References
Alim, MA and Lim, UT (2010).
Ecotoxicological effect of insecticides on Ooencyrtus nezarae
(Hymenoptera: Encyrtidae) an encyrtid parasitoid of Riptortus
pedestris (Hemiptera: Alydidae). In: Book Ecotoxicological effect
of insecticides on Ooencyrtus nezarae (Hymenoptera: Encyrtidae) an
encyrtid parasitoid of Riptortus pedestris (Hemiptera: Alydidae). doi:
10.1080/09583157.2013.851170
Bae, SD, Kim, HJ and Mainali, BP
(2014). Infestation of Riptortus pedestris (Fabricius) decreases
the nutritional quality and germination potential of soybean seeds.J Asia-Pac Entomol , 17 : 477-481. doi:
10.1016/j.aspen.2014.04.006
Bai, L, Wang, L, Vega-Rodríguez, J,
Wang, G and Wang, S (2019). A gut symbiotic bacterium serratia
marcescens renders mosquito resistance to plasmodium infection through
activation of mosquito immune responses. Front Microbiol,10 . doi: 10.3389/fmicb.2019.01580
Bharathimeena, T and Sudharma, K
(2009). Alternate host range and management of riptortus pedestris F.
infesting cowpea. Annal. Plant Protect Sci ,17 :
26-31.
Birney, E, Clamp, M and Durbin, R
(2004). GeneWise and genomewise. Genome Res, 14 :
988-995. doi: 10.1101/gr.1865504
Bolognini, D, Bartalucci, N, Mingrino,
A, Vannucchi, AM and Magi, A (2019). NanoR: A user-friendly R package to
analyze and compare nanopore sequencing data. PLoS One,14 : e0216471. doi: 10.1371/journal.pone.0216471
Capella-Gutiérrez, S, Silla-Martínez,
JM and Gabaldón, T (2009). TrimAl: a tool for automated alignment
trimming in large-scale phylogenetic analyses. Bioinformatics,25 : 1972-1973. doi: 10.1093/bioinformatics/btp348
Chen, S, Blom, J and Walker, ED
(2017). Genomic, physiologic, and symbiotic characterization of serratia
marcescens strains isolated from the mosquito Anopheles
stephensi . Front Microbiol, 8 : 1483. doi:
10.3389/fmicb.2017.01483
De Coster, W, D’Hert, S, Schultz, DT,
Cruts, M and Van Broeckhoven, C (2018). NanoPack: visualizing and
processing long-read sequencing data. Bioinformatics,34 : 2666-2669. doi: 10.1093/bioinformatics/bty149
Dudchenko, O, Batra, SS, Omer, AD,
Nyquist, SK, Hoeger, M, Durand, NC, Shamim, MS, Machol, I, Lander, ES
and Aiden, AP (2017). De novo assembly of the Aedes
aegypti genome using Hi-C yields chromosome-length scaffolds.Science, 356 : 92-95. doi: 10.1126/science.aal3327
Grimont, PA and Grimont, F (1978).
The genus Serratia. Annu. Rev. Microbiol, 32 : 221-248.
doi: 10.1007/0-387-30746-X_11
Haas, BJ, Salzberg, SL, Zhu, W,
Pertea, M, Allen, JE, Orvis, J, White, O, Buell, CR and Wortman, JR
(2008). Automated eukaryotic gene structure annotation using
EVidenceModeler and the program to assemble spliced alignments.Genome Biol, 9 : R7. doi: 10.1186/gb-2008-9-1-r7
Hoff, KJ, Lange, S, Lomsadze, A,
Borodovsky, M and Stanke, M (2016). BRAKER1: unsupervised RNA-Seq-based
genome annotation with GeneMark-ET and AUGUSTUS. Bioinformatics,32 : 767-769. doi: 10.1093/bioinformatics/btv661
Holt, C and Yandell, M (2011).
MAKER2: an annotation pipeline and genome-database management tool for
second-generation genome projects. BMC bioinformatics,12 : 491. doi: 10.1186/1471-2105-12-491
Hu, J, Fan, J, Sun, Z and Liu, S
(2020). NextPolish: a fast and efficient genome polishing tool for long
read assembly. Bioinformatics . doi: 10.1101/2020.04.17.035287
Huang, HJ, Ye, ZX, Lu, G, Zhang, CX,
Chen, JP and Li, JM (2020). Identification of salivary proteins in the
whitefly Bemisia tabaci by transcriptomic and LC-MS/MS analyses.Insect Sci . doi: 10.1111/1744-7917.12856
Itoh, H, Hori, T, Sato, Y, Nagayama,
A, Tago, K, Hayatsu, M and Kikuchi, Y (2018). Infection dynamics of
insecticide-degrading symbionts from soil to insects in response to
insecticide spraying. ISME J, 12 : 909-920. doi:
10.1038/s41396-017-0021-9
Ju, JF, Bing, XL, Zhao, DS, Guo, Y,
Xi, Z, Hoffmann, AA, Zhang, KJ, Huang, HJ, Gong, JT, Zhang, X and Hong,
XY (2020). Wolbachia supplement biotin and riboflavin to enhance
reproduction in planthoppers. ISME J, 14 : 676-687. doi:
10.1038/s41396-019-0559-9
Jung, M, Kim, S, Kim, HG and Lee, DH
(2018). Lethal and sublethal effects of synthetic insecticides on the
locomotory and feeding behavior of Riptortus pedestris(Hemiptera: Alydidae) under laboratory conditions. J Asia-Pac
Entomol, 21 : 179-185. doi: 10.1016/j.aspen.2017.11.019
Jung, M and Lee, D-H (2019).
