- Background: Structural variations (SVs) are a type of mutations that have not been widely detected in plant genomes and studies in animals have shown their role in the process of domestication. - Results: We detected a total of 8083 SVs, including 5260 deletions, 552 tandem duplications and 2271 insertions with deletion being the predominant, indicating the universality of deletion in the evolution of papaya genome.. - Conclusions: SVs played an indispensable role in the process of papaya domestication, especially in the. - Structural variations are ubiquitous in the plant genome and play important roles in several important. - Corn weight directly affects yield and is one of the key selective traits in the process of domestication and im- provement of corn. - The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. - If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. - To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.. - The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.. - It was origin- ally found in the human genome and associated with multiple diseases, and is often used in the prevention and clinical diagnosis of human diseases. - Functional annotation analysis of genes located in the CNV region or overlapping with CNV found that they were closely related to specific biological functions such as cell death, protein phosphorylation, defense re- sponse, and resistance [13]. - Pa- paya female flowers have an ovary and grows on the stem of plant, that is, in the axils of petioles. - They are reproduced in the leaf axils like female flowers, with short peduncles and few secondary flowers. - The genetically modified papaya cultivar ‘SunUp’ is resistant to papaya ring spot virus and is produced from. - There were 1200 large structural variants that were detected through a genome-wide comparative analysis between “SunUp” and “Sunset”, but no gene was found to be related with plant growth and development [24]. - Although SVs have been studied at the level of a single genome, it has not been studied in the papaya population. - Our research reveals the role of structural variation in the domestica- tion process from male papaya to hermaphrodite papaya as well as in the sexual reproduction and environmental adaptability evolution in papaya populations.. - In contrast, a large proportion of SVs were enriched in the middle in chr7.. - Those SVs appearing in the coding regions were identified as large-effect SVs, which overlapped with 761 protein-coding genes. - the positively correlated module genes were highly expressed in the corresponding tissues (trait). - 1 Circle diagram of the distribution of structural variation and copy number variation in the papaya genome. - the distribution of copy number variation in the whole genome of the common cultivated population. - the distribution of copy number variation in the whole genome of the solo cultivated population. - two cultivated populations have similar distributions of copy number variant genes, which are concentrated in the middle and both ends of chromosomes like other structural variants, such as chr1, chr2, chr4, chr8, and chr9. - A total of 55 and 56 CNVs were under artificial selection in the solo and common subpopulations (Supplemental Table S3). - These CNVs regions covers from 108 to 132 kb genomic regions and overlapped with 91 protein-coding genes, which were randomly distributed in different chromosomes in the two subgroups. - These pathways are essential in the growth and develop- ment of plants.. - In addition, the annotation of CNV-genes found that some genes related to reproduction were found in the solo and common subpopulations (Table 2), including AGAMOUS- LIKE 80(AGL80), CELL DIVISION CYCLE 20.1(CDC20.1) and METHIONINE SYNTHASE 2(MS2). - sunup.01G0016040 AT5G16560 KAN1 solo, common the outer integument of the ovule, embryogenesis sunup.07G0005810 AT1G06220 GFA1 solo, common female gametophyte development, female fertility. - sunup.07G0006190 AT1G29300 UNE1 solo defects in pollen tube attraction. - sunup.07G0010620 AT1G69940 PPME1 common pollen tube elongation. - sunup.03G0008270 AT1G04880 HMGBD15 common pollen tube growth. - sunup.01G0016020 AT2G26490 REN4 solo, common negative regulator of pollen germination sunup.06G0003180 AT1G50030 TOR solo, common embryogenesis, water-use efficiency and yield. - sunup.06G0007900 AT1G09730 SPF1 solo embryo development, fertility. - sunup.06G0009160 AT4G38430 ROPGEF1 solo embryos development. - sunup.03G0008500 AT4G13750 EMB2597 common embryo-defective. - sunup.01G0026320 AT3G57230 AGL16 solo flowering time. - sunup.01G0008730 AT3G28860 PGP19/MDR1 solo peduncle growth, multi-branched inflorescence. - sunup.05G0008680 AT2G46240 BAG6 common heat stress, fungal resistance. - sunup.07G0000100 AT4G21320 HSA32 common heat stress associated 32-kD protein. - sunup.08G0015580 AT3G53990 USP solo, common heat shock and oxidative stress. - sunup.03G0007120 AT2G05590 OCR2 solo oxidative stress. - sunup.06G0013090 AT4G38160 MTERF6 solo, common defective chloroplasts or photosynthesis rate. - sunup.01G0002550 AT1G65930 CICDH solo defense responses, pathogen responses. - sunup.07G0001840 AT4G22330 ATCES1 solo, common disease resistance, salt stress. - sunup.02G0014350 AT5G48670 AGL80 solo central cell and endosperm development. - sunup.01G0011520 AT4G33270 CDC20.1 solo indispensable for meiosis and male fertility. - sunup.08G0020230 AT3G11980 MS2 solo, common male sterility. - sunup.03G0024240 AT4G35160 ASMT common enhanced high light stress tolerance and salt tolerance. - sunup.07G0012360 AT2G26150 HSFA2 solo, common heat Tolerance. - sunup.01G0012670 AT5G59550 RDUF2 solo, common tolerance to drought stress. - sunup.04G0018230 AT5G40990 GLIP1 solo, common pathogen resistance. - sunup.06G0008620 AT2G14610 PR1 solo response pathogens. - sunup.08G0014820 AT2G38870 AT2G38870 common PR (pathogenesis-related) peptide sunup.08G0014690 AT5G43570 AT5G43570 common PR (pathogenesis-related) peptide. - Six neu- tral primers were removed in the next statistical analysis (Supplemental Fig. - These candidate genes are very important in the sexual reproduction and agronomic traits of papaya, such as pistil development, female gamete development, pollen tube growth, embryo development, flower time, crop yields, and peduncle elongation. - For example, TOR is involved in embryogen- esis and is expressed in the embryo, endosperm, and meristem under Rapamycin [27, 28]. - PGP19 has an ability to transport auxin through the cell membrane, and pgp19 mutation can lead to abnormal distribution of auxin in the. - Moreover, melatonin is involved in the tolerance of plants under high light stress [34]. - We de- tected a total of 8083 structural variants in the whole genome, including 5260 deletions, 552 duplications, and 2271 insertions. - A total of 1794 coding proteins were de- tected in the SV region, of which of the genes were expressed in at least one tissue. - Gene func- tion analysis found that SV-genes are involved in the growth and development of papaya. - 31 hermaphrodite and 1 male papaya plants were col- lected from China, and fresh leaf tissue were dried on silica gel in the field and stored at 80 °C.. - The ovule, pollen and stamen tissues were collected in the greenhouse, and RNA was extracted. - The minimum number of genes in the module is set to 30, and the threshold of the cutting height is set to 0.2 to merge modules with higher similarity. - Genes of the same gene module may exist in the same metabolic pathway or have similar functions.. - Generally, variation calls for short-read alignments allow us to detect variants without breakpoint using Manta, and some SVs has multiple breakpoints in the population. - The online version contains supplementary material available at https://doi.. - org/10.1186/s . - https://doi.org/10.1093/bfgp/elu016.. - https://doi.org/10.1038/. - https://doi.org/10.1038/s . - https://doi.org/10.1093/gbe/evq033.. - https://doi.org/10.1186/gb-2010-11-1-r4.. - The impact and origin of copy number variations in the Oryza species. - 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