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The evolution and diurnal expression patterns of photosynthetic pathway genes of the invasive alien weed, Mikania micrantha

WANG Kang-kang, JIN Meng-jiao, LI Jing-jing, REN Ye-song, LI Zai-yuan, REN Xing-hai, HUANG Cong, WAN Fang-hao, QIAN Wan-qiang, LIU Bo
2024, 23 (2): 590-604.   DOI: 10.1016/j.jia.2023.04.011
Abstract154)      PDF in ScienceDirect      

Mikania micrantha is a fast-growing global invasive weed species that causes severe damage to natural ecosystems and very large economic losses of forest and crop production.  It has advantages in photosynthesis, including a similar net photosynthetic rate as C4 plants and a higher carbon fixation capacity.  We used a combination of genomics and transcriptomics approaches to study the evolutionary mechanisms and circadian expression patterns of Mmicrantha.  In Mmicrantha, 16 positive selection genes focused on photoreaction and utilization of photoassimilates.  In different tissues, 98.1% of the genes associated with photoresponse had high expression in stems, and more than half of the genes of the C4 cycle had higher expression in stems than in leaves.  In stomatal opening and closing, 2 genes of carbonic anhydrase (CAs) had higher expression at 18:00 than at 8:00, and the slow anion channel 1 (SLAC1) and high-leaf-temperature 1 kinase (HT1) genes were expressed at low levels at 18:00.  In addition, genes associated with photosynthesis had higher expression levels at 7:00 and 17:00.  We hypothesized that Mmicrantha may undergo photosynthesis in the stem and flower organs and that some stomata of the leaves were opening at night by CO2 signals.  In addition, its evolution may attenuate photoinhibition at high light intensities, and enhance more efficient of photosynthesis during low light intensity.  And the tissue-specific photosynthetic types and different diurnal pattern of photosynthetic-related genes may contribute to its rapid colonization of new habitats of Mmicrantha.

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MRUNet: A two-stage segmentation model for small insect targets in complex environments 

WANG Fu-kuan, HUANG Yi-qi, HUANG Zhao-cheng, SHEN Hao, HUANG Cong, QIAO Xi, QIAN Wan-qiang
2023, 22 (4): 1117-1130.   DOI: 10.1016/j.jia.2022.09.004
Abstract316)      PDF in ScienceDirect      

Online automated identification of farmland pests is an important auxiliary means of pest control.  In practical applications, the online insect identification system is often unable to locate and identify the target pest accurately due to factors such as small target size, high similarity between species and complex backgrounds.  To facilitate the identification of insect larvae, a two-stage segmentation method, MRUNet was proposed in this study.  Structurally, MRUNet borrows  the practice of object detection before semantic segmentation from Mask R-CNN and then uses an improved lightweight UNet to perform the semantic segmentation.  To reliably evaluate the segmentation results of the models, statistical methods were introduced to measure the stability of the performance of the models among samples in addition to the evaluation indicators commonly used for semantic segmentation.  The experimental results showed that this two-stage image segmentation strategy is effective in dealing with small targets in complex backgrounds.  Compared with existing state-of-the-art semantic segmentation methods, MRUNet shows better stability and detail processing ability under the same conditions.  This study provides a reliable reference for the automated identification of insect larvae.