Abundance and diversity of gut-symbiotic bacteria, the genusBurkholderia in overwintering Riptortus pedestris(Hemiptera: Alydidae) populations and soil in South Korea. PLoS
One, 14 : e0218240. doi: 10.1371/journal.pone.0218240
Kang, C (2003). Review on true bugs
infesting tree fruits, upland crops, and weeds in Korea. J. Appl.
Entomol, 4 : 269-277.
Katoh, K and Standley, DM (2013).
MAFFT multiple sequence alignment software version 7: improvements in
performance and usability. Mol Biol Evol, 30 : 772-780.
doi: 10.1093/molbev/mst010
Kikuchi, Y and Fukatsu, T (2014).
Live imaging of symbiosis: spatiotemporal infection dynamics of a
GFP-labelled Burkholderia symbiont in. Mol Ecol,23 : 1445-1456. doi: 10.1111/mec.12479
Kikuchi, Y, Hayatsu, M, Hosokawa, T,
Nagayama, A, Tago, K and Fukatsu, T (2012). Symbiont-mediated
insecticide resistance. PNAS, 109 : 8618-8622. doi:
10.1073/pnas.1200231109
Kikuchi, Y, Hosokawa, T and Fukatsu,
T (2007). Insect-microbe mutualism without vertical transmission: a
stinkbug acquires a beneficial gut symbiont from the environment every
generation. Appl Environ Microb, 73 : 4308-4316. doi:
10.1128/AEM.00067-07
Kikuchi, Y, Hosokawa, T and Fukatsu,
T (2011). Specific developmental window for establishment of an
insect-microbe gut symbiosis. Appl Environ Microb, 77 :
4075-4081. doi: 10.1128/AEM.00358-11
Koren, S, Walenz, BP, Berlin, K,
Miller, JR, Bergman, NH and Phillippy, AM (2017). Canu: scalable and
accurate long-read assembly via adaptive k-mer weighting and repeat
separation. Genome Res, 27 : 722-736. doi:
10.1101/gr.215087.116
Korf, I (2004). Gene finding in novel
genomes. BMC bioinformatics, 5 : 59. doi:
10.1186/1471-2105-5-59
Langfelder, P and Horvath, S (2008).
WGCNA: an R package for weighted correlation network analysis. BMC
bioinformatics, 9 : 559. doi: 10.1186/1471-2105-9-559
Lee, DJ, Lee, JB, Jang, HA,
Ferrandon, D and Lee, BL (2017). An antimicrobial protein of theRiptortus pedestris salivary gland was cleaved by a virulence
factor of Serratia marcescens . Dev Comp Immunol,67 : 427-433. doi: 10.1016/j.dci.2016.08.009
Li, H, Handsaker, B, Wysoker, A,
Fennell, T, Ruan, J, Homer, N, Marth, G, Abecasis, G, Durbin, R and
Subgroup, GPDP (2009). The sequence alignment/map format and SAMtools.Bioinformatics, 25 : 2078-2079. doi:
10.1093/bioinformatics/btp352
Li, K, Zhang, X, Guo, J, Penn, H, Wu,
T, Li, L, Jiang, H, Chang, L, Wu, C and Han, T (2019). Feeding ofRiptortus pedestris on soybean plants, the primary cause of
soybean staygreen syndrome in the Huang-Huai-Hai river basin. The
Crop Journal , 7 : 360-367. doi: CNKI:SUN:CROP.0.2019-03-008
Li, W, Gao, Y, Hu, Y, Li, S, Bi,
R,Zhang, J,Shi, S (2020). Effects of the Riptortus pedestris on
staygreen syndrome and yield of soybean. Soybean Science,39 : 116-122. doi: 10.11861
/j. issn.1000-9841.2020.01.0116
Lieberman-Aiden, E, Van Berkum, NL, Williams, L, Imakaev, M, Ragoczy, T,
Telling, A, Amit, I, Lajoie, BR, Sabo, PJ and Dorschner, MO (2009).
Comprehensive mapping of long-range interactions reveals folding
principles of the human genome. Science, 326 : 289-293.
doi: 10.1126/science.1181369
Lomsadze, A, Burns, PD and
Borodovsky, M (2014). Integration of mapped RNA-Seq reads into automatic
training of eukaryotic gene finding algorithm. Nucleic Acids Res,42 : e119-e119. doi: 10.1093/nar/gku557
Longmead, B and Salzberg, S (2012).
