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51. Transcriptome and gene expression analysis of Rhynchophorus ferrugineus (Coleoptera: Curculionidae) during developmental stages

Author

Hongjun Yang, Danping Xu, Zhihang Zhuo, Jiameng Hu, and Baoqian Lu

Subjects
Single-molecule sequencing, RNA-Seq, Transcriptome, Different developmental stage, Differentially expressed genes, Medicine, Biology (General), QH301-705.5
Abstract

Background Red palm weevil, Rhynchophorus ferrugineus Olivier, is one of the most destructive pests harming palm trees. However, genomic resources for R. ferrugineus are still lacking, limiting the ability to discover molecular and genetic means of pest control. Methods In this study, PacBio Iso-Seq and Illumina RNA-seq were used to generate transcriptome from three developmental stages of R. ferrugineus (pupa, 7th-instar larva, adult) to increase the understanding of the life cycle and molecular characteristics of the pest. Results Sequencing generated 625,983,256 clean reads, from which 63,801 full-length transcripts were assembled with N50 of 3,547 bp. Expression analyses revealed 8,583 differentially expressed genes (DEGs). Moreover, gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that these DEGs were mainly related to the peroxisome pathway which associated with metabolic pathways, material transportation and organ tissue formation. In summary, this work provides a valuable basis for further research on the growth and development, gene expression and gene prediction, and pest control of R. ferrugineus.

Published
2020
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52. Influence of climatic factors on the potential distribution of pest Heortia vitessoides Moore in China

Author

Danping Xu, Xinyang Li, Yawen Jin, Zhihang Zhuo, Hongjun Yang, Jiameng Hu, and Rulin Wang

Subjects
Heortia vitessoides Moore, Potential distribution area, Climatic factors, MaxEnt modeling, Ecology, QH540-549.5
Abstract

Heortia vitessoides Moore is one of the predominant pests of Aquilaria sinensis (Lour.) Spreng, which is extremely harmful to this plant, and is also an important quarantine pest around the world. To understand the influence of climate factors on the distribution of this pest, maximum entropy modeling (MaxEnt) was used to predict the potential suitable distribution area under certain climatic conditions. The results showed that H. vitessoides was mainly located in the tropical and southern subtropical climate areas of China under current climatic conditions, with a total suitable distribution area of 107.48 × 104 km2. The highly suitable areas were concentrated in the Pearl River Basin and the south of Lancang River Basin with area of 46.19 × 104 km2. In the future, the suitable area showed a tendency to expand to the north. The total suitable distribution area of this species would reach 136.21 × 104-151.62 × 104 km2, which was 26.62%–40.65% higher than that of the current. The climatic factors of precipitation of warmest quarter, precipitation of wettest quarter, min temperature of coldest month, and mean temperature of warmest quarter were the dominant variables affecting the distribution of H. vitessoides. It can be seen that the suitable area of this pest is relatively large and tends to expand, which poses a threat to the growth of A. sinensis. It is suggested that the relevant afforestation and phytosanitary departments should attach great importance and take necessary measures to control the spread of this pest.

Published
2020
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53. SMRT sequencing of the full-length transcriptome of the Rhynchophorus ferrugineus (Coleoptera: Curculionidae)

Author

Hongjun Yang, Danping Xu, Zhihang Zhuo, Jiameng Hu, and Baoqian Lu

Subjects
Rhynchophorus ferrugineus, Different developmental stage, PacBio Iso-Seq, Illumina RNA-seq, Full-length transcriptome, Medicine, Biology (General), QH301-705.5
Abstract

