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Table 1 Characteristics of RFL genes and predicted properties of RFL proteins in three Gossypium species

From: Genome-wide analysis of Rf-PPR-like (RFL) genes and a new InDel marker development for Rf1 gene in cytoplasmic male sterile CMS-D2 Upland cotton

Gene ID Chromosome number Location Intron Length /aa Domain number Subcellular location
RFL genes in G. hirsutum
 Gh_A02G0346 A02 4061961-4063892(−) 0 643 12 Chloroplast
 Gh_A03G0085 A03 1310395-1312206(+) 0 603 12 Chloroplast
 Gh_A04G0298 A04 6938035-6939906(+) 1 538 14 Signal peptide
 Gh_A04G0299 A04 6958902-6961157(+) 1 740 17 Chloroplast
 Gh_A04G0308 A04 7067031-7068902(+) 0 623 12 Signal peptide
 Gh_A04G1306 scaffold756_A04 11713-13662(+) 0 649 15 _
 Gh_A04G1307 scaffold756_A04 42960-44756(+) 0 598 13 Mitochondrial
 Gh_A08G1858 A08 99291747-99293615(−) 1 538 14 Mitochondrial
 Gh_A08G1886 A08 99594679-99596448(+) 1 557 14 Signal peptide
 Gh_A09G0071 A09 1545143-1547526(−) 1 443 12 _
 Gh_A09G0099 A09 2441359-2443299(+) 0 646 14 Chloroplast
 Gh_A09G1959 A09 72667483-72669399(−) 0 638 10 _
 Gh_A10G1153 A10 58877471-58931193(−) 2 867 20 Signal peptide
 Gh_A10G1192 A10 62428148-62429707(+) 0 519 13 Mitochondrial
 Gh_A10G1204 A10 62755821-62757800(−) 2 485 12 _
 Gh_A10G1206 A10 62766997-62769312(−) 1 726 18 _
 Gh_A11G1174 A11 14344990-14346882(+) 1 558 12 Mitochondrial
 Gh_D02G0409 D02 5265341-5267272(−) 0 643 12 Chloroplast
 Gh_D03G1566 D03 44987228-44989030(−) 0 600 12 Mitochondrial
 Gh_D05G3346 D05 54230340-54232205(−) 0 621 12 Chloroplast
 Gh_D05G3356 D05 54344042-54346277(−) 1 602 13 _
 Gh_D05G3362 D05 54500616-54502460(−) 0 614 14 _
 Gh_D05G3380 D05 54864359-54866280(+) 1 557 13 _
 Gh_D05G3389 D05 55014049-55028124(−) 6 749 14 _
 Gh_D05G3392 D05 55066970-55068568(−) 0 532 13 Signal peptide
 Gh_D08G2249 D08 62092399-62094342(+) 0 647 15 Mitochondrial
 Gh_D09G0096 D09 2499241-2501169(+) 0 642 14 Chloroplast
 Gh_D09G2163 D09 48772802-48774718(−) 0 638 10 _
 Gh_D10G1292 D10 23933234-23935420(+) 0 728 18 _
 Gh_D10G1294 D10 23946799-23948358(+) 0 519 14 _
 Gh_D10G1307 D10 24224714-24226273(−) 0 519 13 Mitochondrial
 Gh_D10G1342 D10 25844049-25845929(+) 0 626 13 Mitochondrial
 Gh_D10G1344 D10 25875652–25882818(+) 6 906 18 _
 Gh_D11G1331 D11 12830305-12832155(+) 0 616 12 Chloroplast
 Gh_D13G0526 D13 6880247-6881917(+) 0 556 14 _
RFL genes in G. arboreum
 Cotton_A_08373 Ca13 57501074-57503005(+) 0 643 13 Chloroplast
 Cotton_A_14708 Ca10 102602256-102604196(−) 0 646 14 Chloroplast
 Cotton_A_14743 Ca10 103472578-103474212(+) 0 544 12 _
