High-quality genome assembly of Pseudocercospora ulei the main threat to natural rubber trees.
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ABSTRACT:
SUBMITTER: Gonzalez-Sayer S
PROVIDER: S-EPMC8762716 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:IntroductionUnderstanding the diversity and assembly of the microbiomes of plant roots is crucial to manipulate them for sustainable ecosystem functioning. However, there are few reports about microbial communities at a continuous fine-scale of roots for rubber trees.MethodsWe investigate the structure, diversity, and assembly of bacterial and fungal communities for the soil (non-rhizosphere), rhizosphere, and rhizoplane as well as root endosphere of rubber trees using the amplicon sequencing of 16S ribosomal ribonucleic acid (rRNA) and Internally Transcribed Spacer (ITS) genes.ResultsWe show that 18.69% of bacterial and 20.20% of fungal operational taxonomic units (OTUs) in the rhizoplane derived from the endosphere and 20.64% of bacterial and 20.60% of fungal OTUs from the soil. This suggests that the rhizoplane microbial community was a mixed community of soil and endosphere microbial communities and that microorganisms can disperse bidirectionally across different compartments of the plant root. On the other hand, in the absence of an enrichment or depletion of core bacterial and fungal OTUs in the rhizosphere, little differences in microbial composition as well as a more shared microbial network structure between the soil and the rhizosphere support the theory that the rhizosphere microbial community is a subset of the soil community. A large number of functional genes (such as nitrogen fixation and nitrite reduction) and more enriched core OTUs as well as a less stable but more complex network structure were observed in the rhizoplane of rubber tree roots. This demonstrated that the rhizoplane is the most active root compartment and a hotspot for plant-soil-environment interactions. In addition, bacterial and fungal communities in the rhizoplane were more stochastic compared to the rhizosphere and soil.DiscussionOur study expands our understanding of root-associated microbial community structure and function, which may provide the scientific basis for sustainable agriculture through biological process management.
| S-EPMC10102524 | biostudies-literature
Project description:We report the acquisition of a high-quality haploid chromosome-scale genome assembly for the first time in a tree species, Eucommia ulmoides, which is known for its rubber biosynthesis and medicinal applications. The assembly was obtained by applying PacBio and Hi-C technologies to a haploid that we specifically generated. Compared to the initial genome release, this one has significantly improved assembly quality. The scaffold N50 (53.15 MB) increased 28-fold, and the repetitive sequence content (520 Mb) increased by 158.24 Mb, whereas the number of gaps decreased from 104,772 to 128. A total of 92.87% of the 26,001 predicted protein-coding genes identified with multiple strategies were anchored to the 17 chromosomes. A new whole-genome duplication event was superimposed on the earlier γ paleohexaploidization event, and the expansion of long terminal repeats contributed greatly to the evolution of the genome. The more primitive rubber biosynthesis of this species, as opposed to that in Hevea brasiliensis, relies on the methylerythritol-phosphate pathway rather than the mevalonate pathway to synthesize isoprenyl diphosphate, as the MEP pathway operates predominantly in trans-polyisoprene-containing leaves and central peels. Chlorogenic acid biosynthesis pathway enzymes were preferentially expressed in leaves rather than in bark. This assembly with higher sequence contiguity can foster not only studies on genome structure and evolution, gene mapping, epigenetic analysis and functional genomics but also efforts to improve E. ulmoides for industrial and medical uses through genetic engineering.
| S-EPMC7603500 | biostudies-literature
Project description:Earthworms enrich the soil and protect the health of their ecological environment. Previous studies on these invertebrates determined their protein content, hormone secretions, medicinal value, and ecological habits, but their whole genomic sequence remains incomplete. We performed whole genome sequencing of Metaphire vulgaris (Chen, 1930), which belongs to the genus Metaphire of the family Megascolecidae. The genome assembly was 729 Mb, with a N50 contig size of 4.2 Mb. In total, 559 contigs were anchored to 41 chromosomes according to the results of Hi-C (High-throughput Chromosome Conformation Capture) technology, which was confirmed by karyological analysis. A comparison of the genomic sequences and genes indicated that there was a whole-genome duplication in M. vulgaris followed by several chromosome fusion events. Hox genes and lumbrokinase genes were identified as partial clusters surrounding the genome. Our high-quality genome assembly of M. vulgaris will provide valuable information for gene function and evolutionary studies in earthworms.
