scholarly journals Deciphering tea tree chloroplast and mitochondrial genomes of Camellia sinensis var. assamica

2019 ◽  
Vol 6 (1) ◽  
Author(s):  
Fen Zhang ◽  
Wei Li ◽  
Cheng-wen Gao ◽  
Dan Zhang ◽  
Li-zhi Gao
Keyword(s):  
Rna Editing ◽  
De Novo ◽  
Comparative Genomic ◽  
Protein Coding ◽  
Tea Tree ◽  
Repeat Sequences ◽  
Genomic Studies ◽  
Cp Genome ◽  
Mt Genome

Abstract Tea is the most popular non-alcoholic caffeine-containing and the oldest beverage in the world. In this study, we de novo assembled the chloroplast (cp) and mitochondrial (mt) genomes of C. sinensis var. assamica cv. Yunkang10 into a circular contig of 157,100 bp and two complete circular scaffolds (701719 bp and 177329 bp), respectively. We correspondingly annotated a total of 141 cp genes and 71 mt genes. Comparative analysis suggests repeat-rich nature of the mt genome compared to the cp genome, for example, with the characterization of 37,878 bp and 149 bp of long repeat sequences and 665 and 214 SSRs, respectively. We also detected 478 RNA-editing sites in 42 protein-coding mt genes, which are ~4.4-fold more than 54 RNA-editing sites detected in 21 protein-coding cp genes. The high-quality cp and mt genomes of C. sinensis var. assamica presented in this study will become an important resource for a range of genetic, functional, evolutionary and comparative genomic studies in tea tree and other Camellia species of the Theaceae family.

scholarly journals Deciphering tea tree chloroplast and mitochondrial genomes of Camellia sinensis var. assamica

2019 ◽  
Author(s):  
Fen Zhang ◽  
Wei Li ◽  
Cheng-wen Gao ◽  
Li-zhi Gao
Keyword(s):  
Rna Editing ◽  
Camellia Sinensis ◽  
De Novo ◽  
Single Copy ◽  
Rrna Genes ◽  
Protein Coding ◽  
Tea Tree ◽  
Protein Coding Genes ◽  
Cp Genome ◽  
Mt Genome

ABSTRACTTea is the most popular non-alcoholic caffeine-containing and the oldest beverage in the world. Despite its enormous industrial, cultural and medicinal values, the chloroplast (cp) and mitochondrial (mt) genomes are not available for Camellia sinensis var. assamica. In this study, we de novo assembled the cp genome sequence of C. sinensis var. assamica into a circular contig of 157,100 bp in length with an overall GC content of 37.29%, comprising a large single-copy region (LSC, 86,649 bp) and a small single-copy region (SSC, 18,285 bp) separated by a pair of inverted repeats (IRs, 26,083 bp). We annotated a total of 141 cp genes, of which 87 are protein-coding genes, 46 are tRNA genes, and eight are rRNA genes. We also de novo assembled the mt genome of C. sinensis var. assamica into two complete circular scaffolds (702,253 bp and 178,082 bp) with overall GC contents of 45.63% and 45.81%, respectively. We annotated a total of 71 mt genes, including 44 protein-coding genes, 24 tRNAs, and 3 rRNAs. Comparative analysis suggests repeat-rich nature of the mt genome compared to the cp genome, for example, with the characterization of 37,878 bp and 149 bp of long repeat sequences and 665 and 214 SSRs, respectively. We also detected 478 RNA-editing sites in 42 protein-coding mt genes, which are ∼4.4-fold more than 54 RNA-editing sites detected in 21 protein-coding cp genes. The high-quality cp and mt genomes of C. sinensis var. assamica presented in this study will become an invaluable resource for a range of genetic, functional, evolutionary and comparative genomic studies in tea tree and other Camellia species of the Theaceae family.

scholarly journals Structural and functional characterization of a putative de novo gene in Drosophila

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Andreas Lange ◽  
Prajal H. Patel ◽  
Brennen Heames ◽  
Adam M. Damry ◽  
Thorsten Saenger ◽  
...  
Keyword(s):  
De Novo ◽  
Functional Characterization ◽  
Comparative Genomic ◽  
Noncoding Dna ◽  
Protein Coding ◽  
Ancestral Sequences ◽  
De Novo Gene ◽  
Genomic Studies ◽  
Biochemical Genetic

