scholarly journals A chromosome-level reference genome of non-heading Chinese cabbage [Brassica campestris (syn. Brassica rapa) ssp. chinensis]

2020 ◽  
Vol 7 (1) ◽  
Author(s):  
Ying Li ◽  
Gao-Feng Liu ◽  
Li-Ming Ma ◽  
Tong-Kun Liu ◽  
Chang-Wei Zhang ◽  
...  
Keyword(s):  
Chinese Cabbage ◽  
Repetitive Sequences ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Sequencing Data ◽  
Long Terminal Repeats ◽  
Protein Coding ◽  
Heading Chinese Cabbage ◽  
Genome Triplication ◽  
Chromosome Level

AbstractNon-heading Chinese cabbage (NHCC) is an important leafy vegetable cultivated worldwide. Here, we report the first high-quality, chromosome-level genome of NHCC001 based on PacBio, Hi-C, and Illumina sequencing data. The assembled NHCC001 genome is 405.33 Mb in size with a contig N50 of 2.83 Mb and a scaffold N50 of 38.13 Mb. Approximately 53% of the assembled genome is composed of repetitive sequences, among which long terminal repeats (LTRs, 20.42% of the genome) are the most abundant. Using Hi-C data, 97.9% (396.83 Mb) of the sequences were assigned to 10 pseudochromosomes. Genome assessment showed that this B. rapa NHCC001 genome assembly is of better quality than other currently available B. rapa assemblies and that it contains 48,158 protein-coding genes, 99.56% of which are annotated in at least one functional database. Comparative genomic analysis confirmed that B. rapa NHCC001 underwent a whole-genome triplication (WGT) event shared with other Brassica species that occurred after the WGD events shared with Arabidopsis. Genes related to ascorbic acid metabolism showed little variation among the three B. rapa subspecies. The numbers of genes involved in glucosinolate biosynthesis and catabolism were higher in NHCC001 than in Chiifu and Z1, due primarily to tandem duplication. The newly assembled genome will provide an important resource for research on B. rapa, especially B. rapa ssp. chinensis.

scholarly journals Brassica carinata genome characterization clarifies U’s triangle model of evolution and polyploidy in Brassica

2021 ◽  
Author(s):  
Xiaoming Song ◽  
Yanping Wei ◽  
Dong Xiao ◽  
Ke Gong ◽  
Pengchuan Sun ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Agronomic Traits ◽  
Repetitive Sequences ◽  
Genomic Analysis ◽  
Brassica Species ◽  
Brassica Carinata ◽  
Comparative Genomic ◽  
Ethiopian Mustard ◽  
A Genome ◽  
Genome Triplication

Abstract Ethiopian mustard (Brassica carinata) in the Brassicaceae family possesses many excellent agronomic traits. Here, the high-quality genome sequence of B. carinata is reported. Characterization revealed a genome anchored to 17 chromosomes with a total length of 1.087 Gb and an N50 scaffold length of 60 Mb. Repetitive sequences account for approximately 634 Mb or 58.34% of the B. carinata genome. Notably, 51.91% of 97,149 genes are confined to the terminal 20% of chromosomes as a result of the expansion of repeats in pericentromeric regions. Brassica carinata shares one whole-genome triplication event with the five other species in U’s triangle, a classic model of evolution and polyploidy in Brassica. Brassica carinata was deduced to have formed ∼0.047 Mya, which is slightly earlier than B. napus but later than B. juncea. Our analysis indicated that the relationship between the two subgenomes (BcaB and BcaC) is greater than that between other two tetraploid subgenomes (BjuB and BnaC) and their respective diploid parents. RNA-seq datasets and comparative genomic analysis were used to identify several key genes in pathways regulating disease resistance and glucosinolate metabolism. Further analyses revealed that genome triplication and tandem duplication played important roles in the expansion of those genes in Brassica species. With the genome sequencing of B. carinata completed, the genomes of all six Brassica species in U’s triangle are now resolved. The data obtained from genome sequencing, transcriptome analysis, and comparative genomic efforts in this study provide valuable insights into the genome evolution of the six Brassica species in U’s triangle.

scholarly journals The chromosome-level Stevia genome provides insights into steviol glycoside biosynthesis

