Al-Jbory, Z., El-Bouhssini, M., Chen, M.S. (2018) Conserved and unique
putative effectors expressed in the salivary glands of three related
gall midges species. Journal of Insect Science 18(5): 15.
https://doi.org/10.1093/jisesa/iey094
Al Jibory, Z., Micheal, J. A., Park, Y., Reeck, G. R., & Chen M. S.
(2020). Differential localization of
Hessian fly candidate effectors in resistant and susceptible wheat
plants. Plant direct, 00: 1-15. https://doi.org/10.1002/pld3.246
Biello,
R., Singh, A., Godfrey, C. J., Fernández, F. F., Mugford, S. T., &
Powell, & G., Hogenhout, S. A., | Mathers, T. C. (2021). A
chromosome level genome assembly of the woolly apple aphid,Eriosoma lanigerum Hausmann (Hemiptera: Aphididae).Molecular Ecology Resources, 21(1), 316-326.
https://doi.org/10.1111/1755-0998.13258
Birney, Ewan, Clamp, Michele, Durbin, & Richard. (2004). GeneWise and
Genomewise. Genome Research, 14(5), 988-995.
https://doi.org/10.1101/gr.1865504
Blackman, R. L., & Eastop, V. F. (2020). Aphids on the world’s
plants: An online identification and information guide. John Wiley &
Sons Ltd. http://www.aphidsonworldsplants.info/.
Blanco,
E., Parra, G., & Guigó, R. (2002). Using geneid to Identify
Genes. John Wiley & Sons, Inc.
Bolger, A. M., Lohse, M., & Usadel, B. (2014). Trimmomatic: a flexible
trimmer for Illumina sequence data. Bioinformatics, 30(15),
2114-2120. doi:10.1093/bioinformatics/btu170
Carolan, J. C., D Caragea, Reardon, K. T., Mutti, N. S., & Edwards, O.
R. (2011). Predicted effector molecules in the salivary secretome of the
pea aphid (Acyrthosiphon pisum): a dual transcriptomic/proteomic
approach. Journal of Proteome Research, 10(4), 1505-18.
https://doi.org/ 10.1021/pr100881q
Castresana,
J. (2000). Selection of conserved blocks from multiple alignments for
their use in phylogenetic analysis. Molecular Biology Evolution,
17(4), 540-552.https://doi.org/10.1093/oxfordjournals.molbev.a026334Chan, P. P., & Lowe, T. M. (2019).
tRNAscan-SE: Searching for tRNA
genes in genomic sequences. Methods in Molecular Biology,
1962:1-14. In book: Gene Prediction.https://doi.org/10.1007/978-1-4939-9173-0_1Chen, C., Chen, H., Y Zhang, Thomas, H. R., & Xia, R. (2020). Tbtools:
an integrative toolkit developed for interactive analyses of big
biological data. Molecular Plant, 13(8).https://doi.org/10.1016/j.molp.2020.06.009Chen, W., Shakir, S., Bigham, M., Fei, Z., & Jander, G. (2019). Genome
sequence of the corn leaf aphid (Rhopalosiphum maidis Fitch).GigaScience, 8(4). https://doi.org/ 10.1093/gigascience/giz033
Chen, X. M., Yang, Z. X., Chen, H., Qi, Q., Liu, J., & Wang, C., Shao,
S. X., Lu, Q., Li, Y., Wu, H. X., King-Jones, K., Chen, M. S. (2020). A
complex nutrient exchange between a gall-forming aphid and its plant
host. Frontiers in Plant Science, 11, 811.
https://doi.org/10.3389/fpls.2020.00811
Clore, A. (2014). gBlocks gene
fragments for gene construction and more. Journal of Immunological
Methods, 188(1), 165-167. https://doi.org/10.1016/0022-1759(95)00229-4
Dudchenko,
O., Batra, S. S., Omer, A. D., Nyquist, S. K., Hoeger, M., Durand, N.
