a haplotype network separated into two clusters. Variation among the NA haplotypes included 93 nonsynonymous single nucleotide polymorphisms. A maximum likelihood tree including all taxa was made using IQtree after the data were partitioned into twenty-two subgroups using PartitionFinder2. Notably, six NA yak haplotypes formed a clade with B. indicus; the other four haplotypes grouped with B. grunniens and fell as a sister clade to bison, gaur and gayal. These data demonstrate two mitochondrial origins of NA yak with genetic variation in protein coding genes. Although these data suggest yak introgression with B. indicus, it appears to date prior to importation into NA. In addition to contributing to our understanding of the species history, these results suggest the two major mtDNA haplotypes in NA yak may functionally differ. Characterization of the impact of these differences on cellular function is currently underway.

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The genome and transcriptome of the Phalaenopsis yield insights into floral organ development and flowering regulation

10.7287/peerj.preprints.1707v1 ◽

2016 ◽

Cited By ~ 1

Author(s):

Jian-Zhi Huang ◽

Chih-Peng Lin ◽

Ting-Chi Cheng ◽

Ya-Wen Huang ◽

Yi-Jung Tsai ◽

...

Keyword(s):

Economic Value ◽

Draft Genome ◽

Floral Organ ◽

Cool Temperature ◽

Organ Development ◽

Nucleotide Polymorphisms ◽

Protein Coding ◽

Draft Genome Assembly ◽

Genome Data ◽

Expression Of Genes

Phalaenopsis orchid is an important potted flower with high economic value around the world. We report the 3.1 Gb draft genome assembly of an important winter flowering Phalaenopsis ‘KHM190’ cultivar. We generated 89.5 Gb RNA-seq and 113 million sRNA-seq reads to use these data to identify 41,153 protein-coding genes and 188 miRNA families. We also generated a draft genome for Phalaenopsis pulcherrima ‘B8802’, a summer flowering species, via resequencing. Comparison of genome data between the two Phalaenopsis cultivars allowed the identification of 691,532 single-nucleotide polymorphisms. In this study, we reveal the key role of PhAGL6b in the regulation of flower organ development involves alternative splicing. We also show gibberellin pathways that regulate the expression of genes control flowering time during the stage in reproductive phase change induced by cool temperature. Our work should contribute a valuable resource for the flowering control, flower architecture development, and breeding of the Phalaenopsis orchids.

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Worldwide tracing of mutations and the evolutionary dynamics of SARS-CoV-2

10.1101/2020.08.07.242263 ◽

2020 ◽

Author(s):

Zhong-Yin Zhou ◽

Hang Liu ◽

Yue-Dong Zhang ◽

Yin-Qiao Wu ◽

Min-Sheng Peng ◽

...

Keyword(s):

Substitution Rate ◽

Evolutionary Dynamics ◽

Vaccine Development ◽

Sequence Data ◽

Immune Recognition ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Protein Coding ◽

Theoretical Support ◽

Recurrent Mutations

AbstractUnderstanding the mutational and evolutionary dynamics of SARS-CoV-2 is essential for treating COVID-19 and the development of a vaccine. Here, we analyzed publicly available 15,818 assembled SARS-CoV-2 genome sequences, along with 2,350 raw sequence datasets sampled worldwide. We investigated the distribution of inter-host single nucleotide polymorphisms (inter-host SNPs) and intra-host single nucleotide variations (iSNVs). Mutations have been observed at 35.6% (10,649/29,903) of the bases in the genome. The substitution rate in some protein coding regions is higher than the average in SARS-CoV-2 viruses, and the high substitution rate in some regions might be driven to escape immune recognition by diversifying selection. Both recurrent mutations and human-to-human transmission are mechanisms that generate fitness advantageous mutations. Furthermore, the frequency of three mutations (S protein, F400L; ORF3a protein, T164I; and ORF1a protein, Q6383H) has gradual increased over time on lineages, which provides new clues for the early detection of fitness advantageous mutations. Our study provides theoretical support for vaccine development and the optimization of treatment for COVID-19. We call researchers to submit raw sequence data to public databases.