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Xiaoyang Xu ◽  
Haiyan Yuan ◽  
Xiaqing Yu ◽  
Suzhen Huang ◽  
Yuming Sun ◽  
...  
Keyword(s):  
Agronomic Traits ◽  
Genomic Analysis ◽  
Stevia Rebaudiana ◽  
Comparative Genomic ◽  
Steviol Glycosides ◽  
Protein Coding ◽  
Steviol Glycoside ◽  
Evolution Analysis ◽  
History Of ◽  
Chromosome Level

AbstractStevia (Stevia rebaudiana Bertoni) is well known for its very sweet steviol glycosides (SGs) consisting of a common tetracyclic diterpenoid steviol backbone and a variable glycone. Steviol glycosides are 150–300 times sweeter than sucrose and are used as natural zero-calorie sweeteners. However, the most promising compounds are biosynthesized in small amounts. Based on Illumina, PacBio, and Hi-C sequencing, we constructed a chromosome-level assembly of Stevia covering 1416 Mb with a contig N50 value of 616.85 kb and a scaffold N50 value of 106.55 Mb. More than four-fifths of the Stevia genome consisted of repetitive elements. We annotated 44,143 high-confidence protein-coding genes in the high-quality genome. Genome evolution analysis suggested that Stevia and sunflower diverged ~29.4 million years ago (Mya), shortly after the whole-genome duplication (WGD) event (WGD-2, ~32.1 Mya) that occurred in their common ancestor. Comparative genomic analysis revealed that the expanded genes in Stevia were mainly enriched for biosynthesis of specialized metabolites, especially biosynthesis of terpenoid backbones, and for further oxidation and glycosylation of these compounds. We further identified all candidate genes involved in SG biosynthesis. Collectively, our current findings on the Stevia reference genome will be very helpful for dissecting the evolutionary history of Stevia and for discovering novel genes contributing to SG biosynthesis and other important agronomic traits in future breeding programs.

scholarly journals Extensive genomic rearrangements mediated by repetitive sequences in plastomes of Medicago and its relatives

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Shuang Wu ◽  
Jinyuan Chen ◽  
Ying Li ◽  
Ai Liu ◽  
Ao Li ◽  
...  
Keyword(s):  
Tandem Repeats ◽  
Genome Instability ◽  
Repetitive Sequences ◽  
Genomic Analysis ◽  
Genomic Rearrangements ◽  
Comparative Genomic ◽  
Length Variation ◽  
Substitution Rates ◽  
Repeat Content ◽  
Plastome Evolution

Abstract Background Although plastomes are highly conserved with respect to gene content and order in most photosynthetic angiosperms, extensive genomic rearrangements have been reported in Fabaceae, particularly within the inverted repeat lacking clade (IRLC) of Papilionoideae. Two hypotheses, i.e., the absence of the IR and the increased repeat content, have been proposed to affect the stability of plastomes. However, this is still unclear for the IRLC species. Here, we aimed to investigate the relationships between repeat content and the degree of genomic rearrangements in plastomes of Medicago and its relatives Trigonella and Melilotus, which are nested firmly within the IRLC. Results We detected abundant repetitive elements and extensive genomic rearrangements in the 75 newly assembled plastomes of 20 species, including gene loss, intron loss and gain, pseudogenization, tRNA duplication, inversion, and a second independent IR gain (IR ~ 15 kb in Melilotus dentata) in addition to the previous first reported cases in Medicago minima. We also conducted comparative genomic analysis to evaluate plastome evolution. Our results indicated that the overall repeat content is positively correlated with the degree of genomic rearrangements. Some of the genomic rearrangements were found to be directly linked with repetitive sequences. Tandem repeated sequences have been detected in the three genes with accelerated substitution rates (i.e., accD, clpP, and ycf1) and their length variation could be explained by the insertions of tandem repeats. The repeat contents of the three localized hypermutation regions around these three genes with accelerated substitution rates are also significantly higher than that of the remaining plastome sequences. Conclusions Our results suggest that IR reemergence in the IRLC species does not ensure their plastome stability. Instead, repeat-mediated illegitimate recombination is the major mechanism leading to genome instability, a pattern in agreement with recent findings in other angiosperm lineages. The plastome data generated herein provide valuable genomic resources for further investigating the plastome evolution in legumes.

