A chromosome‐scale genome assembly of <i>Antheraea pernyi</i> (Saturniidae, Lepidoptera)

Duan, Jianping; Liu, Ying; Du, Jie; Duan, Erzhen; Lei, Yuyu; Liang, Shimei; Zhang, Xian; Zhao, Xin; Kan, Yunchao; Yao, Lunguang; Yang, Xinfeng; Zhang, Xingtan; Wu, Xiangwei

doi:10.1111/1755-0998.13199

Cited by 23 publications

(20 citation statements)

References 106 publications

(137 reference statements)

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“…Vulpes lagopus genomic DNA was extracted from blood samples of a healthy female Finnish blue fox from Changli Jindao Breeding Farm, Qinhuangdao, Hebei, China (Figure S1). To generate enough read data for genome assembly, both PacBio Sequel II and Illumina HiSeq X Ten platforms were used for sequencing (Duan et al, 2020; Guo et al, 2020; Liu, Xiao, et al, 2019; Liu et al, 2019; Zhou et al, 2019; Wei et al, 2020; Yang et al, 2020). The libraries with an average insert sizes of 20 kb were constructed using SMRT bell Template Prep Kits and sequenced using a PacBio Sequel II platform.…”

Section: Methodsmentioning

confidence: 99%

Chromosome‐level genome assembly of the Arctic fox (Vulpes lagopus) using PacBio sequencing and Hi‐C technology

Peng

Liu

et al. 2021

Molecular Ecology Resources

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The Arctic fox (Vulpes lagopus) is the only fox species occurring in the Arctic and has adapted to its extreme climatic conditions. Currently, the molecular basis of its adaptation to the extreme climate has not been characterized. Here, we applied PacBio sequencing and chromosome structure capture technique to assemble the first V. lagopus genome assembly, which is assembled into chromosome fragments. The genome assembly has a total length of 2.345 Gb with a contig N50 of 31.848 Mb and a scaffold N50 of 131.537 Mb, consisting of 25 pseudochromosomal scaffolds. The V. lagopus genome had approximately 32.33% repeat sequences. In total, 21,278 protein-coding genes were predicted, of which 99.14% were functionally annotated.Compared with 12 other mammals, V. lagopus was most closely related to V. Vulpes with an estimated divergence time of ~7.1 Ma. The expanded gene families and positively selected genes potentially play roles in the adaptation of V. lagopus to Arctic extreme environment. This high-quality assembled genome will not only promote future studies of genetic diversity and evolution in foxes and other canids but also provide important resources for conservation of Arctic species.

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Section: Methodsmentioning

confidence: 99%

Chromosome‐level genome assembly of the Arctic fox (Vulpes lagopus) using PacBio sequencing and Hi‐C technology

Peng

Liu

et al. 2021

Molecular Ecology Resources

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“…A total of 3 μg genomic DNA was extracted from the whole body of a female adult, using the standard phenol/ chloroform extraction method (Duan et al, 2020). Whole-genome shotgun sequencing was performed using the PacBio and BGI2000 sequencing platforms.…”

Section: Sample Collection and Sequencingmentioning

confidence: 99%

“…A paired-end library with a 350 bp insert was also constructed and sequenced. The sequencing depth from the BGI2000 platform was about ×108.35 considering the predicted genome size of 1.2 Gb according to the k-mer method (Duan et al, 2020).…”

Section: Sample Collection and Sequencingmentioning

confidence: 99%

A chromosome‐level genome assembly of Paracymoriza distinctalis (Lepidoptera: Crambidae: Acentropinae)

Chen

Zhu

Wang

et al. 2022

Arch Insect Biochem Physiol

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Paracymoriza distinctalis is a semiaquatic lepidopteran insect, which is of great value for studying the differentiation of the Pyraloidea superfamily. However, the understanding of heredity, evolution, and functional genomics of P. distinctalis are limited by few genomewide resources. Here, we applied PacBio sequencing and the chromosome capture technique to assemble the first P. distinctalis genome from a single female individual. The genome size is 1.2 Gb with 32 chromosomes and the N50 is 38.91 Mb. Approximately 576.37 Mb, accounting for 48.93% of the genome, was identified as repeats. The genome comprises 39,003 protein-coding genes, 66.56% of which were functionally annotated. Comparative genomics analysis suggested that the common ancestor of P. distinctalis and Chilo suppressalis lived ~83.5 million years ago. This chromosome-level genome assembly work is not only conducive to the understanding of P. distinctalis, but also may promote the study of the genomes of other lepidopteran species.

