Sequence analysis of Erianthus arundinaceus chromosome 1 isolated by flow sorting after genomic in situ hybridization in suspension

The Crop Journal - Tập 10 - Trang 1746-1754 - 2022
Shan Yang1,2, Petr Cápal3, Jaroslav Doležel3, Xueting Li1, Wang Qian1, Zhiqiang Wang4, Kai Zeng1, Peiting Li1, Hongkai Zhou2, Rui Xia5, Muqing Zhang1,4, Zuhu Deng1,4
1National Engineering Research Center for Sugarcane & State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
2College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, Guangdong, China
3Institute of Experimental Botany of the Czech Academy of Sciences, Center of the Region Haná for Biotechnological and Agricultural Research, Olomouc CZ-77900, Czech Republic
4State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources & Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning 530004, Guangxi, China
5State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou 510642, Guangdong, China

Tài liệu tham khảo

Cai, 2002, Chromosome analysis of Saccharum L. and related plants, Southwest China, J. Agric. Sci., 18, 16 Moore, 2013 Piperidis, 2010, Molecular cytogenetic investigation of chromosome composition and transmission in sugarcane, Mol. Genet. Genomics, 284, 65, 10.1007/s00438-010-0546-3 D’Hont, 1996, Characterisation of the double genome structure of modern sugarcane cultivars (Saccharum spp.) by molecular cytogenetics, Mol. Gen. Genet., 250, 405, 10.1007/s004380050092 C. Grassl, Taxonomy of Saccharum relatives: Sclerostachya, Narenga, and Erianthus, in: Proceedings of 14th Congress of the International Society of Sugar Cane Technologists (ISSCT), New Orleans, LA, USA, 1972, pp. 240–248. Amalraj, 2006, On the taxonomy of the members of ‘Saccharum complex, Genet. Resour. Crop Evol., 53, 35, 10.1007/s10722-004-0581-1 Piperidis, 2000, Molecular contribution to selection of intergeneric hybrids between sugarcane and the wild species Erianthus arundinaceus, Genome, 43, 1033, 10.1139/g00-059 Cai, 2005, Verification of the introgression of Erianthus arundinaceus germplasm into sugarcane using molecular markers, Plant Breed., 124, 322, 10.1111/j.1439-0523.2005.01099.x Hont, 1995, Identification and characterisation of sugarcane intergeneric hybrids, Saccharum officinarum × Erianthus arundinaceus, with molecular markers and DNA in situ hybridisation, Theor. Appl. Genet., 91, 320, 10.1007/BF00220894 J. Wu, Y. Huang, Y. Lin, C. Fu, S. Liu, Z. Deng, Q. Li, Z. Huang, R. Chen, M. Zhang, Unexpected inheritance pattern of Erianthus arundinaceus chromosomes in the intergeneric progeny between Saccharum spp. and Erianthus arundinaceus, PLoS ONE 9 (2014) e110390. Pachakkil, 2019, Cytogenetic and agronomic characterization of intergeneric hybrids between Saccharum spp. hybrid and Erianthus arundinaceus, Sci. Rep., 9, 1748, 10.1038/s41598-018-38316-6 Y. Huang, J. Wu, P. Wang, Y. Lin, C. Fu, Z. Deng, Q. Wang, Q. Li, R. Chen, M. Zhang, Characterization of chromosome inheritance of the intergeneric BC2 and BC3 progeny between Saccharum spp. and Erianthus arundinaceus, PLoS ONE 10 (2015) e0133722. Yang, 2019, Chromosome transmission in BC4 progenies of intergeneric hybrids between Saccharum spp. and Erianthus arundinaceus (Retz.) Jeswiet, Sci. Rep., 9, 2528, 10.1038/s41598-019-38710-8 Wnag, 2017, Analysis on breeding values of sugarcane with consanguinity of E. arundinaceus and their crosses, Chin. J. Trop. Crops, 38, 1274 Shore, 2010, GISH characterization of Erianthus arundinaceus chromosomes in three generations of sugarcane intergeneric hybrids, Genome, 53, 331, 10.1139/G10-010 Fukuhara, 2013, Identification and characterization of intergeneric hybrid of commercial sugarcane (Saccharum spp. hybrid) and Erianthus arundinaceus (Retz.) Jeswiet, Euphytica, 189, 321, 10.1007/s10681-012-0748-3 P.P. Thirugnanasambandam, N.V. Hoang, R.J. Henry, The challenge of analyzing the sugarcane genome, Front. Plant Sci. 9 (2018) 616–616. Garsmeur, 2018, A mosaic monoploid reference sequence for the highly complex genome of sugarcane, Nat. Commun., 9, 2638, 10.1038/s41467-018-05051-5 Souza, 2019, Assembly of the 373k gene space of the polyploid sugarcane genome reveals reservoirs of functional