Chromosome‐level genome assembly of <i>Dastarcus helophoroides</i> provides insights into <scp>CYP450</scp> genes expression upon insecticide exposure

Zhang, Zhengqing; Pei, Pei; Zhang, Meng; Li, Feifei; Tang, Guanghui

doi:10.1002/ps.7319

Cited by 5 publications

(4 citation statements)

References 73 publications

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“…We selected genomes of 11 ladybird beetle (Coccinellidae) species ( Adalia bipunctata (Wellcome Sanger Institute Tree of Life programme, et al 2022), Coccinella septempunctata (Crowley, et al 2021), Cryptolaemus montrouzieri (Li, Huang, et al 2021), Cynegetis impunctata (our unpublished data, NCBI accession: GCA_030704885.1), Halyzia sedecimguttata (Crowley, et al 2023), Harmonia axyridis (Boyes, et al 2021), Henosepilachna vigintioctomaculata (Zhu, et al 2023), Henosepilachna vigintioctopunctata (our unpublished data, NCBI accession: GCA_030704895.1), Micraspis discolor (our unpublished data, NCBI accession: GCA_030674115.1), Novius pumilus (Tang, et al 2022) and Propylea japonica (Zhang, et al 2020)), and one Coccinelloidea outgroup Dastarcus helophoroides (Zhang, et al 2023), as reference species (Table S1). The genomes were downloaded from the NCBI Genome database.…”

Section: Methodsmentioning

confidence: 90%

PhyloAln: a convenient reference-based tool to align sequences and high-throughput reads for phylogeny and evolution in the omic era

Huang,

Sun,

et al. 2024

Preprint

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The current trend in phylogenetic and evolutionary analyses predominantly relies on omic data. However, traditional methods typically involve intricate and time-consuming procedures prior to core analyses. These procedures encompass assembly from high-throughput reads, decontamination, gene prediction, homology search, orthology assignment, multiple alignment, and matrix trimming. Such processes significantly impede the efficiency of research when dealing with extensive datasets. In this study, we present PhyloAln, a convenient reference-based tool capable of directly aligning high-throughput reads or complete sequences with existing alignments as reference for phylogenetic and evolutionary analyses. Through testing with both simulated and authentic datasets, PhyloAln demonstrates consistently robust performance in terms of alignment completeness and identity when compared to other reference-based tools. Additionally, we validate the tool's adeptness in managing foreign and cross-contamination issues prevalent in sequencing data, which are often overlooked by other tools. Moreover, we showcase the broad applicability of PhyloAln by generating alignments and reconstructing phylogenies from transcriptomes of ladybird beetles, plastid genes of peppers, and ultraconserved elements of turtles. These results underscore the versatility of our tool. Leveraging these advantages, PhyloAln stands poised to expedite phylogenetic and evolutionary analyses in the omic era. The tool is accessible at https://github.com/huangyh45/PhyloAln.

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Section: Methodsmentioning

confidence: 90%

PhyloAln: a convenient reference-based tool to align sequences and high-throughput reads for phylogeny and evolution in the omic era

Huang,

Sun,

et al. 2024

Preprint

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“…Therefore, the trapping ability of lights for natural enemies of pests should also be considered in the monitoring and detection of insect pests (Bian et al, 2018). The ectoparasitoid beetle D. helophoroides is an important natural enemy of wood-boring insects and is widely used in controlling cerambycid beetles, including A. glabripennis and M. alternatus (Wang L. et al, 2023;Lyu et al, 2023;Zhang et al, 2023). Therefore, it is vital to explore the response mechanisms of ectoparasitoid beetles to light cue cognition at behavioral and molecular level.…”

Section: Discussionmentioning

confidence: 99%

“…All data have been uploaded in the NCBI Sequence Read Archive (SRA) database (http://www.ncbi.nlm.nih.gov/bioproject/987166). Afterward, the clean data were mapped to the reference genome of D. helophoroides using HISAT2 software (Zhang et al, 2023). All mapped genes were aligned into public databases using Diamond (v0.8.22, E-value 1e-5), including the NCBI non-redundant nucleotide sequences (NR), Swiss-Prot, gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), clusters of orthologous groups of proteins (KOG/COG/eggNOG), and protein family (Pfam) databases as described previously (Liu et al, 2023).…”

Section: Transcriptome Sequencing Assembly and Functional Annotationmentioning

confidence: 99%

Integrated behavior and transcriptomic analysis provide valuable insights into the response mechanisms of Dastarcus helophoroides Fairmaire to light exposure

Jiang,

Li,

Hai

et al. 2023

Front. Physiol.