Background Red palm weevil Rhynchophorus ferrugineus (Coleoptera: Curculionidae) is one of the most destructive insects for palm trees in the world. However, its genome resources are still in the blank stage, which limits the study of molecular and growth development analysis. Methods In this study, we used PacBio Iso-Seq and Illumina RNA-seq to first generate transcriptome from three developmental stages of R. ferrugineus (pupa, 7th larva, female and male) to increase our understanding of the life cycle and molecular characteristics of R. ferrugineus. Results A total of 63,801 nonredundant full-length transcripts were generated with an average length of 2,964 bp from three developmental stages, including the 7th instar larva, pupa, female adult and male adult. These transcripts showed a high annotation rate in seven public databases, with 54,999 (86.20%) successfully annotated. Meanwhile, 2,184 alternative splicing (AS) events, 2,084 transcription factors (TFs), 66,230 simple sequence repeats (SSR) and 9,618 Long noncoding RNAs (lncRNAs) were identified. In summary, our results provide a new source of full-length transcriptional data and information for the further study of gene expression and genetics in R. ferrugineus.

Published
2020
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54. The complete chloroplast genome sequence of Sibiraea angustata, a traditional Chinese medicine in Sichuan Province, China

Author

Jiayong Li, Zhihang Zhuo, Danping Xu, Hongjun Yang, and Tianhui Zhu

Subjects
sibiraea angustata illumina novaseq chloroplast genome phylogenetic analysis, Genetics, QH426-470
Abstract

The complete chloroplast genome of Sibiraea angustata was assembled and subjected to phylogenetic analysis. The chloroplast genome of S. angustata was 155,869 bp in length, containing a large single-copy region (84,343 bp), a small single-copy region (18,820 bp), and two inverted repeat regions (26,353 bp). The overall GC content of S. angustata chloroplast genome was 36.80%. The chloroplast genome of S. angustata contained 127 unique genes, including 83 protein-coding genes, 36 tRNA genes and eight rRNA genes. Phylogenetic analysis revealed that S. angustata was related to Malus ioensis, Malus florentina and Malus trilobata.

Published
2021
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55. Modeling the distribution of Zanthoxylum armatum in China with MaxEnt modeling

Author

Danping Xu, Zhihang Zhuo, Rulin Wang, Meng Ye, and Biao Pu

Subjects
Ecology, QH540-549.5
Abstract

Predicting suitable distribution is an effective way to guide the introduction and cultivation of a species. To explore the climatic suitability of Zanthoxylum armatum, the maximum entropy model was used to model the distribution of this species in China. The results showed that the suitable area for Z. armatum in the current climatic conditions was 85.1–120.4 °E, 20.9–37.7 °N, which was mainly located in the subtropical zone of China. High suitability areas were primarily concentrated in southwestern China in the provinces of Sichuan, Guizhou, Hubei, Hunan, and Chongqing with the region of 102.1–112.8 °E, 22.9–32.8 °N. The total area of suitable habitats accounted for 25% of China's total land area. The suitable ranges of the key environmental factors limiting the distribution of Z. armatum were a maximum temperature for January of 3.8–14.9 °C; a temperature for the driest quarter of 0.5–12.7 °C; a mean temperature for February of 0.2–12.2 °C; a mean temperature for March of 4.0–16.1 °C; a total precipitation for July of 126–500 mm; a minimum temperature for April of 4.1–16.9 °C; a temperature seasonality (standard deviation*100) of 503.1–906.3 °C; and a precipitation seasonality (coefficient of variation) of 43.9–92.2. Keywords: MaxEnt model, Zanthoxylum armatum, Distribution area, Environmental factor

Published
2019
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57. Transcriptome analysis in different developmental stages of Batocera horsfieldi (Coleoptera: Cerambycidae) and comparison of candidate olfactory genes.