C., Shamim, M. S., Machol, I., P., Lander, E. S., Aiden, A. P.,
& Aiden, E. L. (2017). De novo assembly of the Aedes
aegypti genome using Hi-C yields chromosome-length scaffolds.Science, 356, 92-95.https://doi.org/10.1126/science.aal3327Dudchenko, O., Shamim, M. S., Batra, S. S., Durand, N. C. & Aiden, E.
L. (2018). The Juicebox Assembly Tools module facilitates de novo
assembly of mammalian genomes with chromosome-length scaffolds for under
$1000. https://doi.org/ 10.1101/254797
Flynn, J. M., Hubley, R., Goubert, C., Rosen, J., Clark, A. G.,
Feschotte, C., & Smit, A. F. (2020). RepeatModeler2 for automated
genomic discovery of transposable element families. PNAS,
117(17), 9451-9457.https://doi.org/10.1073/pnas.1921046117Ghosh, S., & Chan, C. K. (2016). Analysis of rna-seq data using tophat
and cufflinks. Methods in Molecular Biology, 1374, 339-61.
https://doi.org/ 10.1007/978-1-4939-3167-5_18
Haas, B. J., Salzberg, S. L., Zhu, W., Pertea, M., Allen, J. E., &
Orvis, J., White, O., Buell, C. R., & Wortman J. R. (2008). Automated
eukaryotic gene structure annotation using EVidenceModeler and the
Program to Assemble Spliced Alignments. Genome biology, 9(1), R7.
https://doi.org/10.1186/gb-2008-9-1-r7
Hahn, M. W., Demuth, J. P., & Han, S. G. (2007). Accelerated rate of
gene gain and loss in primates. Genetics, 177(3).
https://doi.org/10.1534/genetics.107.080077
Hirano, T., Kimura, S., Sakamoto, T., Okamoto, A., Nakayama, T.,
Matsuura, T., Ikeda, Y., Takeda, S., Suzuki, Y., OhshimaI., & Sato, M.
H. Reprogramming of the developmental program of Rhus javanicaduring initial stage of gall induction by Schlechtendalia
chinensis. Frontiers in Plant Science, 2020, 11, 471.https://doi.org/10.3389/fpls.2020.00471Hu,
J., Fang, J. P., Su, Z. Y., & Liu, S. L. (2019). NextPolish: a fast and
efficient genome polishing tool for long-read assembly.Bioinformatics, (7), 7.
https://doi.org/10.1093/bioinformatics/btz891
Huang, S. F., Kang, M. J., & Xu, A. L. (2017). HaploMerger2: rebuilding
both haploid sub-assemblies from high-heterozygosity diploid genome
assembly. Bioinformatics 16, 2577.https://doi.org/10.1093/bioinformatics/btx220International Aphid Genomics Consortium. (2010). Genome sequence of the
pea aphid Acyrthosiphon pisum. Plos Biology, 8(2), 1-25.
https://doi.org/10.1371/journal.pbio.1000313
Julca, I., Marcet-Houben, M., Cruz, F., Vargas-Chavez, C., Johnston, J.
S., Gómez-Garrido, J., Frias, L., Corvelo, A., Loska, D., Cámara, F.,
Gut, M., Alioto, T., Latorre, A., & Gabaldón, T. (2020). Phylogenomics
identifies an ancestral burst of gene duplications predating the
diversification of aphidomorpha. Molecular Biology and Evolution,37(3), 730-756. https://doi.org/10.1093/molbe v/msz261
Johnson, K. P., Dietrich, C. H., Friedrich, F., Beutel, R. G., Wipfler,
B., & Peters, R. S., et al. (2018). Phylogenomics and the evolution of
hemipteroid insects. Proceedings of the National Academy of
Sciences of the United States of America, 115(50).
https://doi.org/10.1073/pnas.1815820115
Katoh, K., Misawa, K., Kuma, K., & Miyata, T. (2002). MAFFT: a novel
method for rapid multiple sequence alignment based on fast Fourier
transform. Nucleic Acids Research, 30(14), 3059-3066.
https://doi.org/10.1093/nar/gkf436
Katoh, K., & Standley, D. (2013). MAFFT multiple sequence alignment
software version 7: improvements in performance and usability.Molecular Biology and Evolution, 30(4), 772-780.
https://doi.org/10.1093/molbev/mst010
Kalvari, I., Argasinska, J., Quinones-Olvera, N., Nawrocki, E. P.,
Rivas, E., Eddy, S. R., Bateman, A., Finn, R. D., & Petrov, A. I.