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Light traps have been widely used to monitor and manage pest populations, but natural enemies are also influenced. The Dastarcus helophoroides Fairmaire is an important species of natural enemy for longhorn beetles. However, the molecular mechanism of D. helophoroides in response to light exposure is still scarce. Here, integrated behavioral, comparative transcriptome and weighted gene co-expression network analyses were applied to investigate gene expression profiles in the head of D. helophoroides at different light exposure time. The results showed that the phototactic response rates of adults were 1.67%–22.5% and females and males displayed a negative phototaxis under different light exposure [6.31 × 1018 (photos/m2/s)]; the trapping rates of female and male were influenced significantly by light exposure time, diel rhythm, and light wavelength in the behavioral data. Furthermore, transcriptome data showed that a total of 1,052 significantly differentially expressed genes (DEGs) were identified under different light exposure times relative to dark adaptation. Bioinformatics analyses revealed that the “ECM-receptor interaction,” “focal adhesion,” “PI3K-Akt signaling,” and “lysosome” pathways were significantly downregulated with increasing light exposure time. Furthermore, nine DEGs were identified as hub genes using WGCNA analysis. The results revealed molecular mechanism in negative phototactic behavior response of D. helophoroides under the light exposure with relative high intensity, and provided valuable insights into the underlying molecular response mechanism of nocturnal beetles to light stress.

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“…We selected genomes of 11 ladybird beetle (Coccinellidae) species ( Adalia bipunctata [ Wellcome Sanger Institute Tree of Life Programme et al 2022 ], Coccinella septempunctata [ Crowley et al 2021 ], Cryptolaemus montrouzieri [ Li et al 2021a ], Cynegetis impunctata [our unpublished data, NCBI accession: GCA_030704885.1], Halyzia sedecimguttata [ Crowley et al 2023 ], Harmonia axyridis [ Boyes et al 2021 ], Henosepilachna vigintioctomaculata [ Zhu et al 2023 ], Henosepilachna vigintioctopunctata [our unpublished data, NCBI accession: GCA_030704895.1], M. discolor [our unpublished data, NCBI accession: GCA_030674115.1], Novius pumilus [ Tang et al 2022 ], and Propylea japonica [ Zhang et al 2020 ]) and one Coccinelloidea outgroup Dastarcus helophoroides ( Zhang et al 2023 ), as reference species ( supplementary table S1, Supplementary Material online). The genomes were downloaded from the NCBI Genome database.…”

Section: Methodsmentioning

confidence: 99%

PhyloAln: A Convenient Reference-Based Tool to Align Sequences and High-Throughput Reads for Phylogeny and Evolution in the Omic Era

Huang,

Sun,

et al. 2024

Molecular Biology and Evolution

View full text Add to dashboard Cite

The current trend in phylogenetic and evolutionary analyses predominantly relies on omic data. However, prior to core analyses, traditional methods typically involve intricate and time-consuming procedures, including assembly from high-throughput reads, decontamination, gene prediction, homology search, orthology assignment, multiple sequence alignment, and matrix trimming. Such processes significantly impede the efficiency of research when dealing with extensive datasets. In this study, we develop PhyloAln, a convenient reference-based tool capable of directly aligning high-throughput reads or complete sequences with existing alignments as a reference for phylogenetic and evolutionary analyses. Through testing with simulated datasets of species spanning the tree of life, PhyloAln demonstrates consistently robust performance compared with other reference-based tools across different data types, sequencing technologies, coverages, and species, with percent completeness and identity at least 50 percentage points higher in the alignments. Additionally, we validate the efficacy of PhyloAln in removing a minimum of 90% foreign and 70% cross-contamination issues, which are prevalent in sequencing data but often overlooked by other tools. Moreover, we showcase the broad applicability of PhyloAln by generating alignments (completeness mostly larger than 80%, identity larger than 90%) and reconstructing robust phylogenies using real datasets of transcriptomes of ladybird beetles, plastid genes of peppers, or ultraconserved elements of turtles. With these advantages, PhyloAln is expected to facilitate phylogenetic and evolutionary analyses in the omic era. The tool is accessible at https://github.com/huangyh45/PhyloAln.

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Chromosome‐level genome assembly of Dastarcus helophoroides provides insights into CYP450 genes expression upon insecticide exposure

Cited by 5 publications

References 73 publications

PhyloAln: a convenient reference-based tool to align sequences and high-throughput reads for phylogeny and evolution in the omic era

PhyloAln: a convenient reference-based tool to align sequences and high-throughput reads for phylogeny and evolution in the omic era

Integrated behavior and transcriptomic analysis provide valuable insights into the response mechanisms of Dastarcus helophoroides Fairmaire to light exposure

PhyloAln: A Convenient Reference-Based Tool to Align Sequences and High-Throughput Reads for Phylogeny and Evolution in the Omic Era

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