Author

Hua Yang, Yan Cai, Zhihang Zhuo, Wei Yang, Chunping Yang, Jin Zhang, Yang Yang, Baoxin Wang, and Fengrong Guan

Subjects
Medicine, Science
Abstract

The white-striped longhorn beetle Batocera horsfieldi (Coleoptera: Cerambycidae) is a polyphagous wood-boring pest that causes substantial damage to the lumber industry. Moreover olfactory proteins are crucial components to function in related processes, but the B. horsfieldi genome is not readily available for olfactory proteins analysis. In the present study, developmental transcriptomes of larvae from the first instar to the prepupal stage, pupae, and adults (females and males) from emergence to mating were built by RNA sequencing to establish a genetic background that may help understand olfactory genes. Approximately 199 million clean reads were obtained and assembled into 171,664 transcripts, which were classified into 23,380, 26,511, 22,393, 30,270, and 87, 732 unigenes for larvae, pupae, females, males, and combined datasets, respectively. The unigenes were annotated against NCBI's non-redundant nucleotide and protein sequences, Swiss-Prot, Gene Ontology (GO), Pfam, Clusters of Eukaryotic Orthologous Groups (KOG), and KEGG Orthology (KO) databases. A total of 43,197 unigenes were annotated into 55 sub-categories under the three main GO categories; 25,237 unigenes were classified into 26 functional KOG categories, and 25,814 unigenes were classified into five functional KEGG Pathway categories. RSEM software identified 2,983, 3,097, 870, 2,437, 5,161, and 2,882 genes that were differentially expressed between larvae and males, larvae and pupae, larvae and females, males and females, males and pupae, and females and pupae, respectively. Among them, genes encoding seven candidate odorant binding proteins (OBPs) and three chemosensory proteins (CSPs) were identified. RT-PCR and RT-qPCR analyses showed that BhorOBP3, BhorCSP2, and BhorOBPC1/C3/C4 were highly expressed in the antenna of males, indicating these genes may may play key roles in foraging and host-orientation in B. horsfieldi. Our results provide valuable molecular information about the olfactory system in B. horsfieldi and will help guide future functional studies on olfactory genes.

Published
2018
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58. JUNO Physics and Detector

