Chromosome‐level genome assembly for the horned‐gall aphid provides insights into interactions between gall‐making insect and its host plant

Wei, Hongyuan; Ye, Yuxuan; Huang, Hai‐Jian; Chen, Ming‐Shun; Yang, Zixiang; Xiao-ming, Chen; Zhang, Chuan‐Xi

doi:10.1002/ece3.8815

Cited by 12 publications

(11 citation statements)

References 100 publications

(135 reference statements)

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“…RNA was sequenced using Illumina’s high throughput sequencing platform NovaSeq 6,000 (Illumina, Inc. CA, United States). In order to obtain putative transcripts, clean reads were mapped to S. chinensis genome assembly using Hisat2 (version 2.1.0.5) ( Kim et al, 2015 ; Wei et al, 2022 ). The low-quality alignments were filtered with Sequence Alignment/Map tools (SAMtools) ( Li et al, 2009 ).…”

Section: Methodsmentioning

confidence: 99%

“…Transcripts per million (TPM) expression values were calculated using featureCounts ( Yang et al, 2014 ) and StringTie ( Pertea et al, 2015 ) for transcripts. Transcriptomes of other generations of S. chinensis , autumn migrant, fundatrix, fundatrigenia, overwinter nymph, female and spring migrant (sexuparae) came from the previous research ( Wei et al, 2022 ).…”

Section: Methodsmentioning

confidence: 99%

“…And related to this, what are the energy and material resources used instead? Tackling these questions with transcriptomics is now possible since the genome of S. chinensis has been sequenced recently ( Wei et al, 2022 ). The weighted gene co-expression network analysis (WGCNA) is a powerful method to identify co-expressed groups of genes from large heterogeneous messenger RNA expression data sets ( Clarke et al, 2013 ).…”

Section: Introductionmentioning

confidence: 99%

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Candidate genes potentially involved in molting and body size reduction in the male of the horned gall aphid, Schlechtendalia chinensis

Wei

Xu²,

Gao³

et al. 2023

Front. Physiol.

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In general, insects grow (increase in body size) through molting. To the opposite, the body size of the males of the horned gall aphid, Schlechtendalia chinensis, gets smaller after molting and as they age. To understand the molecular bases of this rare phenomenon, transcriptomes were generated from 1–5 days old male and the data were analyzed via a weighted gene co-expression network analysis (WGCNA). A total of 15 partitioned modules with different topological overlaps were obtained, and four modules were identified as highly significant for male body length (p < 0.05). Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis suggested that a portion of genes in the four modules are likely involved in autophagy and apoptosis. In addition, a total of 40 hub genes were obtained in the four modules, and among them eight genes were highly expressed in males compared to individuals of other generations of S. chinensis. These eight genes were associated with autophagy and apoptosis. Our results reveal the unique negative growth phenomenon in male S. chinensis after molting, and also suggest that the male S. chinensis with no ability to feed probably decompose their own substances via autophagy and apoptosis to provide energy for life activities such as germ cell development.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Candidate genes potentially involved in molting and body size reduction in the male of the horned gall aphid, Schlechtendalia chinensis

Wei

Xu²,

Gao³

et al. 2023

Front. Physiol.

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“…Until recently, no parthenogenetic dipteran had its genome sequenced [64], however, it was possible to make inferences about multiple possible molecular mechanisms from changes in many sequenced obligate parthenogenetic genomes (of varying quality) including: springtail [69], stick insects [70], aphids [71][72][73], ant [74], honeybee [75], wasps [76][77][78][79], mite [80], tick [81], crayfish [82,83], water flea [84,85], seed shrimps [86], nematodes [87][88][89][90][91][92][93][94], rotifers [95,96], tardigrades [97][98][99], snail [100], and fish [101]. We will discuss some of these selected genomes below and a detailed investigation into many of the above genomes can be found elsewhere [102].…”

Section: Genetics and Genomics Of Parthenogenesismentioning

confidence: 99%

Parthenogenesis in dipterans: a genetic perspective

Sperling

Glover

2023

Proc. R. Soc. B.

