Table 1.
Some features of chloroplast genomes in Allioideae and related species.
| Taxa | Accession number | Total length | Number of genes/ pseudogenes |
tRNA | rRNA | LSC-IR junction | SSC-IR junction | |
|---|---|---|---|---|---|---|---|---|
| Length | %GC | |||||||
| Allium siculum | MT348457 | 154,225 | 36.9 | 80/3 | 30 | 4 | rpl22 (35 bp) | ycf1 (1066 bp) gap (151 bp) |
| A. monanthum | MT348452 | 154,306 | 36.9 | 78ab/2 | 30 | 4 | IGS (rps19-rpl22) 19 bp | ycf1 (1136 bp) gap (26 bp) |
| A. ursinum | MH157875 | 153,252 | 37 | 80/2 | 30 | 4 | rpl22 (20 bp) | ycf1-ndhF overlap (55 bp) |
| A. cernuum | MT348440 | 153,750 | 36.9 | 80/1 | 30 | 4 | rpl22 (39 bp) | ycf1-ndhF overlap (48 bp) |
| A. neriniflorum | MT348443 | 154,129 | 36.9 | 80/2 | 30 | 4 | rpl22 (34 bp) | ycf1 (1092 bp) gap (176 bp) |
| A. victorialis | MF687749 | 154,074 | 37 | 80/1 | 30 | 4 | rpl22 (36 bp) | ycf1-ndhF overlap (31 bp) |
| A. tricoccum | MT348456 | 153,565 | 37.1 | 80/1 | 30 | 4 | rpl22 (34 bp) | ycf1-ndhF overlap (31 bp) |
| A. ochotense | MT348451 | 154,048 | 37 | 80/1 | 30 | 4 | rpl22 (34 bp) | ycf1-ndhF overlap (31 bp) |
| A. karataviense | MT348442 | 151,808 | 37 | 79a/2 | 30 | 4 | rps19 (10 bp) | ycf1 (1237 bp) gap (31 bp) |
| A.nigrum | MT348458 | 152,241 | 36.7 | 80/3 | 30 | 4 | rpl22 (32 bp) | ycf1 (1078 bp) gap (60 bp) |
| A. cyathophorum | MT348441 | 153,503 | 36.8 | 80/1 | 30 | 4 | rpl22 (39 bp) | ycf1 (1054 bp) gap (18 bp) |
| A. spicatum | MT348453 | 152,822 | 36.9 | 79a/2 | 30 | 4 | rps19 (10 bp) | ycf1 (1221 bp) gap (15 bp) |
| A. senescens | MT348450 | 153,542 | 36.8 | 80/1 | 30 | 4 | rpl22 (21 bp) | ycf1 (1070 bp) gap (30 bp) |
| A. sativum | NC031829 | 153,172 | 36.7 | 80/2 | 30 | 4 | rpl22 (34 bp) | ycf1 (1070 bp) gap (52 bp) |
| A. koreanum | MT348449 | 153,162 | 36.8 | 80/2 | 30 | 4 | rpl22 (28 bp) | ycf1-ndhF overlap (9 bp) |
| A. obliquum | NC037199 | 152,387 | 36.8 | 80/2 | 30 | 4 | rpl22 (33 bp) | ycf1 (1065 bp) gap (4 bp) |
| A. cepa | KM088013 | 153,529 | 36.8 | 80/2 | 30 | 4 | rpl22 (34 bp) | ycf1-ndhF overlap (1 bp) |
| A. schoenoprasum | MT348444 | 152,852 | 36.8 | 80/2 | 30 | 4 | rpl22 (34 bp) | ycf1-ndhF overlap (8 bp) |
| A. altaicum | MH159130 | 153,129 | 36.8 | 80/1 | 30 | 4 | rpl22 (33 bp) | ycf1-ndhF overlap (3 bp) |