diversity in the world's leading biomass crop, GigaScience, 8, giz129, 10.1093/gigascience/giz129 Zhang, 2012, Genome size variation in three Saccharum species, Euphytica, 185, 511, 10.1007/s10681-012-0664-6 Zhang, 2018, Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L., Nat. Genet., 50, 1565, 10.1038/s41588-018-0237-2 Nascimento, 2019, Unraveling the complex genome of Saccharum spontaneum using polyploid gene assembler, DNA Res., 26, 205, 10.1093/dnares/dsz001 Zeng, 2021, Genome survey sequence and the development of simple sequence repeat (SSR) markers in Erianthus arundinaceus, Sugar Tech, 23, 77, 10.1007/s12355-020-00872-5 J. Yan, J. Zhang, K. Sun, D. Chang, S. Bai, Y. Shen, L. Huang, J. Zhang, Y. Zhang, Y. Dong, Ploidy level and DNA content of Erianthus arundinaceus as determined by flow cytometry and the association with biological characteristics, PLoS ONE 11 (2016) e0151948. Zwyrtková, 2021, Chromosome genomics uncovers plant genome organization and function, Biotechnol. Adv., 46, 10.1016/j.biotechadv.2020.107659 Bansal, 2020, Aegilops umbellulata introgression carrying leaf rust and stripe rust resistance genes Lr76 and Yr70 located to 9.47-Mb region on 5DS telomeric end through a combination of chromosome sorting and sequencing, Theor. Appl. Genet., 133, 903, 10.1007/s00122-019-03514-x Thind, 2017, Rapid cloning of genes in hexaploid wheat using cultivar-specific long-range chromosome assembly, Nat. Biotechnol., 35, 793, 10.1038/nbt.3877 Xiao, 2017, Sequencing flow-sorted short arm of Haynaldia villosa chromosome 4V provides insights into its molecular structure and virtual gene order, BMC Genomics, 18, 791, 10.1186/s12864-017-4211-7 Doležel, 2007, Flow cytometry with plant cells: analysis of genes, chromosomes and genomes, 41 Doležel, 2012, Chromosomes in the flow to simplify genome analysis, Funct. Integr. Genomics, 12, 397, 10.1007/s10142-012-0293-0 Metcalfe, 2019, Flow cytometric characterisation of the complex polyploid genome of Saccharum officinarum and modern sugarcane cultivars, Sci. Rep., 9, 19362, 10.1038/s41598-019-55652-3 Yang, 2020, A flow cytometry-based analysis to establish a cell cycle synchronization protocol for Saccharum spp., Sci. Rep., 10, 5016, 10.1038/s41598-020-62086-9 Cápal, 2015, Multiple displacement amplification of the DNA from single flow-sorted plant chromosome, Plant J., 84, 838, 10.1111/tpj.13035 Kreplak, 2019, A reference genome for pea provides insight into legume genome evolution, Nat. Genet., 51, 1411, 10.1038/s41588-019-0480-1 Giorgi, 2013, FISHIS: fluorescence in situ hybridization in suspension and chromosome flow sorting made easy, PLoS ONE, 8, 10.1371/journal.pone.0057994 Molnár, 2016, Dissecting the U, M, S and C genomes of wild relatives of bread wheat (Aegilops spp.) into chromosomes and exploring their synteny with wheat, Plant J., 88, 452, 10.1111/tpj.13266 Doležel, 1992, A high-yield procedure for isolation of metaphase chromosomes from root tips of Vicia faba L., Planta, 188, 93, 10.1007/BF00198944 Loureiro, 2006, Comparison of four nuclear isolation buffers for plant DNA flow cytometry, Ann. Bot., 98, 679, 10.1093/aob/mcl141 Simková, 2008, Coupling amplified DNA from flow-sorted chromosomes to high-density SNP mapping in barley, BMC Genomics, 9, 294, 10.1186/1471-2164-9-294 Li, 2009, Fast and accurate short read alignment with Burrows-Wheeler transform, Bioinformatics, 25, 1754, 10.1093/bioinformatics/btp324 Li, 2009, Genome project data processing S: the sequence alignment/map format and SAMtools, Bioinformatics, 25, 2078, 10.1093/bioinformatics/btp352 Quinlan, 2010, BEDTools, Bioinformatics, 26, 841, 10.1093/bioinformatics/btq033 Jurka, 2005, Repbase update, a database of eukaryotic repetitive elements, Cytogenet. Genome Res., 110, 462, 10.1159/000084979 Chen, 2004, Using repeatmasker to identify repetitive elements in genomic sequences, Curr. Protoc. Bioinformatics, 5, 4.10.1, 10.1002/0471250953.bi0410s05 Flynn, 2020, RepeatModeler2 for automated genomic discovery of transposable element families, Proc. Natl. Acad. Sci. U. S. A., 117, 9451, 10.1073/pnas.1921046117 Mender, 2015, Telomere restriction fragment (TRF) analysis, Bio-protocol, 5, 