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“…Clean reads were generated by removing adapters and lowquality reads from raw data using Trimmomatic v0.36 (Bolger et al, 2014). All clean reads were aligned to the reference genome of A. pernyi (Duan et al, 2020) using HISAT2 v2.2.1 (Zhang et al, 2021. DEGs were identified by pairwise comparisons at adjacent time points (1 dpi versus 0 dpi, 3 dpi versus 1 dpi, 6 dpi versus 3 dpi, and 9 dpi versus 6 dpi) using the DESeq2 package in R (Love et al, 2014).…”

Section: Identification Of Differential Expressed Genesmentioning

confidence: 99%

Pupal Diapause Termination and Transcriptional Response of Antheraea pernyi (Lepidoptera: Saturniidae) Triggered by 20-Hydroxyecdysone

Zhao

Wang

et al. 2022

Front. Physiol.

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The pupal diapause of univoltine Antheraea pernyi hampers sericultural and biotechnological applications, which requires a high eclosion incidence after artificial diapause termination to ensure production of enough eggs. The effect of pupal diapause termination using 20-hydroxyecdysone (20E) on the eclosion incidence has not been well-documented in A. pernyi. Here, the dosage of injected 20E was optimized to efficiently terminate pupal diapause of A. pernyi, showing that inappropriate dosage of 20E can cause pupal lethality and a low eclosion incidence. The optimal ratio of 20E to 1-month-old pupae was determined as 6 μg/g. Morphological changes showed visible tissue dissociation at 3 days post-injection (dpi) and eye pigmentation at 5 dpi. Comprehensive transcriptome analysis identified 1,355/1,592, 494/203, 584/297, and 1,238/1,404 upregulated and downregulated genes at 1, 3, 6, and 9 dpi, respectively. The 117 genes enriched in the information processing pathways of “signal transduction” and “signaling molecules and interaction” were upregulated at 1 and 3 dpi, including the genes involved in FOXO signaling pathway. One chitinase, three trehalase, and five cathepsin genes related to energy metabolism and tissue dissociation showed high expression levels at the early stage, which were different from the upregulated expression of four other chitinase genes at the later stage. Simultaneously, the expression of several genes involved in molting hormone biosynthesis was also activated between 1 and 3 dpi. qRT-PCR further verified the expression patterns of two ecdysone receptor genes (EcRB1 and USP) and four downstream response genes (E93, Br-C, βFTZ-F1, and cathepsin L) at the pupal and pharate stages, respectively. Taken together, these genes serve as a resource for unraveling the mechanism underlying pupal-adult transition; these findings facilitate rearing of larvae more than once a year and biotechnological development through efficient termination of pupal diapause in A. pernyi in approximately half a month.

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A chromosome‐scale genome assembly of Antheraea pernyi (Saturniidae, Lepidoptera)

Cited by 23 publications

References 106 publications

Chromosome‐level genome assembly of the Arctic fox (Vulpes lagopus) using PacBio sequencing and Hi‐C technology

Chromosome‐level genome assembly of the Arctic fox (Vulpes lagopus) using PacBio sequencing and Hi‐C technology

A chromosome‐level genome assembly of Paracymoriza distinctalis (Lepidoptera: Crambidae: Acentropinae)

Pupal Diapause Termination and Transcriptional Response of Antheraea pernyi (Lepidoptera: Saturniidae) Triggered by 20-Hydroxyecdysone

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