| [1] |
Ozias-Akins P, Jarret RL. 1994. Nuclear DNA content and ploidy levels in the genus Ipomoea. Journal of the American Society for Horticultural Science 119:110−15 doi: 10.21273/JASHS.119.1.110 |
| [2] |
Palumbo F, Galvao AC, Nicoletto C, Sambo P, Barcaccia G. 2019. Diversity analysis of sweet potato genetic resources using morphological and qualitative traits and molecular markers. Genes 10:840 doi: 10.3390/genes10110840 |
| [3] |
Woolfe JA. 1992. Sweet potato: an untapped food resource. Cambridge, New York: Cambridge University Press. https://doi.org/10.1086/417965 |
| [4] |
Kurabachew H. 2015. The role of orange fleshed sweet potato (Ipomea batatas) for combating vitamin A deficiency in Ethiopia: a review. International Journal of Food Science and Nutrition Engineering 5:141−46 |
| [5] |
Yang J, Moeinzadeh MH, Kuhl H, Helmuth J, Xiao P, et al. 2017. Haplotype-resolved sweet potato genome traces back its hexaploidization history. Nature Plants 3:696−703 doi: 10.1038/s41477-017-0002-z |
| [6] |
Hoshino A, Jayakumar V, Nitasaka E, Toyoda A, Noguchi H, et al. 2016. Genome sequence and analysis of the Japanese morning glory Ipomoea nil. Nature Communications 7:13295 doi: 10.1038/ncomms13295 |
| [7] |
Wang D, Liu H, Wang H, Zhang P, Shi C. 2020. A novel sucrose transporter gene IbSUT4 involves in plant growth and response to abiotic stress through the ABF-dependent ABA signaling pathway in Sweetpotato. BMC Plant Biology 20:1−15 doi: 10.1186/s12870-020-02382-8 |
| [8] |
Zhang H, Wang Z, Li X, Gao X, Dai Z, et al. 2022. The IbBBX24–IbTOE3–IbPRX17 module enhances abiotic stress tolerance by scavenging reactive oxygen species in sweet potato. New Phytologist 233:1133−52 doi: 10.1111/nph.17860 |
| [9] |
Cheng CY, Krishnakumar V, Chan AP, Thibaud-Nissen F, Schobel S, et al. 2017. Araport11: a complete reannotation of the Arabidopsis thaliana reference genome. The Plant Journal 89:789−804 doi: 10.1111/tpj.13415 |
| [10] |
Ji CY, Bian X, Lee CJ, Kim HS, Kim SE, et al. 2019. De novo transcriptome sequencing and gene expression profiling of sweet potato leaves during low temperature stress and recovery. Gene 700:23−30 doi: 10.1016/j.gene.2019.02.097 |
| [11] |
Lee IH, Shim D, Jeong JC, Sung YW, Nam KJ, et al. 2019. Transcriptome analysis of root-knot nematode (Meloidogyne incognita)-resistant and susceptible sweetpotato cultivars. Planta 249:431−44 doi: 10.1007/s00425-018-3001-z |
| [12] |
Arisha MH, Aboelnasr H, Ahmad MQ, Liu Y, Tang W, et al. 2020. Transcriptome sequencing and whole genome expression profiling of hexaploid sweetpotato under salt stress. BMC Genomics 21:1−18 doi: 10.1186/s12864-020-6524-1 |
| [13] |
Li Y, Wei W, Feng J, Luo H, Pi M, et al. 2018. Genome re-annotation of the wild strawberry Fragaria vesca using extensive Illumina- and SMRT-based RNA-seq datasets. DNA Research 25:61−70 doi: 10.1093/dnares/dsx038 |
| [14] |
Dong L, Liu H, Zhang J, Yang S, Kong G, et al. 2015. Single-molecule real-time transcript sequencing facilitates common wheat genome annotation and grain transcriptome research. BMC Genomics 16:1039 doi: 10.1186/s12864-015-2257-y |
| [15] |