Author

Angel Abusleme, Thomas Adam, Shakeel Ahmad, Rizwan Ahmed, Sebastiano Aiello, Muhammad Akram, Fengpeng An, Guangpeng An, Qi An, Giuseppe Andronico, Nikolay Anfimov, Vito Antonelli, Tatiana Antoshkina, Burin Asavapibhop, João Pedro Athay de Marcondes de André, Didier Auguste, Andrej Babic, Wander Baldini, Andrea Barresi, Eric Baussan, Marco Bellato, Antonio Bergnoli, Enrico Bernieri, Thilo Birkenfeld, Sylvie Blin, David Blum, Simon Blyth, Anastasia Bolshakova, Mathieu Bongrand, Clément Bordereau, Dominique Breton, Augusto Brigatti, Riccardo Brugnera, Riccardo Bruno, Antonio Budano, Mario Buscemi, Jose Busto, Ilya Butorov, Anatael Cabrera, Hao Cai, Xiao Cai, Yanke Cai, Zhiyan Cai, Antonio Cammi, Agustin Campeny, Chuanya Cao, Guofu Cao, Jun Cao, Rossella Caruso, Cédric Cerna, Jinfan Chang, Yun Chang, Pingping Chen, Po-An Chen, Shaomin Chen, Xurong Chen, Yi-Wen Chen, Yixue Chen, Yu Chen, Zhang Chen, Jie Cheng, Yaping Cheng, Alexey Chetverikov, Davide Chiesa, Pietro Chimenti, Artem Chukanov, Gérard Claverie, Catia Clementi, Barbara Clerbaux, Selma Conforti Di Lorenzo, Daniele Corti, Salvatore Costa, Flavio Dal Corso, Olivia Dalager, Christophe de la Taille, Jiawei Deng, Zhi Deng, Ziyan Deng, Wilfried Depnering, Marco Diaz, Xuefeng Ding, Yayun Ding, Bayu Dirgantara, Sergey Dmitrievsky, Tadeas Dohnal, Dmitry Dolzhikov, Georgy Donchenko, Jianmeng Dong, Evgeny Doroshkevich, Marcos Dracos, Frédéric Druillole, Shuxian Du, Stefano Dusini, Martin Dvorak, Timo Enqvist, Heike Enzmann, Andrea Fabbri, Lukas Fajt, Donghua Fan, Lei Fan, Can Fang, Jian Fang, Wenxing Fang, Marco Fargetta, Dmitry Fedoseev, Vladko Fekete, Li-Cheng Feng, Qichun Feng, Richard Ford, Andrey Formozov, Amélie Fournier, Haonan Gan, Feng Gao, Alberto Garfagnini, Christoph Genster, Marco Giammarchi, Agnese Giaz, Nunzio Giudice, Maxim Gonchar, Guanghua Gong, Hui Gong, Oleg Gorchakov, Yuri Gornushkin, Alexandre Göttel, Marco Grassi, Christian Grewing, Vasily Gromov, Minghao Gu, Xiaofei Gu, Yu Gu, Mengyun Guan, Nunzio Guardone, Maria Gul, Cong Guo, Jingyuan Guo, Wanlei Guo, Xinheng Guo, Yuhang Guo, Paul Hackspacher, Caren Hagner, Ran Han, Yang Han, Muhammad Sohaib Hassan, Miao He, Wei He, Tobias Heinz, Patrick Hellmuth, Yuekun Heng, Rafael Herrera, Daojin Hong, Yuenkeung Hor, Shaojing Hou, Yee Hsiung, Bei-Zhen Hu, Hang Hu, Jianrun Hu, Jun Hu, Shouyang Hu, Tao Hu, Zhuojun Hu, Chunhao Huang, Guihong Huang, Hanxiong Huang, Qinhua Huang, Wenhao Huang, Xin Huang, Xingtao Huang, Yongbo Huang, Jiaqi Hui, Lei Huo, Wenju Huo, Cédric Huss, Safeer Hussain, Antonio Insolia, Ara Ioannisian, Roberto Isocrate, Beatrice Jelmini, Kuo-Lun Jen, Ignacio Jeria, Xiaolu Ji, Xingzhao Ji, Huihui Jia, Junji Jia, Siyu Jian, Di Jiang, Xiaoshan Jiang, Ruyi Jin, Xiaoping Jing, Cécile Jollet, Jari Joutsenvaara, Sirichok Jungthawan, Leonidas Kalousis, Philipp Kampmann, Li Kang, Michael Karagounis, Narine Kazarian, Waseem Khan, Khanchai Khosonthongkee, Denis Korablev, Konstantin