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Repli-seq: genome-wide analysis of replication timing by next-generation sequencing

10.1101/104653 ◽

2017 ◽

Cited By ~ 8

Author(s):

Claire Marchal ◽

Takayo Sasaki ◽

Daniel Vera ◽

Korey Wilson ◽

Jiao Sima ◽

...

Keyword(s):

Next Generation Sequencing ◽

Replication Timing ◽

Nucleotide Polymorphisms ◽

Robust Methods ◽

Next Generation ◽

Single Nucleotide ◽

Cellular Processes ◽

Genome Wide ◽

Next Generation Sequencing Ngs ◽

Generation Sequencing

ABSTRACTCycling cells duplicate their DNA content during S phase, following a defined program called replication timing (RT). Early and late replicating regions differ in terms of mutation rates, transcriptional activity, chromatin marks and sub-nuclear position. Moreover, RT is regulated during development and is altered in disease. Exploring mechanisms linking RT to other cellular processes in normal and diseased cells will be facilitated by rapid and robust methods with which to measure RT genome wide. Here, we describe a rapid, robust and relatively inexpensive protocol to analyze genome-wide RT by next-generation sequencing (NGS). This protocol yields highly reproducible results across laboratories and platforms. We also provide computational pipelines for analysis, parsing phased genomes using single nucleotide polymorphisms (SNP) for analyzing RT allelic asynchrony, and for direct comparison to Repli-chip data obtained by analyzing nascent DNA by microarrays.

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The Mitochondrial Genomes of 18 New Pleurosticti (Coleoptera: Scarabaeidae) Exhibit a Novel trnQ-NCR-trnI-trnM Gene Rearrangement and Clarify Phylogenetic Relationships of Subfamilies within Scarabaeidae

Insects ◽

10.3390/insects12111025 ◽

2021 ◽

Vol 12 (11) ◽

pp. 1025

Author(s):

Sam Pedro Galilee Ayivi ◽

Yao Tong ◽

Kenneth B. Storey ◽

Dan-Na Yu ◽

Jia-Yong Zhang

Keyword(s):

Next Generation Sequencing ◽

Gene Order ◽

Phylogenetic Relationships ◽

Gene Rearrangement ◽

Next Generation ◽

Protein Coding ◽

Protein Coding Genes ◽

Next Generation Sequencing Ngs ◽

Mt Genome ◽

Generation Sequencing

The availability of next-generation sequencing (NGS) in recent years has facilitated a revolution in the availability of mitochondrial (mt) genome sequences. The mt genome is a powerful tool for comparative studies and resolving the phylogenetic relationships among insect lineages. The mt genomes of phytophagous scarabs of the subfamilies Cetoniinae and Dynastinae were under-represented in GenBank. Previous research found that the subfamily Rutelinae was recovered as a paraphyletic group because the few representatives of the subfamily Dynastinae clustered into Rutelinae, but the subfamily position of Dynastinae was still unclear. In the present study, we sequenced 18 mt genomes from Dynastinae and Cetoniinae using next-generation sequencing (NGS) to re-assess the phylogenetic relationships within Scarabaeidae. All sequenced mt genomes contained 37 sets of genes (13 protein-coding genes, 22 tRNAs, and two ribosomal RNAs), with one long control region, but the gene order was not the same between Cetoniinae and Dynastinae species. All mt genomes of Dynastinae species showed the same gene rearrangement of trnQ-NCR-trnI-trnM, whereas all mt genomes of Cetoniinae species showed the ancestral insect gene order of trnI-trnQ-trnM. Phylogenetic analyses (IQ-tree and MrBayes) were conducted using 13 protein-coding genes based on nucleotide and amino acid datasets. In the ML and BI trees, we recovered the monophyly of Rutelinae, Cetoniinae, Dynastinae, and Sericinae, and the non-monophyly of Melolonthinae. Cetoniinae was shown to be a sister clade to (Dynastinae + Rutelinae).

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A multiparametric approach to improve the prediction of response to immunotherapy in patients with metastatic NSCLC

Cancer Immunology Immunotherapy ◽

10.1007/s00262-020-02810-6 ◽

2020 ◽

Author(s):

Marzia Del Re ◽

Federico Cucchiara ◽

Eleonora Rofi ◽

Lorenzo Fontanelli ◽

Iacopo Petrini ◽

...