Liu T, Li M, Liu Z, Ai X, Li Y. 2021. Reannotation of the cultivated strawberry genome and establishment of a strawberry genome database. Horticulture Research 8:41 doi: 10.1038/s41438-021-00476-4 |
| [16] |
Xiong J, Tang X, Wei M, Yu W. 2022. Comparative full-length transcriptome analysis by Oxford Nanopore Technologies reveals genes involved in anthocyanin accumulation in storage roots of sweet potatoes (Ipomoea batatas L.). PeerJ 10:e13688 doi: 10.7717/peerj.13688 |
| [17] |
Li Y, Pi M, Gao Q, Liu Z, Kang C. 2019. Updated annotation of the wild strawberry Fragaria vesca V4 genome. Horticulture Research 6:1 doi: 10.1038/s41438-018-0066-6 |
| [18] |
Wang F, Tan WF, Song W, Yang ST, Qiao S. 2022. Transcriptome analysis of sweet potato responses to potassium deficiency. BMC Genomics 23:655 doi: 10.1186/s12864-022-08870-5 |
| [19] |
Suematsu K, Tanaka M, Kurata R, Kai Y. 2020. Comparative transcriptome analysis implied a ZEP paralog was a key gene involved in carotenoid accumulation in yellow-fleshed sweetpotato. Scientific Reports 10:20607 doi: 10.1038/s41598-020-77293-7 |
| [20] |
Tadda SA, Li C, Ding J, Li JA, Wang J, et al. 2023. Integrated metabolome and transcriptome analyses provide insight into the effect of red and blue LEDs on the quality of sweet potato leaves. Frontiers in Plant Science 14:1181680 doi: 10.3389/fpls.2023.1181680 |
| [21] |
Tang C, Han R, Zhou Z, Yang Y, Zhu M, et al. 2020. Identification of candidate miRNAs related in storage root development of sweet potato by high throughput sequencing. Journal of Plant Physiology 251:153224 doi: 10.1016/j.jplph.2020.153224 |
| [22] |
Li H. 2018. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34:3094−100 doi: 10.1093/bioinformatics/bty191 |
| [23] |
Chen S, Zhou Y, Chen Y, Gu J. 2018. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34:i884−i890 doi: 10.1093/bioinformatics/bty560 |
| [24] |
Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, et al. 2013. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29:15−21 doi: 10.1093/bioinformatics/bts635 |
| [25] |
Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT, et al. 2015. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nature Biotechnology 33:290−+ doi: 10.1038/nbt.3122 |
| [26] |
Wu TD, Watanabe CK. 2005. GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics 21:1859−75 doi: 10.1093/bioinformatics/bti310 |
| [27] |
Haas BJ, Delcher AL, Mount SM, Wortman JR, Smith RK Jr, et al. 2003. Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Research 31:5654−66 doi: 10.1093/nar/gkg770 |
| [28] |
Hoff KJ, Lomsadze A, Borodovsky M, Stanke M. 2019. Whole-genome annotation with BRAKER. In Gene Prediction, ed. Kollmar M. New York: Humana. pp. 65−95. https://doi.org/10.1007/978-1-4939-9173-0_5 |
| [29] |
Haas BJ, Salzberg SL, Zhu W, Pertea M, Allen JE, et al. 2008. Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments. Genome biology 9:R7 doi: 10.1186/gb-2008-9-1-r7 |
| [30] |
Xia R, Meyers BC, Liu Z, Beers EP, Ye S, et al. 2013. MicroRNA superfamilies descended from miR390 and their roles in secondary small interfering RNA biogenesis in eudicots. The Plant Cell 25:1555−72 doi: 10.1105/tpc.113.110957 |
| [31] |
Xia R, Xu J, Arikit S, Meyers BC. 2015. Extensive families of miRNAs and PHAS loci in Norway spruce demonstrate the origins of complex phasiRNA networks in seed plants. Molecular Biology and Evolution 32:2905−18 doi: 10.1093/molbev/msv164 |