(2018). Rfam 13.0: shifting to a genome-centric resource for non-coding
RNA families. Nucleic Acids Research 46 (Database issue),
D335-D342. http://dx.doi.org/10.1093/nar/gkx1038
Karin, L., Peter, H., Rodland, E. A., Stærfeldt, H. H., Rognes, T., &
Ussery, D. W. (2007). RNAmmer:
consistent and rapid annotation of ribosomal RNA genes. Nucleic
Acids Research, 35(9), 3100-3108.https://doi.org/10.1093/nar/gkm160Korgaonkar, A., Han, C., Lemire, A. L., Siwanowicz, I., & Stern, D. L.
(2021). A novel family of secreted insect proteins linked to plant gall
development. Current Biology (D1).
Kim, D., Landmead, B., & Salzberg, S. L. (2015). HISAT: a fast spliced
aligner with low memory requirements. Nature Methods,12(4), 357-360. https://doi.org/ 10.1038/nmeth.3317
Kurosu, U., & Aoki, S. (1992).
Gall cleaning by the aphid Hormaphis betulae. Journal of Ethology,9, 51-55. https://doi.org/10.1007/BF02350191.Li, F., Zhao, X.,
Li, M., He, K., Huang, C., Zhou, Y., Li, Z., & Walters, J. R. (2019).
Insect
genomes: progress and challenges. Insect Molecular Biology,
28(6), 739-758. https://doi.org/10.1111/imb.12599
Li, L., Stoeckert, C. J., & Roos, D. (2003). OrthoMCL: identification
of ortholog groups for eukaryotic genomes. Genome Research,
13(9), 2178-2189. https://doi.org/10.1101/gr.1224503
Liu, P., Yang, Z. X., Chen, X. M., Foottit, R. G. (2014). The Effect of
the gall-forming aphid Schlechtendalia chinensis (Hemiptera:
Aphididae) on leaf wing ontogenesis in Rhus chinensis(Sapindales: Anacardiaceae). Annals of the Entomological Society
of America, 107(1), 242-250.
http://www.bioone.org/doi/full/10.1603/AN13118
Li, Y., Park, H., Smith, T. E., & Moran, N. A. (2019). Gene family
evolution in the pea aphid based on chromosome-level genome assembly.Molecular Biology and Evolution, 36(10), 2143-2156.https://doi.org/10.1093/molbev/msz138Li, Y., Zhang, B., & Moran, N. A. (2020). The aphid x chromosome is a
dangerous place for functionally important genes: diverse evolution of
hemipteran genomes based on chromosome-level assemblies. Molecular
Biology and Evolution, 37(8), 2357-2368. https://doi.org/
10.1093/molbev/msaa095
Mathers, T. C. (2020). Improved genome assembly and annotation of the
soybean aphid (Aphis glycines Matsumura). G3: Genes,
Genomes, Genetics, 10(3), g3.400954.2019. https://doi.org/10.1534/
g3.119.400954
Mathers, T. C., Chen, Y., Kaithakottil, G., Legeai, F., Mugford, S. T.,
Baa-Puyoulet, P., Bretaudeau, A., Clavijo, B., Colella, S., Collin, O.,
Dalmay, T., Derrien, T., Feng, H., Gabaldón, T., Jordan, A., Julca, I.,
Kettles, G. J., Kowitwanich, K., Lavenier, D., … Hogenhout, S. A.
(2017). Rapid transcriptional plasticity of duplicated gene clusters
enables a clonally reproducing aphid to colonise diverse plant species.Genome Biology, 18(1), 27. https://doi.org/10.1186/s1305
9-016-1145-3
Mathers, T. C., Mugford, S. T., Hogenhout, S. A. T., & Tripathi, L.