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Biology, invasion and management of the agricultural invader: Fall armyworm, Spodoptera frugiperda (Lepidoptera: Noctuidae)
Jing WAN, HUANG Cong, LI Chang-you, ZHOU Hong-xu, REN Yong-lin, LI Zai-yuan, XING Long-sheng, ZHANG Bin, QIAO Xi, LIU Bo, LIU Cong-hui, XI Yu, LIU Wan-xue, WANG Wen-kai, QIAN Wan-qiang, Simon MCKIRDY, WAN Fang-hao
2021, 20 (3): 646-663.   DOI: 10.1016/S2095-3119(20)63367-6
Abstract181)      PDF in ScienceDirect      
The fall armyworm (FAW), Spodoptera frugiperda (J. E. Smith), is native to the Americas.  It has rapidly invaded 47 African countries and 18 Asian countries since the first detection of invasion into Nigeria and Ghana in 2016.  It is regarded as a super pest based on its host range (at least 353 host plants), its inherent ability to survive in a wide range of habitats, its strong migration ability, high fecundity, rapid development of resistance to insecticides/viruses and its gluttonous characteristics.  The inherently superior biological characteristics of FAW contribute to its invasiveness.  Integrated pest management (IPM) of FAW has relied on multiple applications of monitoring and scouting, agricultural control, chemical pesticides, viral insecticides, sex attractants, bio-control agents (parasitoids, predators and entomopathogens) and botanicals.  Knowledge gaps remain to be filled to: (1) understand the invasive mechanisms of S. frugiperda; (2) understand how to prevent its further spread and (3) provide better management strategies.  This review summarizes the biological characters of FAW, their association with its invasiveness and IPM strategies, which may provide further insights for future management.
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InvasionDB: A genome and gene database of invasive alien species
HUANG Cong, LANG Kun, QIAN Wan-qiang, WANG Shu-ping, CAO Xiao-mei, HE Rui, ZHAN An-ran, CHEN Meng-yao, YANG Nian-wan, LI Fei
2021, 20 (1): 191-200.   DOI: 10.1016/S2095-3119(20)63231-2
Abstract280)      PDF in ScienceDirect      
Invasive alien species (IAS) are species whose introduction to areas outside of their native range cause harm to economics, biodiversity, and the environment.  Understanding the genetic basis of invasiveness is critical for preventing invasion by an alien species and managing IAS with eco-friendly control methods.  In addition, uncovering the genomic features of IAS is essential for accurately predicting invasiveness.  However, even though increasing efforts have been devoted to sequencing the genomes of IAS, there is still not an integrated genome database for the invasive biology community.  Here, we first determined a list of invasive plants and animals by mining references and databases.  Then, we retrieved the genomic and gene data of these IAS, and constructed a database, InvasionDB.  InvasionDB encompasses 131 IAS genomes, 76 annotated IAS assemblies, and links these data to conventional functions such as searching for gene coding sequences and Pfam, KEGG, NR annotations, BLAST server, JBrowse, and downloads services.  Next, we analyzed 19 invasiveness-related gene families which confer invasiveness in insects.  To study the roles of noncoding RNA in invasiveness, we also annotated 135 494 miRNAs, 89 294 rRNAs, and 2 671 941 tRNAs from these IAS.  In summary, InvasionDB is useful for studying the invasiveness at the genomic level, and thus helps to develop novel management strategies to control IAS.
 
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Identification and developmental expression of putative gene encoding juvenile hormone esterase (CpJHE-like) in codling moth, Cydia pomonella (L.)
HUANG Cong, WU Qiang, JIANG Chun-yan, XING Long-sheng, SHI Guo-liang, ZHANG Bin, QIAN Wan-qiang, LI You-zhi, XI Yu, YANG Nian-wan, WAN Fang-hao
2019, 18 (7): 1624-1633.   DOI: 10.1016/S2095-3119(19)62682-1
Abstract201)      PDF in ScienceDirect      
Juvenile hormone esterase (JHE) is a key enzyme for insects, playing an important role in the regulation of insect growth, development, diapause and reproduction.  We identified a complete putative JHE of Cydia pomonella (CpJHE-like) which is comprised of a 1 761 bp coding sequence (CDS) encoding 587 amino acid residues from the transcriptome data.  The deduced protein sequence of CpJHE-like showed the highest identity of 60.44% with the Adoxophyes honmai JHE (AhJHE) and the minimal identity of 25.81% with Aedes aegypti JHE (AaJHE).  CpJHE-like exhibited all the seven typical motifs of the functional JHEs and had the highly consistent tertiary structure with Manduca sexta JHE (MsJHE).  Phylogenetic analysis showed that the CpJHE-like was close to two JHEs from the family Tortricidae.  The CpJHE-like transcript level take a leap in the 3-day-old fifth instar larva, increased about 300-fold compared to the basal level.  Tissue-specific expression profile showed that the CpJHE-like transcript was expressed mainly in the fat body.  This study indicates that the CpJHE-like is the functional JHE, which may play vital roles in the development and reproduction of C. pomonella.
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