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. 2023 Aug 8;18(8):e0285430. doi: 10.1371/journal.pone.0285430

Fig 5. Presence or absence of numts in beet nuDNA.

Fig 5

Numts are indicated by boxes. Yellow boxes are numts of the query sequence used for database searching. Dashed lines show numt coordination. Horizontal bars depict non-numt sequences. Homology among sequences is shown by color identity except for thin black lines, which are unique sequences. Each panel has a scale bar. A. Nucleotide sequence comparison of EL10 chromosome 9 (nucleotide position 17,504,107 to 17,505,958 of NC_064025.1), DH1440 scaffold78 (104,751 to 106,319 of KI697145.1), and M4021 cha_scaffold3517 (346,240 to 347,876 of JADNRI010003657.1). The corresponding locus of KWS2320 chromosome 9 is unknown because of a complex rearrangement. The query sequence was 68,238 to 68,316 of TK-81mm-O_mtDNA Ref. B. Nucleotide sequence comparison of EL10 chromosome 7 (51,162,715 to 51,161,579 of NC_064023.1), KWS2320 chromosome 7 (33,117,373 to 33,116,380 of CM002327.2), DH1440 scaffold5603 (48,257 to 36,467 of KI701583.1), and M4021 cha_scaffold7580 (3,999 to 4,992 of JADNRI010007566.1). Two regions are omitted but are shown as ‘14 kbp’ and ‘3.8 kbp’ in the DH1440_scaffold5603 and M4021_cha_scaffold7580, respectively. The query sequence was 241,343 to 241,452 of TK-81mm-O_mtDNA Ref. C. Nucleotide sequence comparison of EL10 chromosome 6 (56,357,154 to 56,356,569 of NC_064022.1), DH1440 scaffold2859 (13,701 to 13,144 of KI699428.1), M4021 cha_scaffold7843 (168,404 to 168,698 of JADNRI010008189.1), and KWS2320 chromosome 6 (51,174,328 to 51,175,018 of CM002326.2). The query sequence was 241,651 to 242,111 of TK-81mm-O_mtDNA Ref. D. Nucleotide sequence comparison of EL10 chromosome 5 (4,722,313 to 4,716,515 of NC_064021.1), KWS2320 chromosome 5 (46,2840,42 to 46,286,102 of CM002325.2), and DH1440_scaffold19588 (24,930 to 26,990 of KI710041.1). The M4021 scaffold covering the region shown here was not identified. The query sequence was 253,612 to 253,858 of TK-81mm-O_mtDNA Ref. E. Nucleotide sequence comparison of EL10 chromosome 6 (49,897,315 to 49,898,565 of NC_064022.1), KWS2320 chromosome 6 (16,480,712 to 16,478,931 of CM002326.2), DH1440_scaffold1512 (115,775 to 111,051 of KI698314.1) and M4021 cha_scaffold1776 (384,189 to 390,380 of JADNRI010001789.1). The query sequence was 285,369 to 285,865 of TK-81mm-O_mtDNA Ref. F. Nucleotide sequence comparison of EL10 chromosome 7 (36,164,741 to 36,160,763 of NC_064023.1), KWS2320 chromosome 7 (17,345,068 to 17,349,049 of CM002327.2), M4021 cha_scaffold1720 (190,289 to 195,270 of JADNRI010001714.1), and DH1440 scaffold4651 (221 to 7,397 of KI700858.1). The query sequences were 286,732 to 286,944 (the asterisk indicates its cognate numt) and 328,503 to 328,908 of TK-81mm-O_mtDNA Ref.