| A. ampeloprasum | NC_044666 | 152,732 | 36.7 | 79a | 30 | 4 | rpl22 (33 bp) | ycf1 (1070 bp) gap (38 bp) |
| A. fistulosum | LT674586 | 152,859 | 36.9 | 80 | 30 | 4 | rpl22 (28 bp) | ycf1 (1074 bp) gap (6 bp) |
| A. macleanii | LT699703 | 152,633 | 36.9 | 79a | 30 | 4 | rpl22 (34 bp) | ycf1 (1234 bp) gap (41 bp) |
| A. paradoxum | MH053150 | 145,819 | 37.1 | 77bcd/9 | 30 | 4 | rps3 (39 bp) | ycf1 (522 bp) |
| A. platyspathum | LT673892 | 152,529 | 36.8 | 79e | 30 | 4 | rps3 (45 bp) | ycf1 (1066 bp) gap (13 bp) |
| A. caeruleum | MK820610 | 153,267 | 36.8 | 80/1 | 30 | 4 | rpl22 (16 bp) | ycf1 (1038 bp) gap (29 bp) |
| A. chrysocephalum | MH992109 | 153,710 | 36.8 | 80/1 | 30 | 4 | rpl22 (16 bp) | ycf1 (1041 bp) gap (2 bp) |
| A. chrysanthum | MH992108 | 153,621 | 36.8 | 80/1 | 30 | 4 | rpl22 (16 bp) | ycf1 (1041 bp) gap (2 bp) |
| A. chinense | MK096442 | 152,525 | 36.8 | 80/1 | 30 | 4 | rpl22 (16 bp) | ycf1 (1075 bp) gap (45 bp) |
| A. fetisowii | MK820612 | 154,018 | 36.9 | 80/1 | 30 | 4 | rpl22 (34 bp) | ycf1 (1037 bp) gap (6 bp) |
| A. forrestii | MK820613 | 153,186 | 36.8 | 80/1 | 30 | 4 | rpl22 (15 bp) | ycf1 (1043 bp) gap (12 bp) |
| A. herderianum | MH992110 | 153,605 | 36.8 | 80/1 | 30 | 4 | rpl22 (16 bp) | ycf1 (1042 bp) gap (1 bp) |
| A. macranthum | MK820614 | 152,876 | 37.1 | 80/1 | 30 | 4 | rpl22 (34 bp) | ycf1 (1031 bp) gap (33 bp) |
| A. mairei | MK820615 | 152,913 | 36.9 | 80/1 | 30 | 4 | rpl22 (34 bp) | ycf1 (942 bp) gap (98 bp) |
| A. maowenense | MH992111 | 153,608 | 36.8 | 80/1 | 30 | 4 | rpl22 (16 bp) | ycf1 (1042 bp) gap (1 bp) |
| A. nanodes | MK820616 | 154,077 | 37.0 | 80/4 | 30 | 4 | rpl22 (34 bp) | ycf1 (1023 bp) gap (11 bp) |
| A. oschaninii | MK411816 | 153,580 | 36.8 | 80/1 | 30 | 4 | rpl22 (33 bp) | ycf1 (1066 bp) gap (1 bp) |
| A. polyrhizum | MK820618 | 153,086 | 36.9 | 80/1 | 30 | 4 | rpl22 (16 bp) | ycf1 (910 bp) gap (28 bp) |
| A. prattii | MG739457 | 154,482 | 37.0 | 80/3 | 30 | 4 | rpl22 (16 bp) | ycf1 (1072 bp) gap (95 bp) |
| A. przewalskianum | MK820619 | 153,245 | 36.9 | 80/1 | 30 | 4 | rpl22 (16 bp) | ycf1 (1021 bp) gap (10 bp) |
| A. rude | MH992112 | 153,697 | 36.7 | 80/1 | 30 | 4 | rpl22 (16 bp) | ycf1 (1041 bp) gap (2 bp) |