10.21769/BioProtoc.1658 Stanke, 2003, Gene prediction with a hidden Markov model and a new intron submodel, Bioinformatics, 19, ii215, 10.1093/bioinformatics/btg1080 Korf, 2004, Gene finding in novel genomes, BMC Bioinformatics, 5, 59, 10.1186/1471-2105-5-59 Altschul, 1990, Basic local alignment search tool, J. Mol. Biol., 215, 403, 10.1016/S0022-2836(05)80360-2 Birney, 2004, GeneWise and Genomewise, Genome Res., 14, 988, 10.1101/gr.1865504 Campbell, 2006, Comprehensive analysis of alternative splicing in rice and comparative analyses with Arabidopsis, BMC Genomics, 7, 327, 10.1186/1471-2164-7-327 Haas, 2008, Automated eukaryotic gene structure annotation using EVidenceModeler and the program to assemble spliced alignments, Genome Biol., 9, R7, 10.1186/gb-2008-9-1-r7 Griffiths-Jones, 2005, Rfam: annotating non-coding RNAs in complete genomes, Nucleic Acids Res., 33, D121, 10.1093/nar/gki081 Lowe, 1997, tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence, Nucleic Acids Res., 25, 955, 10.1093/nar/25.5.955 Bairoch, 2000, The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000, Nucleic Acids Res., 28, 45, 10.1093/nar/28.1.45 Marchler-Bauer, 2011, CDD: a Conserved Domain Database for the functional annotation of proteins, Nucleic Acids Res., 39, D225, 10.1093/nar/gkq1189 Finn, 2013, Pfam: the protein families database, Nucleic Acids Res., 42, D222, 10.1093/nar/gkt1223 Jensen, 2007, eggNOG: automated construction and annotation of orthologous groups of genes, Nucleic Acids Res., 36, D250, 10.1093/nar/gkm796 Koonin, 2004, A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes, Genome Biol., 5, R7, 10.1186/gb-2004-5-2-r7 Dimmer, 2011, The UniProt-GO annotation database in 2011, Nucleic Acids Res., 40, D565, 10.1093/nar/gkr1048 Ogata, 1999, KEGG: kyoto encyclopedia of genes and genomes, Nucleic Acids Res., 27, 29, 10.1093/nar/27.1.29 Wang, 2012, MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity, Nucleic Acids Res., 40, 10.1093/nar/gkr1293 Chen, 2020, TBtools: an integrative toolkit developed for interactive analyses of big biological data, Mol. Plant, 13, 1194, 10.1016/j.molp.2020.06.009 K. Katoh, K. Misawa, K.i. Kuma, T. Miyata, MAFFT: a novel method for rapid multiple sequence alignment based on fast fourier transform, Nucleic Acids Res. 30 (2002) 3059–3066. Talavera, 2007, Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments, Syst. Biol., 56, 564, 10.1080/10635150701472164 Kalyaanamoorthy, 2017, ModelFinder: fast model selection for accurate phylogenetic estimates, Nat. Methods, 14, 587, 10.1038/nmeth.4285 L.T. Nguyen, H.A. Schmidt, A. von Haeseler, B.Q. Minh, IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies, Mol. Biol. Evol. 32 (2015) 268–274. Hao, 2020, The resurgence of introgression breeding, as exemplified in wheat improvement, Front. Plant Sci., 11, 252, 10.3389/fpls.2020.00252 Dolezel, 2007, Chromosome-based genomics in the cereals, Chromosome Res., 15, 51, 10.1007/s10577-006-1106-x Doležel, 2014, Advances in plant chromosome genomics, Biotechnol. Adv., 32, 122, 10.1016/j.biotechadv.2013.12.011 Tsuruta, 2017, Complete chloroplast genomes of Erianthus arundinaceus and Miscanthus sinensis: comparative genomics and evolution of the Saccharum complex, PLoS ONE, 12, 10.1371/journal.pone.0169992 Vrána, 2016 Kopecký, 2013, Flow sorting and sequencing Meadow fescue chromosome 4F, Plant Physiol., 163, 1323, 10.1104/pp.113.224105 Akpinar, 2015, Sequencing chromosome 5D of Aegilops tauschii and comparison with its allopolyploid descendant bread wheat (Triticum aestivum), Plant Biotechnol. J., 13, 740, 10.1111/pbi.12302 Paterson, 2009, The Sorghum bicolor genome and the diversification of grasses, Nature, 457, 551, 10.1038/nature07723 Wright, 2005, The effects of artificial selection on the maize genome, Science, 308, 1310, 10.1126/science.1107891 Goff, 2002, A draft sequence of the rice genome (Oryza sativa L. ssp. japonica), Science, 296, 92, 10.1126/science.1068275 Cooper, 2019, A new reference genome for Sorghum bicolor reveals high levels of sequence similarity between sweet and grain genotypes: implications for the genetics of sugar metabolism, BMC Genomics, 20, 13, 10.1186/s12864-019-5734-x