 Cotton_A_16847 Ca7 9513817-9515736(−) 1 573 13 _
 Cotton_A_18522 Ca7 61596824-61598692(−) 0 622 14 Chloroplast
 Cotton_A_23070 Ca8 78350187-78351653(+) 0 488 13 Signal peptide
 Cotton_A_23084 Ca8 78693577-78695556(−) 0 659 15 Mitochondrial
 Cotton_A_24432 Ca8 85527702-85529582(−) 0 626 13 Mitochondrial
 Cotton_A_24724 Ca10 34691224-34693117(−) 1 630 10 Mitochondrial
 Cotton_A_26557 Ca3 23320169-23321491(−) 0 440 10 Signal peptide
 Cotton_A_26837 Ca5 136263118-136264365(+) 0 415 11 _
 Cotton_A_29292 Ca6 90346627-90348504(−) 0 625 13 Chloroplast
 Cotton_A_29299 Ca6 90193385-90195133(−) 0 582 14 _
 Cotton_A_29300 Ca6 90149515-90151278(−) 0 587 12 Mitochondrial
 Cotton_A_30591 Ca4 116495782-116497152(+) 0 456 11 Mitochondrial
 Cotton_A_33520 Ca6 91413647-91415518(+) 0 623 12 Mitochondrial
RFL genes in G. raimondii
 Cotton_D_gene_10000174 scaffold587 10218-12381(+) 1 698 15 Chloroplast
 Cotton_D_gene_10000410 scaffold520 19372–20826(−) 0 484 13 Signal peptide
 Cotton_D_gene_10000446 scaffold516 21891-23345(+) 0 484 13 Signal peptide
 Cotton_D_gene_10000448 scaffold516 47453-49639(+) 0 540 11 Chloroplast
 Cotton_D_gene_10000451 scaffold516 90985-92439(+) 0 484 13 Signal peptide
 Cotton_D_gene_10000822 scaffold512 92947-94929(+) 0 660 13 Chloroplast
 Cotton_D_gene_10000826 scaffold512 134156-135944(+) 1 564 10 Chloroplast
 Cotton_D_gene_10002529 scaffold461 131009-132463(−) 0 484 13 Signal peptide
 Cotton_D_gene_10003142 Chr9 41720023-41721747(+) 1 520 9 Signal peptide
 Cotton_D_gene_10003980 scaffold288 253425-255650(−) 0 623 14 Mitochondrial
 Cotton_D_gene_10003981 scaffold288 259126-260817(−) 1 479 11 _
 Cotton_D_gene_10004373 scaffold326 137744-139303(−) 1 519 13 Mitochondrial
 Cotton_D_gene_10005258 Chr5 742735-745217(+) 0 641 12 Chloroplast
 Cotton_D_gene_10007940 Chr4 2510485-2512428(+) 0 647 15 Mitochondrial
 Cotton_D_gene_10009676 Chr7 41367207-41369072(−) 0 621 12 Chloroplast
 Cotton_D_gene_10009740 Chr3 1451913-1453283(+) 0 456 10 Mitochondrial
 Cotton_D_gene_10013435 scaffold333 1235526-1237394(−) 0 622 12 Chloroplast
 Cotton_D_gene_10013437 scaffold333 1247144-1249009(−) 0 621 12 Mitochondrial
 Cotton_D_gene_10014531 scaffold324 965465-968260(+) 1 579 13 _
 Cotton_D_gene_10014534 scaffold324 998554-1000283(+) 1 541 13 _
 Cotton_D_gene_10021157 Chr6 45498703-45500927(−) 0 638 10 _
 Cotton_D_gene_10026507 Chr11 23161755-23163734(+) 0 659 15 Mitochondrial
 Cotton_D_gene_10027032 Chr6 2797685-2799676(+) 1 555 12 _
 Cotton_D_gene_10027066 Chr6 2028765-2030705(−) 0 646 14 Mitochondrial