Kouzakov, Alexey Krasnoperov, Zinovy Krumshteyn, Andre Kruth, Nikolay Kutovskiy, Pasi Kuusiniemi, Tobias Lachenmaier, Cecilia Landini, Sébastien Leblanc, Victor Lebrin, Frederic Lefevre, Ruiting Lei, Rupert Leitner, Jason Leung, Demin Li, Fei Li, Fule Li, Haitao Li, Huiling Li, Jiaqi Li, Mengzhao Li, Min Li, Nan Li, Qingjiang Li, Ruhui Li, Shanfeng Li, Tao Li, Weidong Li, Weiguo Li, Xiaomei Li, Xiaonan Li, Xinglong Li, Yi Li, Yufeng Li, Zhaohan Li, Zhibing Li, Ziyuan Li, Hao Liang, Jingjing Liang, Daniel Liebau, Ayut Limphirat, Sukit Limpijumnong, Guey-Lin Lin, Shengxin Lin, Tao Lin, Jiajie Ling, Ivano Lippi, Fang Liu, Haidong Liu, Hongbang Liu, Hongjuan Liu, Hongtao Liu, Hui Liu, Jianglai Liu, Jinchang Liu, Min Liu, Qian Liu, Qin Liu, Runxuan Liu, Shuangyu Liu, Shubin Liu, Shulin Liu, Xiaowei Liu, Xiwen Liu, Yan Liu, Yunzhe Liu, Alexey Lokhov, Paolo Lombardi, Claudio Lombardo, Kai Loo, Chuan Lu, Haoqi Lu, Jingbin Lu, Junguang Lu, Shuxiang Lu, Xiaoxu Lu, Bayarto Lubsandorzhiev, Sultim Lubsandorzhiev, Livia Ludhova, Fengjiao Luo, Guang Luo, Pengwei Luo, Shu Luo, Wuming Luo, Vladimir Lyashuk, Bangzheng Ma, Qiumei Ma, Si Ma, Xiaoyan Ma, Xubo Ma, Jihane Maalmi, Yury Malyshkin, Fabio Mantovani, Francesco Manzali, Xin Mao, Yajun Mao, Mari, Stefano M., Filippo Marini, Sadia Marium, Cristina Martellini, Gisele Martin-Chassard, Agnese Martini, Davit Mayilyan, Ints Mednieks, Yue Meng, Anselmo Meregaglia, Emanuela Meroni, David Meyhöfer, Mauro Mezzetto, Jonathan Miller, Lino Miramonti, Salvatore Monforte, Paolo Montini, Michele Montuschi, Axel Müller, Pavithra Muralidharan, Massimiliano Nastasi, Naumov, Dmitry V., Elena Naumova, Diana Navas-Nicolas, Igor Nemchenok, Minh Thuan Nguyen Thi, Feipeng Ning, Zhe Ning, Hiroshi Nunokawa, Lothar Oberauer, Juan Pedro Ochoa-Ricoux, Alexander Olshevskiy, Domizia Orestano, Fausto Ortica, Rainer Othegraven, Hsiao-Ru Pan, Alessandro Paoloni, Nina Parkalian, Sergio Parmeggiano, Yatian Pei, Nicomede Pelliccia, Anguo Peng, Haiping Peng, Frédéric Perrot, Pierre-Alexandre Petitjean, Fabrizio Petrucci, Oliver Pilarczyk, Luis Felipe Piñeres Rico, Artyom Popov, Pascal Poussot, Wathan Pratumwan, Ezio Previtali, Fazhi Qi, Ming Qi, Sen Qian, Xiaohui Qian, Zhen Qian, Hao Qiao, Zhonghua Qin, Shoukang Qiu, Muhammad Usman Rajput, Gioacchino Ranucci, Neill Raper, Alessandra Re, Henning Rebber, Abdel Rebii, Bin Ren, Jie Ren, Taras Rezinko, Barbara Ricci, Markus Robens, Mathieu Roche, Narongkiat Rodphai, Aldo Romani, Bedřich Roskovec, Christian Roth, Xiangdong Ruan, Xichao Ruan, Saroj Rujirawat, Arseniy Rybnikov, Andrey Sadovsky, Paolo Saggese, Giuseppe Salamanna, Simone Sanfilippo, Anut Sangka, Nuanwan Sanguansak, Utane Sawangwit, Julia Sawatzki, Fatma Sawy, Michaela Schever, Jacky Schuler, Cédric Schwab, Konstantin Schweizer, Alexandr Selyunin, Andrea Serafini, Giulio Settanta, Mariangela Settimo, Zhuang Shao, Vladislav Sharov, Arina Shaydurova, Jingyan Shi, Yanan Shi, Vitaly Shutov, Andrey