(2020). Genome sequence of the banana aphid, Pentalonia
nigronervosa Coquerel (Hemiptera: Aphididae) and its symbionts.G3: Genes, Genomes, Genetics, 10(12), 4315-4321.
https://doi.org/10.1534/g3.120.401358
Mathers, T. C., Wouters, R. H. M., Mugford, S. T., Swarbreck, D., Van
Oosterhout, C., & Hogenhout, S. A. (2020).
Chromosome-scale genome assemblies
of aphids reveal extensively rearranged autosomes and long-term
conservation of the X chromosome. Molecular Biology and Evolution,
38(3):856-875.https://doi.org/10.1093/molbev/msaa246Marçais, Guillaume, Kingsford, & Carl. (2011). A fast, lock-free
approach for efficient parallel counting of occurrences of k-mers.Bioinformatics, 27, 764-770.
https://doi.org/10.1093/bioinformatics/btr011
Moran, N. A. (1989). A
48-million-year-old aphid-host plant association and complex life cycle:
biogeographic evidence. Science, 245(4914), 173-175.
https://doi.org/10.1126/science.245.4914.173
Nicholson,
S. J., Nickerson, M. L., Dean, M., Song, Y., Hoyt, P. R., Rhee, H., Kim,
C., & Puterka, G. J. (2015). The genome of Diuraphis noxia, a
global aphid pest of small grains. BMC Genomics, 16(1), 1-16.
https:// doi.org/10.1186/s1286 4-015-1525-1
Quan, Q. M., Hu, X., Pan, B. H., Zeng, B. S., Wu, N. N., Fang, G. Q.,
Cao, Y. H., Chen, X. Y., Li, X., Huang, Y. P., & Zhan, S. (2019).
Draft genome of the cotton aphidAphis gossypii. Insect Biochemistry and Molecular Biology,
105, 25-32. https://doi.org/10.1016/j.ibmb.2018.12.007
Rao, S. S. P., Huntley, M. H., Durand, N. C., Stamenova, E. K., Bochkov,
I. D., Robinson, J. T., Sanborn, A. L., Machol, I., Omer, A. D., &
Lander, E. S. (2014). A 3D map of the human genome at Kilobase
resolution reveals principles of chromatin looping. Cell, 158,
1-6. https://doi.org/10.1016/j.cell.2014.11.021
Ranallo-Benavidez, T. R., Jaron, K. S., & Schatz, M. C. (2020).
GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid
genomes. Nature Communications, 11(1), 1432.
https://doi.org/10.1038/s41467-020-14998-3
Ruan, J., & Li, H. (2020). Fast and
accurate long-read assembly with wtdbg2. Nature Methods, 17(Supp
l 6), 1-4.https://doi.org/10.1101/530972Roach, M. J., Schmidt, S. A., & Borneman, A. R. (2018). Purge
haplotigs: allelic contig reassignment for third-gen diploid genome
assemblies. BMC Bioinformatics, 19(1). https://doi.org/
10.1186/s12859-018-2485-7
Stamatakis, A. (2014). RAxML version 8: a tool for phylogenetic analysis
and post-analysis of large phylogenies. Bioinformatics, 30(9),
1312-1313. https://doi.org/10.1093/bioinformatics/btu033
Stanke,
M., Keller, O., Gunduz, I., Hayes, A., Waack, S., & Morgenstern, B.