Keyword(s):

Mutational Load ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Synonymous Mutations ◽

Metastatic Nsclc ◽

Molecular Determinants ◽

Droplet Pcr ◽

Ifn Γ ◽

Nsclc Patients ◽

Next Generation Sequencing Ngs

Abstract Background It is still unclear how to combine biomarkers to identify patients who will truly benefit from anti-PD-1 agents in NSCLC. This study investigates exosomal mRNA expression of PD-L1 and IFN-γ, PD-L1 polymorphisms, tumor mutational load (TML) in circulating cell-free DNA (cfDNA) and radiomic features as possible predictive markers of response to nivolumab and pembrolizumab in metastatic NSCLC patients. Methods Patients were enrolled and blood (12 ml) was collected at baseline before receiving anti-PD-1 therapy. Exosome-derived mRNA and cfDNA were extracted to analyse PD-L1 and IFN-γ expression and tumor mutational load (TML) by digital droplet PCR (ddPCR) and next-generation sequencing (NGS), respectively. The PD-L1 single nucleotide polymorphisms (SNPs) c.-14-368 T > C and c.*395G > C, were analysed on genomic DNA by Real-Time PCR. A radiomic analysis was performed on the QUIBIM Precision® V3.0 platform. Results Thirty-eight patients were enrolled. High baseline IFN-γ was independently associated with shorter median PFS (5.6 months vs. not reached p = 0.0057), and levels of PD-L1 showed an increase at 3 months vs. baseline in patients who progressed (p = 0.01). PD-L1 baseline levels showed significant direct and inverse relationships with radiomic features. Radiomic features also inversely correlated with PD-L1 expression in tumor tissue. In subjects receiving nivolumab, median PFS was shorter in carriers of c.*395GG vs. c.*395GC/CC genotype (2.3 months vs. not reached, p = 0.041). Lastly, responders had higher non-synonymous mutations and more links between co-occurring genetic somatic mutations and ARID1A alterations as well. Conclusions A combined multiparametric approach may provide a better understanding of the molecular determinants of response to immunotherapy.

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A New High-Quality Draft Genome Assembly of the Chinese Cordyceps Ophiocordyceps sinensis

Genome Biology and Evolution ◽

10.1093/gbe/evaa112 ◽

2020 ◽

Vol 12 (7) ◽

pp. 1074-1079 ◽

Cited By ~ 1

Author(s):

Ruihao Shu ◽

Jihong Zhang ◽

Qian Meng ◽

Huan Zhang ◽

Guiling Zhou ◽

...

Keyword(s):

Single Molecule ◽

Genome Assembly ◽

Draft Genome ◽

Gene Clusters ◽

Tibet Plateau ◽

Protein Coding ◽

Draft Genome Assembly ◽

Ophiocordyceps Sinensis ◽

Homologous Protein ◽

Genome Features

Abstract Ophiocordyceps sinensis (Berk.) is an entomopathogenic fungus endemic to the Qinghai-Tibet Plateau. It parasitizes and mummifies the underground ghost moth larvae, then produces a fruiting body. The fungus-insect complex, called Chinese cordyceps or “DongChongXiaCao,” is not only a valuable traditional Chinese medicine, but also a major source of income for numerous Himalayan residents. Here, taking advantage of rapid advances in single-molecule sequencing, we assembled a highly contiguous genome assembly of O. sinensis. The assembly of 23 contigs was ∼110.8 Mb with a N50 length of 18.2 Mb. We used RNA-seq and homologous protein sequences to identify 8,916 protein-coding genes in the IOZ07 assembly. Moreover, 63 secondary metabolite gene clusters were identified in the improved assembly. The improved assembly and genome features described in this study will further inform the evolutionary study and resource utilization of Chinese cordyceps.

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Draft genome sequence of Solanum aethiopicum provides insights into disease resistance, drought tolerance, and the evolution of the genome

GigaScience ◽

10.1093/gigascience/giz115 ◽

2019 ◽

Vol 8 (10) ◽

Cited By ~ 3

Author(s):

Bo Song ◽

Yue Song ◽

Yuan Fu ◽

Elizabeth Balyejusa Kizito ◽

Sandra Ndagire Kamenya ◽

...