scholarly journals Quantification of aneuploidy in targeted sequencing data using ASCETS

2020 ◽  
Author(s):  
Liam F Spurr ◽  
Mehdi Touat ◽  
Alison M Taylor ◽  
Adrian M Dubuc ◽  
Juliann Shih ◽  
...  
Keyword(s):  
Copy Number ◽  
Large Scale ◽  
Genomic Analysis ◽  
Targeted Sequencing ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Sequencing Data ◽  
Copy Number Changes ◽  
Panel Sequencing ◽  
Chromosome Level

Abstract Summary The expansion of targeted panel sequencing efforts has created opportunities for large-scale genomic analysis, but tools for copy-number quantification on panel data are lacking. We introduce ASCETS, a method for the efficient quantitation of arm and chromosome-level copy-number changes from targeted sequencing data. Availability and implementation ASCETS is implemented in R and is freely available to non-commercial users on GitHub: https://github.com/beroukhim-lab/ascets, along with detailed documentation. Supplementary information Supplementary data are available at Bioinformatics online.

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 Predicting Insect Invasiveness With Whole-genome Sequencing Data

2020 ◽  
Author(s):  
Cong Huang ◽  
Nianwan Yang ◽  
Shuping Wang ◽  
Xiaodan Fan ◽  
Cong Pian ◽  
...  
Keyword(s):  
Insect Pest ◽  
Genomic Analysis ◽  
Gene Families ◽  
Insect Species ◽  
Whole Genome Sequencing Data ◽  
Comparative Genomic ◽  
Nucleic Acid Metabolism ◽  
Sequencing Data ◽  
Invasive Insects ◽  
Invasive Insect

Abstract Background Invasive alien insects threaten agriculture, biodiversity, and human livelihoods globally. Unfortunately, insect invasiveness still cannot be reliably predicted. Empirical policies of insect pest quarantine and inspection are mainly designed against species that are already problematic. Results We conducted a comparative genomic analysis of 37 invasive insect species and six non-invasive insect species, showing that the gene families associated with defense, protein and nucleic acid metabolism, chemosensory function, and transcriptional regulation were significantly expanded in invasive insects, suggesting that enhanced abilities in self-protection, nutrition exploitation, and locating food or mates are intrinsic features conferring invasiveness in insects. By using these intrinsic genome features, we proposed an invasiveness index and estimated the invasiveness of 99 other insect species with genome data, classifying them as highly, moderately, or minimally invasive. Insects possessing all these aforementioned enhanced abilities are predicted to be highly invasive, and vice versa. Next, a logistic-regression classifier was trained to predict insect invasiveness, achieving 93.2% accuracy. Conclusions We present evidence that several traits may confer invasiveness in insects and these features can be used to predict insect invasiveness accurately, and we quantify insect invasiveness with an invasiveness index.

scholarly journals Mitochondrial Genomes of Hestina persimilis and Hestinalis nama (Lepidoptera, Nymphalidae): Genome Description and Phylogenetic Implications

Insects ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 754
Author(s):  
Yupeng Wu ◽  
Hui Fang ◽  
Jiping Wen ◽  
Juping Wang ◽  
Tianwen Cao ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Genomic Analysis ◽  
Mitochondrial Genomes ◽  
Comparative Genomic ◽  
Trna Genes ◽  
Cox1 Gene ◽  
Protein Coding ◽  
Phylogenetic Implications ◽  
Typical Composition

