Table 2.
Summary of Major Features of Eleocharis, Hypolytrum, and Basal Poales Plastid Genomes
| Family |
Cyperaceae |
Bromeliaceae |
Typhaceae |
||
|---|---|---|---|---|---|
| Taxon | Eleocharis dulcis (Type 2) | Eleocharis cellulosa (Type 2) | Hypolytrum nemorum | Ananas comosus | Typha latifolia |
| Genome size (bp) | 199,561 | 193,234 | 180,648 | 159,636 | 161,572 |
| LSC (% of genome) | 117,896 (59.1) | 112,881 (58.4) | 95,644 (52.9) | 87,482 (54.8) | 89,140 (55.2) |
| SSC (% of genome) | 9,601 (4.8) | 10,311 (5.3) | 8,150 (4.5) | 18,622 (11.7) | 19,652 (12.2) |
| IR (% of genome) | 36,032 (18.1) | 35,021 (18.1) | 38,427 (21.3) | 26,766 (16.8) | 26,390 (16.3) |
| Total number of genes | 139 | 132 | 135 | 131 | 131 |
| Number of unique genes | 105 | 105 | 110 | 113 | 113 |
| Number of unique protein-coding genes (duplicated in IR) | 72 (14) | 72 (12) | 76 (12) | 79 (6) | 79 (6) |
| Number of unique tRNA genes (duplicated in IR) | 29 (10) | 29 (9) | 30 (8) | 30 (8) | 30 (8) |
| Number of unique rRNA genes (duplicated in IR) | 4 (4) | 4 (4) | 4 (4) | 4 (4) | 4 (4) |
| Number of genes with introns | 17 | 17 | 18 | 18 | 18 |
| GC content (%) | 32.6 | 32.8 | 34.9 | 37.4 | 36.6 |
| GC content of IR/LSC/SSC (%) | 37.6/30.2/25.5 | 37.8/30.4/25.8 | 38.5/32.6/28.1 | 42.7/35.4/31.4 | 42.4/34.4/30.5 |
| Genic DNA (% of genome, GC [%]) | 76,207 (38.2, 38.4) | 74,394 (38.5, 38.5) | 98,905 (54.8, 38.1) | 91,317 (57.2, 40.2) | 91,212 (56.4, 39.9) |
| Intergenic spacers (% of genome, GC [%]) | 123,354 (61.8, 29.1) | 118,840 (61.5, 29.3) | 81,743 (45.2, 31.1) | 68,611 (42.8, 33.7) | 70,541 (43.6, 32.4) |
| Gene density | 0.70 | 0.68 | 0.75 | 0.82 | 0.81 |
| Putative gene losses | accD, clpP, rpl23, rps18, ycf1, ycf2, infA, and trnT-GGU | accD, clpP, rpl23, rps18, ycf1, ycf2, infA, and trnT-GGU | accD, rps18, and infA | — | — |
| Putative gene duplications | rpoA (2) rpl36 (4), trnfM-CAU (6), trnH-GUG (3), trnP-UGG (3), and trnV-GAC (3) | rpl36 (2)* trnfM-CAU (3), trnH-GUG (3), and trnV-GAC (3) | trnV-GAC (3) | — | — |
Note.—The number in ( ) in putative gene duplications indicates the number of copies. Asterisk (*) on rpl36 gene indicates gene duplication in only plastome type 4 of E. cellulosa.