(2006). AUGUSTUS: ab initio prediction of alternative
transcripts. Nucleic Acids Research, 34 (Web Server issue),
W435-439. https://doi.org/10.1093/nar/gkl200
Thorpe, P., Escudero-Martinez, C. M., Cock, P. J. A., Eves-van den
Akker, S., & Bos, J. I. B. (2018). Shared transcriptional control and
disparate gain and loss of aphid parasitism genes. Genome Biology
and Evolution, 10(10), 2716-2733. https://doi.org/10.1093/gbe/evy183
Takeda, S., Yoza, M., Amano, T., Ohshima, I., Hirano, T., Sato, M. H.,
Sakamoto, T., & Seisuke Kimura, S. (2019) Comparative transcriptome
analysis of galls from four different host plants suggests the molecular
mechanism of gall development. PLoS One, 14(10), e0223686.https://doi.org/10.1371/journal.pone.0223686Tarailo-Graovac, M., & Chen, N. (2009). Using RepeatMasker to identify
repetitive elements in genomic sequences. Current protocols in
bioinformatics, Chapter 4, Unit 4.10.https://doi.org/10.1002/0471250953.bi0410s25Walker,
B. J., Abeel, T., Shea, T., Priest, M., Abouelliel, A., Sakthikumar, S.,
Cuomo, C. A., Zeng, Q. D., Wortman, J., Young, S. K., & Earl, A. M.
(2014). Pilon: an integrated tool for comprehensive microbial variant
detection and genome assembly improvement. PLoS One, 9(11),
e112963.https://doi.org/10.1371/journal.pone.0112963Waterhouse, R. M., Seppey, M., Simao, F. A., Manni, M., Ioannidis, P.,
Klioutchnikov, G., . . . Zdobnov, E. M. (2018). BUSCO applications from
quality assessments to gene prediction and phylogenomics. Molecular
Biology and Evolution, 35(3), 543-548.
https://doi.org/10.1093/molbev/msx319
Wang,
Z., Ge, J., Chen, H., Cheng, X., Yang, Y., Li, J., Whitworth, R. J., &
Chen M. C. S. (2018). An insect
nucleoside diphosphate kinase (NDK) functions as an effector protein in
wheat - Hessian fly interactions. Insect Biochemistry and
Molecular Biology, 100, 30-38.
https://doi.org/10.1016/j.ibmb.2018.06.003
Wenger,
J. A., Cassone, B. J., Legeai, F., Johnston, J. S., Bansal, R., Yates,
A. D., Coates, B. S., Pavinato, V. A. C., & Michel, A. (2016). Whole
genome sequence of the soybean aphid, Aphis glycines.Insect Biochemistry and Molecular Biology, 123, 102917.
https://doi.org/10.1016/j.ibmb.2017.01.005
Wool, D. Galling aphids: specialization, biological complexity, and
variation. (2004). Annual Review of Entomology, 49(1), 175.
https://doi.org/10.1146/annurev.ento.49.061802.123236
Yang,
Z. H. (2007). PAML 4: phylogenetic analysis by maximum likelihood.Molecular Biology and Evolution, 24(8), 1586-1591.
https://doi.org/10.1093/molbev/msm088
Yang, Z. X., Ma, L., Francis, F., Yang, Y., Chen, H., Wu, H. X., &
Chen, X. M. (2018). Proteins
identified from saliva and salivary glands of the Chinese gall aphidSchlectendalia chinensis. Proteomics, 18, 1700378.
https://doi.org/10.1002/pmic.201700378
Zhang, C. X., Tang, X. D., & Cheng, J. A. (2008). The utilization and
industrialization of insect resources in China. Entomological
research, 38, S38-S47. https://doi.org/10.1111/j.1748-5967.2008.00173.x
Zhang,
G. X., Qiao, G. X., Zhong, T. S., & Zhang, W. Y. (1999). Fauna
Sinica, Insecta Vol. 14 Homoptera, Mindaridae and Pemphigidae. Science
Press, Beijing.
Zhao, C. Y., Escalante, L.N., Chen, H., Benatti, T. R., Qu, J. X.,
Chellapilla, S., Waterhouse, R. M., Wheeler, D., Andersson, M. N., Bao,
R., Batterton, M., Behura, S. K., Blankenburg, K. P., Caragea, D.,
Carolan, J. C., Coyle, M., El-Bouhssini M., Francisco L., …
Richards S. (2015) A massive expansion of effector genes underlies
gall-formation in the wheat pest Mayetiola destructor .Current Biology 25 (5): 613-620.
https://doi.org/10.1016/j.cub.2014.12.057