In this study, the complete mitochondrial genomes (mitogenomes) of Hestina persimilis and Hestinalis nama (Nymphalidae: Apaturinae)were acquired. The mitogenomes of H. persimilis and H. nama are 15,252 bp and 15,208 bp in length, respectively. These two mitogenomes have the typical composition, including 37 genes and a control region. The start codons of the protein-coding genes (PCGs) in the two mitogenomes are the typical codon pattern ATN, exceptCGA in the cox1 gene. Twenty-one tRNA genes show a typical clover leaf structure, however, trnS1(AGN) lacks the dihydrouridine (DHU) stem. The secondary structures of rrnL and rrnS of two species were predicted, and there are several new stem loops near the 5’ of rrnL secondary structure. Based on comparative genomic analysis, four similar conservative structures can be found in the control regions of these two mitogenomes. The phylogenetic analyses were performed on mitogenomes of Nymphalidae. The phylogenetic trees show that the relationships among Nymphalidae are generally identical to previous studies, as follows: Libytheinae\Danainae + ((Calinaginae + Satyrinae) + Danainae\Libytheinae + ((Heliconiinae + Limenitidinae) + (Nymphalinae + (Apaturinae + Biblidinae)))). Hestinalisnama isapart fromHestina, andclosely related to Apatura, forming monophyly.

scholarly journals Chromosome-level genome assembly of a butterflyfish, Chelmon rostratus

2019 ◽  
Author(s):  
Xiaoyun Huang ◽  
Yue Song ◽  
Suyu Zhang ◽  
A Yunga ◽  
Mengqi Zhang ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Repetitive Sequences ◽  
Ecological Environment ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
A Genome ◽  
Genome Information ◽  
Adaptation Evolution ◽  
Core Genes ◽  
Chromosome Level

AbstractChelmon rostratus (Teleostei, Perciformes, Chaetodontidae) is a copperband butterflyfish. As an ornamental fish, the genome information for this species might help understanding the genome evolution of Chaetodontidae and adaptation/evolution of coral reef fish.In this study, using the stLFR co-Barcode reads data, we assembled a genome of 638.70 Mb in size with contig and scaffold N50 sizes of 294.41 kb and 2.61 Mb, respectively. 94.40% of scaffold sequences were assigned to 24 chromosomes using Hi-C data and BUSCO analysis showed that 97.3% (2,579) of core genes were found in our assembly. Up to 21.47 % of the genome was found to be repetitive sequences and 21,375 protein-coding genes were annotated. Among these annotated protein-coding genes, 20,163 (94.33%) proteins were assigned with possible functions.As the first genome for Chaetodontidae family, the information of these data helpfully to improve the essential to the further understanding and exploration of marine ecological environment symbiosis with coral and the genomic innovations and molecular mechanisms contributing to its unique morphology and physiological features.

scholarly journals Chromosome-Level Genome Assembly Reveals Significant Gene Expansion in the Toll and IMD Signaling Pathways of Dendrolimus kikuchii

2021 ◽  
Vol 12 ◽  
Author(s):  
Jielong Zhou ◽  
Peifu Wu ◽  
Zhongping Xiong ◽  
Naiyong Liu ◽  
Ning Zhao ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Phylogenetic Analyses ◽  
Repetitive Sequences ◽  
Gene Families ◽  
Thaumetopoea Pityocampa ◽  
High Quality ◽  
Protein Coding ◽  
Peptidoglycan Recognition Protein ◽  
Recognition Protein ◽  
Chromosome Level

A high-quality genome is of significant value when seeking to control forest pests such as Dendrolimus kikuchii, a destructive member of the order Lepidoptera that is widespread in China. Herein, a high quality, chromosome-level reference genome for D. kikuchii based on Nanopore, Pacbio HiFi sequencing and the Hi-C capture system is presented. Overall, a final genome assembly of 705.51 Mb with contig and scaffold N50 values of 20.89 and 24.73 Mb, respectively, was obtained. Of these contigs, 95.89% had unique locations on 29 chromosomes. In silico analysis revealed that the genome contained 15,323 protein-coding genes and 63.44% repetitive sequences. Phylogenetic analyses indicated that D. kikuchii may diverged from the common ancestor of Thaumetopoea. Pityocampa, Thaumetopoea ni, Heliothis virescens, Hyphantria armigera, Spodoptera frugiperda, and Spodoptera litura approximately 122.05 million years ago. Many gene families were expanded in the D. kikuchii genome, particularly those of the Toll and IMD signaling pathway, which included 10 genes in peptidoglycan recognition protein, 19 genes in MODSP, and 11 genes in Toll. The findings from this study will help to elucidate the mechanisms involved in protection of D. kikuchii against foreign substances and pathogens, and may highlight a potential channel to control this pest.

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