| [32] |
Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25:1754−60 doi: 10.1093/bioinformatics/btp324 |
| [33] |
Meyers BC, Green PJ (eds.). 2010. Plant microRNAs: methods and protocols. Totowa, NJ: Humana Press. https://doi.org/10.1007/978-1-4939-9042-9 |
| [34] |
Xia R, Zhu H, An YQ, Beers EP, Liu Z. 2012. Apple miRNAs and tasiRNAs with novel regulatory networks. Genome Biology 13:R47 doi: 10.1186/gb-2012-13-6-r47 |
| [35] |
Holt C, 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 |
| [36] |
Simão FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM. 2015. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31:3210−12 doi: 10.1093/bioinformatics/btv351 |
| [37] |
Jones P, Binns D, Chang HY, Fraser M, Li W, et al. 2014. InterProScan 5: genome-scale protein function classification. Bioinformatics 30:1236−40 doi: 10.1093/bioinformatics/btu031 |
| [38] |
Powell S, Forslund K, Szklarczyk D, Trachana K, Roth A, et al. 2014. eggNOG v4.0: nested orthology inference across 3686 organisms. Nucleic Acids Research 42:D231−D239 doi: 10.1093/nar/gkt1253 |
| [39] |
Zheng Y, Jiao C, Sun H, Rosli HG, Pombo MA, et al. 2016. iTAK: A program for genome-wide prediction and classification of plant transcription factors, transcriptional regulators, and protein kinases. Molecular Plant 9:1667−70 doi: 10.1016/j.molp.2016.09.014 |
| [40] |
Cabreira-Cagliari C, Fagundes DGS, Dias NCF, Bohn B, Margis-Pinheiro M, et al. 2018. GILP family: a stress-responsive group of plant proteins containing a LITAF motif. Functional & integrative genomics 18:55−66 doi: 10.1007/s10142-017-0574-8 |
| [41] |
Lee SG, Nwumeh R, Jez JM. 2016. Structure and mechanism of isopropylmalate dehydrogenase from Arabdiopsis thaliana: insights on leucine and aliphatic glucosinolate biosynthesis. Journal of Biological Chemistry 291(26):13421−30 |
| [42] |
Murphy AS, Hoogner KR, Peer WA, Taiz L. 2002. Identification, purification, and molecular cloning of N-1-naphthylphthalmic acid-binding plasma membrane-associated aminopeptidases from Arabidopsis. Plant Physiology 128:935−50 doi: 10.1104/pp.010519 |
| [43] |
Jin S, Kim SY, Susila H, Nasim Z, Youn G, et al. 2022. FLOWERING LOCUS M isoforms differentially affect the subcellular localization and stability of SHORT VEGETATIVE PHASE to regulate temperature-responsive flowering in Arabidopsis. Molecular Plant 15:1696−709 doi: 10.1016/j.molp.2022.08.007 |
| [44] |
Xia R, Ye S, Liu Z, Meyers BC, Liu Z. 2015. Novel and recently evolved microRNA clusters regulate expansive F-BOX gene networks through phased small interfering RNAs in wild diploid strawberry. Plant Physiology 169:594−610 doi: 10.1104/pp.15.00253 |
| [45] |
Chen C, Chen H, Zhang Y, Thomas HR, Frank MH, et al. 2020. TBtools: an integrative toolkit developed for interactive analyses of big biological data. Molecular plant 13:1194−202 doi: 10.1016/j.molp.2020.06.009 |
| [46] |
Bo X, Wang S. 2005. TargetFinder: a software for antisense oligonucleotide target site selection based on MAST and secondary structures of target mRNA. Bioinformatics 21:1401−2 doi: 10.1093/bioinformatics/bti211 |