scholarly journals Hybrid Genome Assembly of a Regenerative Chordate

2020 ◽  
Vol 34 (S1) ◽  
pp. 1-1
Author(s):  
Jack Thomas Sumner ◽  
Sarah Wax ◽  
Cassidy Andrasz ◽  
Paul Anderson ◽  
Elena Keeling ◽  
...  
2019 ◽  
Author(s):  
Hanno Schmidt ◽  
Ann-Marie Waldvogel ◽  
Sören Lukas Hellmann ◽  
Barbara Feldmeyer ◽  
Thomas Hankeln ◽  
...  

AbstractBackgroundChironomus riparius is of great importance as a study species in various fields like ecotoxicology, molecular genetics, developmental biology and ecology. However, only a fragmented draft genome exists to date, hindering the recent rush of population genomic studies in this species.FindingsMaking use of 50 NGS datasets, we present a hybrid genome assembly from short and long sequence reads that make C. riparius’ genome one of the most contiguous Dipteran genomes published, the first complete mitochondrial genome of the species and the respective recombination rate as one of the first insect recombination rates at all.ConclusionsThe genome and associated resources will be highly valuable to the broad community working with dipterans in general and chironomids in detail. The estimated recombination rate will help evolutionary biologist gain a better understanding of commonalities and differences of genomic patterns in insects.


2021 ◽  
Author(s):  
Sabrina Simon ◽  
Thijmen Breeschoten ◽  
Hans J Jansen ◽  
Ron P Dirks ◽  
M. Eric Schranz ◽  
...  

Background: The genus Spodoptera (Lepidoptera: Noctuidae) includes some of the most infamous insect pests of cultivated plants including Spodoptera frugiperda, Spodoptera litura and Spodoptera exigua. To effectively develop targeted pest control strategies for diverse Spodoptera species, genomic resources are highly desired. To this aim, we provide the genome assembly and developmental transcriptome comprising all major life stages of S. exigua, the beet armyworm. Spodoptera exigua is a polyphagous herbivore that can feed from > 130 host plants including several economically important crops. Results: The 419 Mb beet armyworm genome was sequenced from a female S. exigua pupa. Using a hybrid genome sequencing approach (Nanopore long read data and Illumina short read), a high-quality genome assembly was achieved (N50=1.1 Mb). An official gene set (OGS, 18,477 transcripts) was generated by automatic annotation and by using transcriptomic RNA-seq data sets of 18 S. exigua samples as supporting evidence. In-depth analyses of developmental stage-specific expression in combination with gene tree analyses of identified homologous genes across Lepidoptera genomes revealed potential Spodoptera-specific genes of interest such as mg7 and REPAT46 upregulated during 1st and 3rd instar larval stages for targeted pest-outbreak management. Conclusions: The beet armyworm genome sequence and developmental transcriptome covering all major developmental stages provides critical insights into the biology of this devastating polyphagous insect pest species with a worldwide distribution. In addition, comparative genomic analyses across Lepidoptera significantly advance our knowledge to further control other invasive Spodoptera species and reveals potential lineage-specific target genes for pest control strategies.


2020 ◽  
Vol Volume 13 ◽  
pp. 199-206 ◽  
Author(s):  
Zhi Ruan ◽  
Jianyong Wu ◽  
Hangfei Chen ◽  
Mohamed S Draz ◽  
Juan Xu ◽  
...  

2019 ◽  
Vol 6 (1) ◽  
Author(s):  
Mykola Kadobianskyi ◽  
Lisanne Schulze ◽  
Markus Schuelke ◽  
Benjamin Judkewitz

PLoS ONE ◽  
2018 ◽  
Vol 13 (1) ◽  
pp. e0189993 ◽  
Author(s):  
Alessandro Passera ◽  
Luca Marcolungo ◽  
Paola Casati ◽  
Milena Brasca ◽  
Fabio Quaglino ◽  
...  

Author(s):  
LONG PENG ◽  
Xiaoliang Shan ◽  
Yuchen Wang ◽  
Francis Martin ◽  
Rytas Vilgalys ◽  
...  

Clitopilus hobsonii (Entolomataceae, Agaricales, Basidiomycetes) is a common soil saprotroph. There is also evidence that C. hobsonii can act as a root endophyte benefiting tree growth. Here, we report the genome assembly of C. hobsonii QYL-10 isolated from ectomycorrhizal root tips of Quercus lyrata. The genome size is 36.93 Mb, consisting of 13 contigs (N50=3.3 Mb) with 49.2% GC-content. Of them, 10 contigs approached the length of intact chromosomes, and 3 had telomeres at one end only. BUSCO analysis reported a completeness score of 98.4% using the Basidiomycota_odb10. Combining ab-initio, RNA-seq data, and homology-based predictions, we identified 12,710 protein-coding genes. Approximately, 1.43 Mb of Transposable elements (TEs) (3.88% of the assembly), 36 secondary metabolite biosynthetic gene clusters and 361 genes encoding putative CAZymes were identified. This genomic resource will allow functional studies aimed to characterize the symbiotic interactions between C. hobsonii and its host trees, but will also provide a valuable foundation for further research on comparative genomics of the Entolomataceae.


2020 ◽  
Vol 10 (4) ◽  
pp. 1151-1157 ◽  
Author(s):  
Hanno Schmidt ◽  
Sören Lukas Hellmann ◽  
Ann-Marie Waldvogel ◽  
Barbara Feldmeyer ◽  
Thomas Hankeln ◽  
...  

Chironomus riparius is of great importance as a study species in various fields like ecotoxicology, molecular genetics, developmental biology and ecology. However, only a fragmented draft genome exists to date, hindering the recent rush of population genomic studies in this species. Making use of 50 NGS datasets, we present a hybrid genome assembly from short and long sequence reads that make C. riparius’ genome one of the most contiguous Dipteran genomes published, the first complete mitochondrial genome of the species, and the respective recombination rate among the first insect recombination rates at all. The genome assembly and associated resources will be highly valuable to the broad community working with dipterans in general and chironomids in particular. The estimated recombination rate will help evolutionary biologists gaining a better understanding of commonalities and differences of genomic patterns in insects.


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