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Parthenogenesis has been documented in almost every phylum of animals, and yet this phenomenon is largely understudied. It has particular importance in dipterans since some parthenogenetic species are also disease vectors and agricultural pests. Here, we present a catalogue of parthenogenetic dipterans, although it is likely that many more remain to be identified, and we discuss how their developmental biology and interactions with diverse environments may be linked to different types of parthenogenetic reproduction. We discuss how the advances in genetics and genomics have identified chromosomal loci associated with parthenogenesis. In particular, a polygenic cause of facultative parthenogenesis has been uncovered in Drosophila mercatorum, allowing the corresponding genetic variants to be tested for their ability to promote parthenogenesis in another species, Drosophila melanogaster . This study probably identifies just one of many routes that could be followed in the evolution of parthenogenesis. We attempt to account for why the phenomenon has evolved so many times in the dipteran order and why facultative parthenogenesis appears particularly prevalent. We also discuss the significance of coarse genomic changes, including non-disjunction, aneuploidy, and polyploidy and how, together with changes to specific genes, these might relate to both facultative and obligate parthenogenesis in dipterans and other parthenogenetic animals.

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“…Gall-forming aphids induce galls on the woody host plant and live inside the gall for several generations. The complex life cycles and host specificity of gall-forming aphids make them intriguing models for studying the evolution of insect-plant interactions [ 7 – 9 ].…”

Section: Introductionmentioning

confidence: 99%

A chromosome-level genome assembly of the Rhus gall aphid Schlechtendalia chinensis provides insight into the endogenization of Parvovirus-like DNA sequences

Ahmad,

von Dohlen,

Ren

2024

BMC Genomics

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The Rhus gall aphid, Schlechtendalia chinensis, feeds on its primary host plant Rhus chinensis to induce galls, which have economic importance in medicines and the food industry. Rhus gall aphids have a unique life cycle and are economically beneficial but there is huge gap in genomic information about this group of aphids. Schlechtendalia chinensis induces rich-tannin galls on its host plant and is emerging as a model organism for both commercial applications and applied research in the context of gall production by insects. Here, we generated a high-quality chromosome-level assembly for the S. chinensis genome, enabling the comparison between S. chinensis and non-galling aphids. The final genome assembly is 344.59 Mb with 91.71% of the assembled sequences anchored into 13 chromosomes. We predicted 15,013 genes, of which 14,582 (97.13%) coding genes were annotated, and 99% of the predicted genes were anchored to the 13 chromosomes. This assembly reveals the endogenization of parvovirus-related DNA sequences (PRDs) in the S. chinensis genome, which could play a role in environmental adaptations. We demonstrated the characterization and classification of cytochrome P450s in the genome assembly, which are functionally crucial for sap-feeding insects and have roles in detoxification and insecticide resistance. This genome assembly also revealed the whole genome duplication events in S. chinensis, which can be considered in comparative evolutionary analysis. Our work represents a reference genome for gall-forming aphids that could be used for comparative genomic studies between galling and non-galling aphids and provides the first insight into the endogenization of PRDs in the genome of galling aphids. It also provides novel genetic information for future research on gall-formation and insect-plant interactions.

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Chromosome‐level genome assembly for the horned‐gall aphid provides insights into interactions between gall‐making insect and its host plant

Abstract: This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

Cited by 12 publications

References 100 publications

Candidate genes potentially involved in molting and body size reduction in the male of the horned gall aphid, Schlechtendalia chinensis

Candidate genes potentially involved in molting and body size reduction in the male of the horned gall aphid, Schlechtendalia chinensis

Parthenogenesis in dipterans: a genetic perspective

A chromosome-level genome assembly of the Rhus gall aphid Schlechtendalia chinensis provides insight into the endogenization of Parvovirus-like DNA sequences

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