Elucidating the ecophysiology of soybean pod-sucking stinkbug Riptortus pedestris (Hemiptera: Alydidae) based on de novo genome assembly and transcriptome analysis

Chade Li; Wenyan Nong; Delbert Almerick T Boncan; Wai Lok So; Ho Yin Yip; Thomas Swale; Qi Jia; Ignacio G Vicentin; Gyuhwa Chung; William G Bendena; Jacky C K Ngo; Ting Fung Chan; Hon-Ming Lam; Jerome H L Hui

doi:10.1186/s12864-024-10232-2

Elucidating the ecophysiology of soybean pod-sucking stinkbug Riptortus pedestris (Hemiptera: Alydidae) based on de novo genome assembly and transcriptome analysis

BMC Genomics. 2024 Apr 2;25(1):327. doi: 10.1186/s12864-024-10232-2.

Authors

Chade Li^#^{1

2}, Wenyan Nong^#^{1

2}, Delbert Almerick T Boncan^#¹, Wai Lok So^{1

2}, Ho Yin Yip^{1

2}, Thomas Swale³, Qi Jia⁴, Ignacio G Vicentin⁵, Gyuhwa Chung⁶, William G Bendena⁷, Jacky C K Ngo⁸, Ting Fung Chan^{9

10}, Hon-Ming Lam^{11

12}, Jerome H L Hui^{13

14

15}

Affiliations

¹ Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, HKSAR, China.
² Simon F.S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Shat-in, HKSAR, China.
³ Dovetail Genomics, Scotts Valley, CA, USA.
⁴ Key Laboratory for Genetics Breeding and Multiple Utilization of Crops, Ministry of Education/College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, PR China.
⁵ Instituto Nacional de Tecnologia Agropecuaria, Avenida Rivadavia, Ciudad de Buenos, 1439, Argentina.
⁶ Department of Biotechnology, Chonnam National University, Yeosu, 59626, Korea.
⁷ Department of Biology, Queen's University, 116 Barrie St, Kingston, ON K7L 3N6, Canada.
⁸ Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, HKSAR, China. jackyngo@cuhk.edu.hk.
⁹ Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, HKSAR, China. tf.chan@cuhk.edu.hk.
¹⁰ Institute of Environment, Institute of Energy and Sustainability, The Chinese University of Hong Kong, Shatin, HKSAR, China. tf.chan@cuhk.edu.hk.
¹¹ Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, HKSAR, China. honming@cuhk.edu.hk.
¹² Institute of Environment, Institute of Energy and Sustainability, The Chinese University of Hong Kong, Shatin, HKSAR, China. honming@cuhk.edu.hk.
¹³ Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, HKSAR, China. jeromehui@cuhk.edu.hk.
¹⁴ Simon F.S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Shat-in, HKSAR, China. jeromehui@cuhk.edu.hk.
¹⁵ Institute of Environment, Institute of Energy and Sustainability, The Chinese University of Hong Kong, Shatin, HKSAR, China. jeromehui@cuhk.edu.hk.

^# Contributed equally.

Abstract

Food security is important for the ever-growing global population. Soybean, Glycine max (L.) Merr., is cultivated worldwide providing a key source of food, protein and oil. Hence, it is imperative to maintain or to increase its yield under different conditions including challenges caused by abiotic and biotic stresses. In recent years, the soybean pod-sucking stinkbug Riptortus pedestris has emerged as an important agricultural insect pest in East, South and Southeast Asia. Here, we present a genomics resource for R. pedestris including its genome assembly, messenger RNA (mRNA) and microRNA (miRNA) transcriptomes at different developmental stages and from different organs. As insect hormone biosynthesis genes (genes involved in metamorphosis) and their regulators such as miRNAs are potential targets for pest control, we analyzed the sesquiterpenoid (juvenile) and ecdysteroid (molting) hormone biosynthesis pathway genes including their miRNAs and relevant neuropeptides. Temporal gene expression changes of these insect hormone biosynthesis pathways were observed at different developmental stages. Similarly, a diet-specific response in gene expression was also observed in both head and salivary glands. Furthermore, we observed that microRNAs (bantam, miR-14, miR-316, and miR-263) of R. pedestris fed with different types of soybeans were differentially expressed in the salivary glands indicating a diet-specific response. Interestingly, the opposite arms of miR-281 (-5p and -3p), a miRNA involved in regulating development, were predicted to target Hmgs genes of R. pedestris and soybean, respectively. These observations among others highlight stinkbug's responses as a function of its interaction with soybean. In brief, the results of this study not only present salient findings that could be of potential use in pest management and mitigation but also provide an invaluable resource for R. pedestris as an insect model to facilitate studies on plant-pest interactions.

Keywords: Ecdysteroid; MicroRNA; Neuropeptide; Sesquiterpenoid; Soybean; Stinkbug; Transcriptome.

MeSH terms

Animals
Gene Expression Profiling
Glycine max / genetics
Heteroptera* / genetics
Insect Hormones*
MicroRNAs* / genetics
Transcriptome

Substances

MicroRNAs
Insect Hormones