Sidorenkov, Fedor Šimkovic, Chiara Sirignano, Jaruchit Siripak, Monica Sisti, Maciej Slupecki, Mikhail Smirnov, Oleg Smirnov, Thiago Sogo-Bezerra, Sergey Sokolov, Julanan Songwadhana, Boonrucksar Soonthornthum, Albert Sotnikov, Ondřej Šrámek, Warintorn Sreethawong, Achim Stahl, Luca Stanco, Konstantin Stankevich, Dušan Štefánik, Hans Steiger, Jochen Steinmann, Tobias Sterr, Matthias Raphael Stock, Virginia Strati, Alexander Studenikin, Gongxing Sun, Shifeng Sun, Xilei Sun, Yongjie Sun, Yongzhao Sun, Narumon Suwonjandee, Michal Szelezniak, Jian Tang, Qiang Tang, Quan Tang, Xiao Tang, Alexander Tietzsch, Igor Tkachev, Tomas Tmej, Marco Danilo Claudio Torri, Konstantin Treskov, Andrea Triossi, Giancarlo Troni, Wladyslaw Trzaska, Cristina Tuve, Nikita Ushakov, Johannes van den Boom, Stefan van Waasen, Guillaume Vanroyen, Nikolaos Vassilopoulos, Vadim Vedin, Giuseppe Verde, Maxim Vialkov, Benoit Viaud, Moritz Vollbrecht, Cristina Volpe, Vit Vorobel, Dmitriy Voronin, Lucia Votano, Pablo Walker, Caishen Wang, Chung-Hsiang Wang, En Wang, Guoli Wang, Jian Wang, Jun Wang, Kunyu Wang, Lu Wang, Meifen Wang, Meng Wang, Ruiguang Wang, Siguang Wang, Wei Wang, Wenshuai Wang, Xi Wang, Xiangyue Wang, Yangfu Wang, Yaoguang Wang, Yi Wang, Yifang Wang, Yuanqing Wang, Yuman Wang, Zhe Wang, Zheng Wang, Zhimin Wang, Zongyi Wang, Muhammad Waqas, Apimook Watcharangkool, Lianghong Wei, Wei Wei, Wenlu Wei, Yadong Wei, Liangjian Wen, Christopher Wiebusch, Steven Chan-Fai Wong, Bjoern Wonsak, Diru Wu, Fangliang Wu, Qun Wu, Wenjie Wu, Zhi Wu, Michael Wurm, jacques wurtz, Christian Wysotzki, Yufei Xi, Dongmei Xia, Yuguang Xie, Zhangquan Xie, Zhizhong Xing, Benda Xu, Cheng Xu, Donglian Xu, Fanrong Xu, Hangkun Xu, Jilei Xu, Jing Xu, Meihang Xu, Yin Xu, Yu Xu, Baojun Yan, Taylor Yan, Wenqi Yan, Xiongbo Yan, Yupeng Yan, Anbo Yang, Changgen Yang, Huan Yang, Jie Yang, Lei Yang, Xiaoyu Yang, Yifan Yang, Haifeng Yao, Zafar Yasin, Jiaxuan Ye, Mei Ye, Ziping Ye, Ugur Yegin, Frédéric Yermia, Peihuai Yi, Na Yin, Xiangwei Yin, Zhengyun You, Boxiang Yu, Chiye Yu, Chunxu Yu, Hongzhao Yu, Miao Yu, Xianghui Yu, Zeyuan Yu, Chengzhuo Yuan, Ying Yuan, Zhenxiong Yuan, Ziyi Yuan, Baobiao Yue, Noman Zafar, Andre Zambanini, Vitalii Zavadskyi, Shan Zeng, Tingxuan Zeng, Yuda Zeng, Liang Zhan, Aiqiang Zhang, Feiyang Zhang, Guoqing Zhang, Haiqiong Zhang, Honghao Zhang, Jiawen Zhang, Jie Zhang, Jingbo Zhang, Jinnan Zhang, Peng Zhang, Qingmin Zhang, Shiqi Zhang, Shu Zhang, Tao Zhang, Xiaomei Zhang, Xuantong Zhang, Xueyao Zhang, Yan Zhang, Yinhong Zhang, Yiyu Zhang, Yongpeng Zhang, Yuanyuan Zhang, Yumei Zhang, Zhenyu Zhang, Zhijian Zhang, Fengyi Zhao, Jie Zhao, Rong Zhao, Shujun Zhao, Tianchi Zhao, Dongqin Zheng, Hua Zheng, Minshan Zheng, Yangheng Zheng, Weirong Zhong, Jing Zhou, Li Zhou, Nan Zhou, Shun Zhou, Xiang Zhou, Jiang Zhu, Kangpu Zhu, Kejun Zhu, Zhihang Zhu, Bo Zhuang, Honglin Zhuang, Liang Zong, and Jiaheng Zou

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