| S-EPMC7666815 | biostudies-literature
Project description:BackgroundThe channel catfish (Ictalurus punctatus), a species native to North America, is one of the most important commercial freshwater fish in the world, especially in the United States' aquaculture industry. Since its introduction into China in 1984, both cultivation area and yield of this species have been dramatically increased such that China is now the leading producer of channel catfish. To aid genomic research in this species, data sets such as genetic linkage groups, long-insert libraries, physical maps, bacterial artificial clones (BAC) end sequences (BES), transcriptome assemblies, and reference genome sequences have been generated. Here, using diverse assembly methods, we provide a comparable high-quality genome assembly for a channel catfish from a breeding stock inbred in China for more than three generations, which was originally imported to China from North America.FindingsApproximately 201.6 gigabases (Gb) of genome reads were sequenced by the Illumina HiSeq 2000 platform. Subsequently, we generated high quality, cost-effective and easily assembled sequences of the channel catfish genome with a scaffold N50 of 7.2 Mb and 95.6 % completeness. We also predicted that the channel catfish genome contains 21,556 protein-coding genes and 275.3 Mb (megabase pairs) of repetitive sequences.ConclusionsWe report a high-quality genome assembly of the channel catfish, which is comparable to a recent report of the "Coco" channel catfish. These generated genome data could be used as an initial platform for molecular breeding to obtain novel catfish varieties using genomic approaches.
| S-EPMC4994213 | biostudies-literature
Project description:Diospyros oleifera Cheng, of the family Ebenaceae, is an economically important tree. Phylogenetic analyses indicate that D. oleifera is closely related to Diospyros kaki Thunb. and could be used as a model plant for studies of D. kaki. Therefore, development of genomic resources of D. oleifera will facilitate auxiliary assembly of the hexaploid persimmon genome and elucidate the molecular mechanisms of important traits. The D. oleifera genome was assembled with 443.6 Gb of raw reads using the Pacific Bioscience Sequel and Illumina HiSeq X Ten platforms. The final draft genome was ∼812.3 Mb and had a high level of continuity with N50 of 3.36 Mb. Fifteen scaffolds corresponding to the 15 chromosomes were assembled to a final size of 721.5 Mb using 332 scaffolds, accounting for 88.81% of the genome. Repeat sequences accounted for 54.8% of the genome. By de novo sequencing and analysis of homology with other plant species, 30,530 protein-coding genes with an average transcript size of 7,105.40 bp were annotated; of these, 28,580 protein-coding genes (93.61%) had conserved functional motifs or terms. In addition, 171 candidate genes involved in tannin synthesis and deastringency in persimmon were identified; of these chalcone synthase (CHS) genes were expanded in the D. oleifera genome compared with Diospyros lotus, Camellia sinensis, and Vitis vinifera. Moreover, 186 positively selected genes were identified, including chalcone isomerase (CHI) gene, a key enzyme in the flavonoid-anthocyanin pathway. Phylogenetic tree analysis indicated that the split of D. oleifera and D. lotus likely occurred 9.0 million years ago. In addition to the ancient γ event, a second whole-genome duplication event occurred in D. oleifera and D. lotus. We generated a high-quality chromosome-level draft genome for D. oleifera, which will facilitate assembly of the hexaploid persimmon genome and further studies of major economic traits in the genus Diospyros.
| S-EPMC6964648 | biostudies-literature
Project description:Closing gaps in draft genome assemblies can be costly and time-consuming, and published genomes are therefore often left 'unfinished.' Here we show that genome-wide chromosome conformation capture (3C) data can be used to overcome these limitations, and present a computational approach rooted in polymer physics that determines the most likely genome structure using chromosomal contact data. This algorithm--named GRAAL--generates high-quality assemblies of genomes in which repeated and duplicated regions are accurately represented and offers a direct probabilistic interpretation of the computed structures. We first validated GRAAL on the reference genome of Saccharomyces cerevisiae, as well as other yeast isolates, where GRAAL recovered both known and unknown complex chromosomal structural variations. We then applied GRAAL to the finishing of the assembly of Trichoderma reesei and obtained a number of contigs congruent with the know karyotype of this species. Finally, we showed that GRAAL can accurately reconstruct human chromosomes from either fragments generated in silico or contigs obtained from de novo assembly. In all these applications, GRAAL compared favourably to recently published programmes implementing related approaches.