AbstractComparative genomic studies have repeatedly shown that new protein-coding genes can emerge de novo from noncoding DNA. Still unknown is how and when the structures of encoded de novo proteins emerge and evolve. Combining biochemical, genetic and evolutionary analyses, we elucidate the function and structure of goddard, a gene which appears to have evolved de novo at least 50 million years ago within the Drosophila genus. Previous studies found that goddard is required for male fertility. Here, we show that Goddard protein localizes to elongating sperm axonemes and that in its absence, elongated spermatids fail to undergo individualization. Combining modelling, NMR and circular dichroism (CD) data, we show that Goddard protein contains a large central α-helix, but is otherwise partially disordered. We find similar results for Goddard’s orthologs from divergent fly species and their reconstructed ancestral sequences. Accordingly, Goddard’s structure appears to have been maintained with only minor changes over millions of years.

scholarly journals Structural and functional characterization of a putative de novo gene in Drosophila

2021 ◽  
Author(s):  
Andreas Lange ◽  
Prajal H. Patel ◽  
Brennen Heames ◽  
Adam M. Damry ◽  
Thorsten Saenger ◽  
...  
Keyword(s):  
De Novo ◽  
Functional Characterization ◽  
Comparative Genomic ◽  
Protein Coding ◽  
Ancestral Sequences ◽  
De Novo Gene ◽  
Genomic Studies ◽  
Biochemical Genetic ◽  
Α Helix

AbstractComparative genomic studies have repeatedly shown that new protein-coding genes can emerge de novo from non-coding DNA. Still unknown is how and when the structures of encoded de novo proteins emerge and evolve. Combining biochemical, genetic and evolutionary analyses, we elucidate the function and structure of goddard, a gene which appears to have evolved de novo at least 50 million years ago within the Drosophila genus.Previous studies found that goddard is required for male fertility. Here, we show that Goddard protein localizes to elongating sperm axonemes and that in its absence, elongated spermatids fail to undergo individualization. Combining modelling, NMR and CD data, we show that Goddard protein contains a large central α-helix, but is otherwise partially disordered. We find similar results for Goddard’s orthologs from divergent fly species and their reconstructed ancestral sequences. Accordingly, Goddard’s structure appears to have been maintained with only minor changes over millions of years.

scholarly journals Whole-genome sequence of the Tibetan frog Nanorana parkeri and the comparative evolution of tetrapod genomes

2015 ◽  
Vol 112 (11) ◽  
pp. E1257-E1262 ◽  
Author(s):  
Yan-Bo Sun ◽  
Zi-Jun Xiong ◽  
Xue-Yan Xiang ◽  
Shi-Ping Liu ◽  
Wei-Wei Zhou ◽  
...  
Keyword(s):  
De Novo ◽  
Structural Evolution ◽  
Whole Genome Sequence ◽  
Comparative Genomic ◽  
Whole Genome ◽  
Protein Coding ◽  
Comparable Rate ◽  
Evolutionary Studies ◽  
Genomic Studies ◽  
The Difference

The development of efficient sequencing techniques has resulted in large numbers of genomes being available for evolutionary studies. However, only one genome is available for all amphibians, that of Xenopus tropicalis, which is distantly related from the majority of frogs. More than 96% of frogs belong to the Neobatrachia, and no genome exists for this group. This dearth of amphibian genomes greatly restricts genomic studies of amphibians and, more generally, our understanding of tetrapod genome evolution. To fill this gap, we provide the de novo genome of a Tibetan Plateau frog, Nanorana parkeri, and compare it to that of X. tropicalis and other vertebrates. This genome encodes more than 20,000 protein-coding genes, a number similar to that of Xenopus. Although the genome size of Nanorana is considerably larger than that of Xenopus (2.3 vs. 1.5 Gb), most of the difference is due to the respective number of transposable elements in the two genomes. The two frogs exhibit considerable conserved whole-genome synteny despite having diverged approximately 266 Ma, indicating a slow rate of DNA structural evolution in anurans. Multigenome synteny blocks further show that amphibians have fewer interchromosomal rearrangements than mammals but have a comparable rate of intrachromosomal rearrangements. Our analysis also identifies 11 Mb of anuran-specific highly conserved elements that will be useful for comparative genomic analyses of frogs. The Nanorana genome offers an improved understanding of evolution of tetrapod genomes and also provides a genomic reference for other evolutionary studies.