| A. schoenoprasides | MK820620 | 153,583 | 36.7 | 80/1 | 30 | 4 | rpl22 (34 bp) | ycf1 (1042 bp) gap (22 bp) |
| A. praemixtum | MK411817 | 153,226 | 36.8 | 80/1 | 30 | 4 | rpl22 (33 bp) | ycf1 (1066 bp) gap (26 bp) |
| A. pskemense | MK411815 | 153,788 | 36.7 | 80 | 30 | 4 | rpl22 (33 bp) | ycf1-ndhF overlap (2 bp) |
| A. strictum | MK820622 | 152,962 | 36.8 | 80/1 | 30 | 4 | rpl22 (29 bp) | ycf1 (1010 bp) gap (39 bp) |
| A. tuberosum | MK820623 | 157,735 | 36.9 | 80/1 | 30 | 4 | rpl22 (34 bp) | ycf1 (1044 bp) gap (2 bp) |
| A. xichuanense | MH992113 | 153,673 | 36.7 | 80/1 | 30 | 4 | rpl22 (16 bp) | ycf1 (1041 bp) gap (2 bp) |
| Nothoscordum bonariense | MT348455 | 156,559 | 37.5 | 80 | 30 | 4 | IGS (trnH-GUG-rps19) 51 bp | ycf1-ndhF overlap (14 bp) |
| Tulbagia violacea | MT323239 | 156,449 | 37.6 | 80/3 | 30 | 4 | rpl22 (9 bp) | ycf1-ndhF overlap (50 bp) |
| Gillesia graminea | MT348447 | 154,067 | 37.8 | 80/1 | 30 | 4 | rpl22 (23 bp) | ycf1-ndhF overlap (29 bp) |
| Agapanthus coddii | MT348439 | 157,055 | 37.5 | 80 | 30 | 4 | IGS (rps19-rpl22) 52 bp | ycf1-ndhF overlap (49 bp) |
| Lycoris radiata | MT348454 | 158,355 | 37.8 | 80 | 30 | 4 | IGS (rps19-rpl22) 16 bp | ycf1 (982 bp) gap (0 bp) |
| Zephyranthes mesochloa | MT323238 | 158,768 | 38 | 80 | 30 | 4 | rpl22 (3 bp) | ycf1-ndhF overlap (77 bp) |
| Calostemma purpureum | MT348445 | 159,500 | 37.7 | 80 | 30 | 4 | rpl22 (9 bp) | ycf1-ndhF overlap (38 bp) |
| Crinum asiaticum var pendunculatum | MT348448 | 158,683 | 37.8 | 80 | 30 | 4 | rpl22 (6 bp) | ycf1-ndhF overlap (8 bp) |
| Cyrtanthus mackenii | MT348446 | 159,998 | 37.6 | 80 | 30 | 4 | rpl22 (24 bp) | ycf1-ndhF overlap (3 bp) |
| Asparagus officinalis | NC034777 | 156,699 | 37.6 | 80 | 30 | 4 | IGS (rps19-rpl22) 53 bp | ycf1 (802 bp) gap (9 bp) |
| Hosta yingeri | NC039976 | 156,756 | 37.8 | 80/2 | 30 | 4 | rpl22 (29 bp) | ycf1-ndhF overlap (26 bp) |
| Yucca filamentosa | KX931467 | 157,785 | 37.8 | 80 | 30 | 4 | IGS (rps19-rpl22) 26 bp | ycf1 (959 bp) gap (9 bp) |
| Xanthorrhorea preissii | NC035996 | 158,116 | 37.9 | 80 | 30 | 4 | IGS (rps19-rpl22) 46 bp | ycf1-ndhF overlap (51 bp) |
| Iris sanguinea | KT626943 | 150,862 | 38 | 80 | 30 | 4 | IGS (rps19-rpl22) 37 bp | ycf1-ndhF overlap (49 bp) |
a: infA loss; b: rpl22 loss; c: ndhF loss; d: ndhG loss; e: rps16 loss.