| S-EPMC4284522 | biostudies-literature
Project description:ObjectivesLasiodiplodia pseudotheobromae is an important fungal pathogen associated with die-back, canker and shoot blight in many plant hosts with a wide geographic distribution. The aim of our study was to provide high-quality genome assemblies and sequence annotation resources of L. pseudotheobromae, to facilitate future studies on the systematics, population genetics and genomics of the fungal pathogen L. pseudotheobromae.Data descriptionHigh-quality genomes of five L. pseudotheobromae isolates were sequenced based on Oxford Nanopore technology (ONT) and Illumina HiSeq sequencing platform. The total size of each assembly ranged from 43 Mb to 43.86 Mb and over 11,000 protein-coding genes were predicted from each genome. The proteins of predicted genes were annotated using multiple public databases, among the annotated protein-coding genes, more than 4,300 genes were predicted as potential virulence genes by the Pathogen Host Interactions (PHI) database. Moreover, the genome comparative analysis among L. pseudotheobromae and other closely related species revealed that 7,408 gene clusters were shared among them and 152 gene clusters unique to L. pseudotheobromae. This genome and associated datasets provided here will serve as a useful resource for further analyses of this fungal pathogen species.
| S-EPMC10759541 | biostudies-literature
Project description:The decreasing costs of next-generation sequencing and the improvements in de novo sequence assemblers have made it possible to obtain reference genomes for most eukaryotes, including minor crops such as the blueberry (Vaccinium corymbosum). Nevertheless, these genomes are at various levels of completeness and few have been anchored to chromosome scale and/or are haplotype-phased. We highlight the impact of a high-quality genome assembly for plant breeding and genetic research by showing how it affects our understanding of the genetic architecture of important traits and aids marker selection and candidate gene detection. We compared the results of genome-wide association studies and genomic selection that were already published using a blueberry draft genome as reference with the results using the recent released chromosome-scale and haplotype-phased blueberry genome. We believe that the benefits shown herein reinforce the importance of genome assembly projects for other non-model species.
| S-EPMC6558523 | biostudies-literature
Project description:Sweet sorghum (Sorghum dochna) is a high-quality bio-energy crop that also serves as food for humans and animals. However, there is little information on the genomic characteristics of S. dochna. In this study, we presented a high-quality assembly of S. dochna with PacBio long reads, Illumina short reads, high-throughput chromosome capture technology (Hi-C) sequencing data, gene annotation, and a comparative genome analysis. The results showed that the genome of S. dochna was assembled to 777 Mb with a contig N50 of 553.47 kb and a scaffold N50 of 727.11 kb. In addition, the gene annotation predicted 37,971 genes and 39,937 transcripts in the genome of S. dochna. A Venn analysis revealed a set of 7,988 common gene annotations by integrating five databases. A Cafe software analysis showed that 191 gene families were significantly expanded, while 3,794 were significantly contracted in S. dochna. A GO enrichment analysis showed that the expanded gene families were primarily clustered in the metabolic process, DNA reconstruction, and DNA binding among others. The high-quality genome map constructed in this study provides a biological basis for the future analysis of the biological characteristics of S. dochna, which is crucial for its breeding.
| S-EPMC9412107 | biostudies-literature
Project description:Monocercomonoides exilis is considered the first known eukaryote to completely lack mitochondria. This conclusion is based primarily on a genomic and transcriptomic study which failed to identify any mitochondrial hallmark proteins. However, the available genome assembly has limited contiguity and around 1.5 % of the genome sequence is represented by unknown bases. To improve the contiguity, we re-sequenced the genome and transcriptome of M. exilis using Oxford Nanopore Technology (ONT). The resulting draft genome is assembled in 101 contigs with an N50 value of 1.38 Mbp, almost 20 times higher than the previously published assembly. Using a newly generated ONT transcriptome, we further improve the gene prediction and add high quality untranslated region (UTR) annotations, in which we identify two putative polyadenylation signals present in the 3'UTR regions and characterise the Kozak sequence in the 5'UTR regions. All these improvements are reflected by higher BUSCO genome completeness values. Regardless of an overall more complete genome assembly without missing bases and a better gene prediction, we still failed to identify any mitochondrial hallmark genes, thus further supporting the hypothesis on the absence of mitochondrion.
| S-EPMC8767320 | biostudies-literature