scholarly journals Subtelomeric Rearrangements: Presentation of 21 Probands with Emphasis on Familial Cases

2019 ◽  
Vol 32 (7-8) ◽  
pp. 529
Author(s):  
Ana Rita Soares ◽  
Gabriela Soares ◽  
Manuela Mota-Freitas ◽  
Natália Oliva-Teles ◽  
Ana Maria Fortuna
Keyword(s):  
Intellectual Disability ◽  
Comparative Genomic Hybridization ◽  
Chromosomal Abnormality ◽  
Array Comparative Genomic Hybridization ◽  
De Novo ◽  
Family Members ◽  
Comparative Genomic ◽  
Genomic Hybridization ◽  
Subtelomeric Rearrangements

Introduction: Intellectual disability affects 2% – 3% of the general population, with a chromosomal abnormality being found in 4% – 28% of these patients and a cryptic subtelomeric abnormality in 3% – 16%. In most cases, these subtelomeric rearrangements are submicroscopic, requiring techniques other than conventional karyotype for detection. They may be de novo or inherited from an affected parent or from a healthy carrier of a balanced chromosomal abnormality. The aim of this study was to characterize patients from our medical genetics center, in whom both a deletion and duplication in subtelomeric regions were found.Material and Methods: Clinical and cytogenetic characterization of 21 probands followed at our center, from 1998 until 2017, with subtelomeric rearrangements.Results: There were 21 probands from 19 families presenting with intellectual disability and facial dysmorphisms. Seven had behavior changes, five had epilepsy and 14 presented with some other sign or symptom. Four had chromosomal abnormalities detected by conventional karyotype and four were diagnosed by array-comparative genomic hybridization. In four cases, parental studies were not possible. The online mendelian inheritance in man classification was provided whenever any of the phenotypes (deletion or duplication syndrome) was dominant.Discussion: Patients and relevant family members were clinically and cytogenetically characterized. Although rare, subtelomeric changes are a substantial cause of syndromic intellectual disability with important familial repercussions. It is essential to remember that a normal array-comparative genomic hybridization result does not exclude a balanced rearrangement in the parents.Conclusion: Parental genetic studies are essential not only for a complete characterization of the rearrangement, but also for accurate genetic counselling and screening of family members at risk for recurrence.

scholarly journals High-Quality Genome Assembly of Peronospora destructor, the Causal Agent of Onion Downy Mildew

2020 ◽  
Vol 33 (5) ◽  
pp. 718-720
Author(s):  
Karthi Natesan ◽  
Ji Yeon Park ◽  
Cheol-Woo Kim ◽  
Dong Suk Park ◽  
Young-Seok Kwon ◽  
...  
Keyword(s):  
Downy Mildew ◽  
De Novo ◽  
Gc Content ◽  
Comparative Genomic ◽  
High Quality ◽  
Sequencing Platform ◽  
Peronospora Destructor ◽  
Genomic Studies ◽  
Genome Assemblies ◽  
High Quality Genome

Peronospora destructor is an obligate biotrophic oomycete that causes downy mildew on onion (Allium cepa). Onion is an important crop worldwide, but its production is affected by this pathogen. We sequenced the genome of P. destructor using the PacBio sequencing platform, and de novo assembly resulted in 74 contigs with a total contig size of 29.3 Mb and 48.48% GC content. Here, we report the first high-quality genome sequence of P. destructor and its comparison with the genome assemblies of other oomycetes. The genome is a very useful resource to serve as a reference for analysis of P. destructor isolates and for comparative genomic studies of the biotrophic oomycetes.

scholarly journals Genome Sequence Resource for Elsinoë ampelina, the Causal Organism of Grapevine Anthracnose