Fast gapped-read alignment with Bowtie2. Nat Methods , 9:357–359.
doi: 10.1038/nmeth.1923
Ma, W, Le, X, Hua, H, Chen, M, Guo,
M, He, K, Zhao, J and Li, F (2020). Chromosomal-level genomes of three
rice planthoppers provide new insights into sex chromosome evolution.Mol Ecol Resour , doi: 10.1111/1755-0998.13242
Muramoto, N (1978). A chromosome
study of thirty Japanese heteropterans (Heteroptera). Genetica,49 : 37-44. doi: 10.1007/BF00187812
Nguyen, L-T, Schmidt, HA, Von
Haeseler, A and Minh, BQ (2015). IQ-TREE: a fast and effective
stochastic algorithm for estimating maximum-likelihood phylogenies.Mol Biol Evol, 32 : 268-274. doi: 10.1093/molbev/msu300
Ohbayashi, T, Futahashi, R,
Terashima, M, Barriere, Q, Lamouche, F, Takeshita, K, Meng, XY, Mitani,
Y, Sone, T, Shigenobu, S, Fukatsu, T, Mergaert, P and Kikuchi, Y (2019).
Comparative cytology, physiology and transcriptomics ofBurkholderia insecticola in symbiosis with the bean bugRiptortus pedestris and in culture. ISME J, 13 :
1469-1483. doi: 10.1038/s41396-019-0361-8
Rahman, MM and Lim, UT (2017).
Evaluation of mature soybean pods as a food source for two pod-sucking
bugs, Riptortus pedestris (Hemiptera: Alydidae) andHalyomorpha halys (Hemiptera: Pentatomidae). PLoS One,12 : e0176187. doi: 10.1371/journal.pone.0176187
Sakuraoka, R, Suzuki, T and
Morohoshi, T (2019). Distribution and genetic diversity of genes
involved in quorum sensing and prodigiosin biosynthesis in the complete
genome sequences of Serratia marcescens . Genome Biol Evol,11 : 931-936. doi: 10.1093/gbe/evz046
Schmidt, MH-W, Vogel, A, Denton, AK,
Istace, B, Wormit, A, van de Geest, H, Bolger, ME, Alseekh, S, Maß, J
and Pfaff, C (2017). De novo assembly of a new Solanum
pennellii accession using Nanopore sequencing. Plant Cell,29 : 2336-2348. doi: 10.1105/tpc.17.00521
Stanke, M, Keller, O, Gunduz, I,
Hayes, A, Waack, S and Morgenstern, B (2006). AUGUSTUS: ab initio
prediction of alternative transcripts. Nucleic Acids Res,34 : W435-W439. doi: 10.1093/nar/gkl200
Takeshita, K and Kikuchi, Y (2017).Riptortus pedestris and Burkholderia symbiont: an ideal
model system for insect-microbe symbiotic associations. Res
Microbiol, 168 : 175-187. doi: 10.1016/j.resmic.2016.11.005
Takeshita, K, Shibata, TF, Nikoh, N,
Nishiyama, T, Hasebe, M, Fukatsu, T, Shigenobu, S and Kikuchi, Y (2014).
Whole-genome sequence of Burkholderia sp. strain RPE67, a
bacterial gut symbiont of the bean bug Riptortus pedestris .Genome A, 2 . doi: 10.1128/genomeA.00556-14
Takeshita, K, Tamaki, H, Ohbayashi,
T, Meng, X-Y, Sone, T, Mitani, Y, Peeters, C, Kikuchi, Y and Vandamme, P
(2018). Burkholderia insecticola sp. nov., a gut symbiotic
bacterium of the bean bug Riptortus pedestris . Int J Syst
Evol Micr, 68 : 2370-2374. doi: 10.1099/ijsem.0.002848
Wu, TD and Watanabe, CK (2005). GMAP:
a genomic mapping and alignment program for mRNA and EST sequences.Bioinformatics, 21 : 1859-1875. doi:
10.1093/bioinformatics/bti310
Xue, J, Zhou, X, Zhang, C-X, Yu, L-L,
Fan, H-W, Wang, Z, Xu, H-J, Xi, Y, Zhu, Z-R, Zhou, W-W, Pan, P-L, Li,
B-L, Colbourne, JK, Noda, H, Suetsugu, Y, Kobayashi, T, Zheng, Y, Liu,
S, Zhang, R, Liu, Y, Luo, Y-D, Fang, D-M, Chen, Y, Zhan, D-L, Lv, X-D,
Cai, Y, Wang, Z-B, Huang, H-J, Cheng, R-L, Zhang, X-C, Lou, Y-H, Yu, B,
Zhuo, J-C, Ye, Y-X, Zhang, W-Q, Shen, Z-C, Yang, H-M, Wang, J, Wang, J,
Bao, Y-Y and Cheng, J-A (2015). Genomes of the rice pest brown
planthopper and its endosymbionts reveal complex complementary.Genome Biol, 15 : 521. doi: 10.1186/s13059-014-0521-0
Yang, Z (1997). PAML: a program
package for phylogenetic analysis by maximum likelihood. Comput
Appl Biosci, 13 : 555-556. doi: 10.1093/bioinformatics/13.5.555