Keyword(s):

Disease Resistance ◽

Single Nucleotide Polymorphisms ◽

Drought Tolerance ◽

Resistance Genes ◽

Draft Genome ◽

Disease Resistance Genes ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Protein Coding ◽

Protein Coding Genes

Abstract Background The African eggplant (Solanum aethiopicum) is a nutritious traditional vegetable used in many African countries, including Uganda and Nigeria. It is thought to have been domesticated in Africa from its wild relative, Solanum anguivi. S. aethiopicum has been routinely used as a source of disease resistance genes for several Solanaceae crops, including Solanum melongena. A lack of genomic resources has meant that breeding of S. aethiopicum has lagged behind other vegetable crops. Results We assembled a 1.02-Gb draft genome of S. aethiopicum, which contained predominantly repetitive sequences (78.9%). We annotated 37,681 gene models, including 34,906 protein-coding genes. Expansion of disease resistance genes was observed via 2 rounds of amplification of long terminal repeat retrotransposons, which may have occurred ∼1.25 and 3.5 million years ago, respectively. By resequencing 65 S. aethiopicum and S. anguivi genotypes, 18,614,838 single-nucleotide polymorphisms were identified, of which 34,171 were located within disease resistance genes. Analysis of domestication and demographic history revealed active selection for genes involved in drought tolerance in both “Gilo” and “Shum” groups. A pan-genome of S. aethiopicum was assembled, containing 51,351 protein-coding genes; 7,069 of these genes were missing from the reference genome. Conclusions The genome sequence of S. aethiopicum enhances our understanding of its biotic and abiotic resistance. The single-nucleotide polymorphisms identified are immediately available for use by breeders. The information provided here will accelerate selection and breeding of the African eggplant, as well as other crops within the Solanaceae family.

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Complete Genome Sequence of Yersinia pestis Strains Antiqua and Nepal516: Evidence of Gene Reduction in an Emerging Pathogen

Journal of Bacteriology ◽

10.1128/jb.00124-06 ◽

2006 ◽

Vol 188 (12) ◽

pp. 4453-4463 ◽

Cited By ~ 114

Author(s):

Patrick S. G. Chain ◽

Ping Hu ◽

Stephanie A. Malfatti ◽

Lyndsay Radnedge ◽

Frank Larimer ◽

...

Keyword(s):

Single Nucleotide Polymorphisms ◽

Yersinia Pestis ◽

Yersinia Pseudotuberculosis ◽

Open Reading Frames ◽

Genomic Diversity ◽

Avirulent Strain ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Protein Coding ◽

Definition Of

ABSTRACT Yersinia pestis, the causative agent of bubonic and pneumonic plagues, has undergone detailed study at the molecular level. To further investigate the genomic diversity among this group and to help characterize lineages of the plague organism that have no sequenced members, we present here the genomes of two isolates of the “classical” antiqua biovar, strains Antiqua and Nepal516. The genomes of Antiqua and Nepal516 are 4.7 Mb and 4.5 Mb and encode 4,138 and 3,956 open reading frames, respectively. Though both strains belong to one of the three classical biovars, they represent separate lineages defined by recent phylogenetic studies. We compare all five currently sequenced Y. pestis genomes and the corresponding features in Yersinia pseudotuberculosis. There are strain-specific rearrangements, insertions, deletions, single nucleotide polymorphisms, and a unique distribution of insertion sequences. We found 453 single nucleotide polymorphisms in protein-coding regions, which were used to assess the evolutionary relationships of these Y. pestis strains. Gene reduction analysis revealed that the gene deletion processes are under selective pressure, and many of the inactivations are probably related to the organism's interaction with its host environment. The results presented here clearly demonstrate the differences between the two biovar antiqua lineages and support the notion that grouping Y. pestis strains based strictly on the classical definition of biovars (predicated upon two biochemical assays) does not accurately reflect the phylogenetic relationships within this species. A comparison of four virulent Y. pestis strains with the human-avirulent strain 91001 provides further insight into the genetic basis of virulence to humans.

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