2020 ◽  
Vol 33 (4) ◽  
pp. 576-579 ◽  
Author(s):  
Zhi Li ◽  
Yanchun Fan ◽  
Pingping Chang ◽  
Linlin Gao ◽  
Xiping Wang
Keyword(s):  
Genome Sequence ◽  
Management Strategies ◽  
Comparative Genomic ◽  
Causal Organism ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Elsinoe Ampelina ◽  
Genomic Studies ◽  
High Quality Genome ◽  
Ascomycetous Fungus

Elsinoë ampelina is an ascomycetous fungus that causes grape anthracnose, a potentially devastating disease worldwide. Here, we report a 28.29 Mb high-quality genome sequence of E. ampelina YL-1 that encodes 8,057 predicted protein-coding genes and represents the first sequenced genome assembly of E. ampelina. This study adds to the current genomic resources for the genus Elsinoë and paves the way for research on comparative genomic studies, E. ampelina–grape interactions, and improvement of management strategies.

scholarly journals ELFN1-AS1: A Novel Primate Gene with Possible MicroRNA Function Expressed Predominantly in Human Tumors

2014 ◽  
Vol 2014 ◽  
pp. 1-10 ◽  
Author(s):  
Dmitrii E. Polev ◽  
Iuliia K. Karnaukhova ◽  
Larisa L. Krukovskaya ◽  
Andrei P. Kozlov
Keyword(s):  
De Novo ◽  
Human Gene ◽  
Homo Sapiens ◽  
Genomic Analysis ◽  
Structure Characteristic ◽  
Comparative Genomic ◽  
Protein Coding ◽  
Regulatory Motifs ◽  
Normal Tissues ◽  
Microrna Function

Human geneLOC100505644 uncharacterized LOC100505644 [Homo sapiens](Entrez Gene ID 100505644) is abundantly expressed in tumors but weakly expressed in few normal tissues. Till now the function of this gene remains unknown. Here we identified the chromosomal borders of the transcribed region and the major splice form of theLOC100505644-specific transcript. We characterised the major regulatory motifs of the gene and its splice sites. Analysis of the secondary structure of the major transcript variant revealed a hairpin-like structure characteristic for precursor microRNAs. Comparative genomic analysis of the locus showed that it originated in primatesde novo. Taken together, our data indicate that human geneLOC100505644encodes some non-protein coding RNA, likely a microRNA. It was assigned a gene symbolELFN1-AS1(ELFN1 antisense RNA 1 (non-protein coding)). This gene combines features of evolutionary novelty and predominant expression in tumors.

scholarly journals Characterization of testis-specific LINC01016 gene reveals isoform-specific roles in controlling biological processes

2021 ◽  
Author(s):  
Enrique I Ramos ◽  
Barbara Yang ◽  
Yasmin M Vasquez ◽  
Ken Y Lin ◽  
Ramesh Choudhari ◽  
...  
Keyword(s):  
De Novo ◽  
Biological Processes ◽  
Detailed Characterization ◽  
Aberrant Expression ◽  
Protein Coding ◽  
Lncrna Gene ◽  
Gene Expression Analyses ◽  
Uterine Cancers ◽  
Exon Usage

Abstract Long noncoding RNAs (lncRNAs) have emerged as critical regulators of biological processes. However, the aberrant expression of an isoform from the same lncRNA gene could lead to RNA with altered functions due to changes in their conformations, leading to diseases. Here, we describe a detailed characterization of the gene which encodes long intergenic non-protein coding RNA 01016 (LINC01016, a.k.a., LncRNA1195) with a focus on its structure, exon usage, and expression in human and macaque tissues. In this study, we show that it is among the highly expressed lncRNAs in the testis, exclusively conserved among non-human primates, suggesting its recent evolution and is expressed and processed into 12 distinct RNAs in testis, cervix, and uterus tissues. Further, we integrate de novo annotation of expressed LINC01016 transcripts and isoform-dependent gene expression analyses to show that human LINC01016 is a multi-exon gene, processed through differential exon usage with isoform-specific roles. Furthermore, in cervical, testicular, and uterine cancers, LINC01016 isoforms are differentially expressed, and their expression is predictive of survival in these cancers. The study has revealed an essential aspect of lncRNA biology, which is rarely associated with coding RNAs that lncRNA genes are precisely processed to generate isoforms with distinct biological roles in specific tissues.

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