@ARTICLE{TreeBASE2Ref29629,
author = {yunxia li and Xiao-Hua Jin},
title = {Phylogenomics of Orchidaceae based on plastid and mitochondrial genomes.},
year = {2019},
keywords = {Cypripedioideae, mitochondrial genome, mycoheterotrophic orchids, Orchidaceae, plastid genome, Vanilloideae},
doi = {10.1016/j.ympev.2019.106540},
url = {http://},
pmid = {},
journal = {Molecular Phylogenetics and Evolution},
volume = {139},
number = {},
pages = {106540},
abstract = {To advance our knowledge of orchid relationships and timing of their relative divergences, we used 76 protein-coding genes from plastomes (ptCDS) and 38 protein-coding genes from mitochondrial genomes (mtCDS) of 74 orchids representing the five subfamilies and 18 tribes of Orchidaceae, to reconstruct the phylogeny and temporal evolution of the Orchidaceae. Our results indicated the backbone of Orchidaceae is well supported with both datasets, but there are conflicts between these trees. The phylogenetic positions of two subfamilies (Vanilloideae and Cypripedioideae) are reversed in these two analyses. The phylogenetic positions of several tribes and subtribes, such as Epipogiinae, Gastrodieae, Nerviliinae, and Tropidieae, are well resolved in mtCDS tree. Thaieae have a different position among higher Epidendroideae, instead of sister to the higher Epidendroideae. Interrelationships of several recently radiated tribes within Epidendroideae, including Vandeae, Collabieae, Cymbidieae, Epidendreae, Podochileae, and Vandeae, were resolved with good support in the ptCDS tree, but most are not in the mtCDS tree. Conflicts between the two datasets may be attributed to the different substitution rates in these two genomes and heterogeneity of substitution rate of plastome. Molecular dating indicated that the first three subfamilies, Apostasioideae, Cypripedioideae and Vanilloideae, diverged relatively quickly, and then there was a longer period before the last two subfamilies, Orchidoideae and Epidendroideae, began to radiate. Most mycoheterotrophic clades of Orchidaceae evolved in the last 30 million years with the exception of Gastrodieae. }
}
Taxa for Study 24472
Citation title:
"Phylogenomics of Orchidaceae based on plastid and mitochondrial genomes.".
Study name:
"Phylogenomics of Orchidaceae based on plastid and mitochondrial genomes.".
This study is part of submission 24472
(Status: Published).
Taxa
ID |
Taxon Label |
NCBI taxid |
uBIO namebankID |
3888443 |
Allium cepa |
4679
|
2662403
|
3888437 |
Anguloa rukerii |
|
|
3888412 |
Anthogonium gracile |
159935
|
5965118
|
3888458 |
Aphyllorchis montana |
666370
|
5778013
|
3888419 |
Apostasia odorata |
280455
|
5978822
|
3888454 |
Arundina graminifolia |
78703
|
2664287
|
3888426 |
Bletilla formosana |
466243
|
1883808
|
3888481 |
Brachycorythis henryi |
|
|
3888455 |
Bulbophyllum helenae |
|
|
3888466 |
Calanthe labrosa |
|
|
3888467 |
Calanthe mannii |
|
|
3888460 |
Cephalanthera humilis |
|
|
3888453 |
Ceratostylis himalaica |
|
|
3888474 |
Cheirostylis yunnanensis |
|
|
3888444 |
Chrysoglossum ornatum |
|
|
3888450 |
Cleisostoma scolopendrifolium |
331189
|
5983944
|
3888414 |
Coelogyne fimbriata |
141728
|
5784097
|
3888447 |
Collabium formosanum |
|
|
3888476 |
Corybas taliensis |
|
|
3888478 |
Corymborkis veratrifolia |
256354
|
3491654
|
3888472 |
Cremastra appendiculata |
459596
|
5893138
|
3888461 |
Cryptochilus luteus |
|
|
3888465 |
Cryptostylis arachnites |
256355
|
1883898
|
3888436 |
Cymbidium macrorhizon |
|
|
3888440 |
Cypripedilum lichiangense |
|
|
3888409 |
Cypripedium henryi |
476167
|
5990271
|
3888441 |
Cypripedium tibeticum |
|
|
3888433 |
Dactylorhiza viride |
230577
|
9351041
|
3888475 |
Danxiaorchis singchii |
|
|
3888424 |
Dendrobium hainanense |
467197
|
5784200
|
3888483 |
Dendrobium moniliforme |
142614
|
3491777
|
3888470 |
Epigeneium amplum |
234050
|
1883995
|
3888416 |
Epipactis mairei |
|
8401069
|
3888484 |
Epipactis royleana |
|
8590279
|
3888427 |
Epipactis veratrifolia |
|
8584445
|
3888415 |
Epipogium aphyllum |
449980
|
5768929
|
3888445 |
Eria amica |
|
|
3888442 |
Eriodes barbata |
|
|
3888479 |
Eulophia nuda |
78774
|
5780070
|
3888410 |
Galeola lindleyana |
|
|
3888446 |
Gastrodia elata |
91201
|
5769072
|
3888423 |
Gennaria griffthii |
|
|
3888428 |
Habenaria glaucifolia |
|
|
3888431 |
Hancockia uniflora |
|
|
3888430 |
Hemipilia cordifolia |
|
|
3888429 |
Holcoglossum amesianum |
536147
|
8916132
|
3888473 |
Holcoglossum himalaicum |
|
|
3888435 |
Holcoglossum quasipinifolium |
|
|
3888439 |
Hsenhsua chrysea |
|
|
3888408 |
Hygrochilus parishii |
331205
|
5983950
|
3888451 |
Liparis bootanensis |
|
|
3888482 |
Malaxis monophyllos |
426910
|
2663116
|
3888425 |
Maxillaria variablis |
|
|
3888432 |
Neottia alternifolia |
|
|
3888471 |
Neottia cordata |
669720
|
8914163
|
3888456 |
Nervilia aragoana |
152892
|
5775606
|
3888413 |
Neuwiedia veratrifolia |
38223
|
5779947
|
3888420 |
Pelatantheria rivesii |
|
|
3888422 |
Phaius flavus |
679630
|
3508988
|
3888485 |
Phalaenopsis marriottiana var parishii |
|
|
3888468 |
Phalaenopsis zhejiangensis |
|
|
3888457 |
Phoenix dactylifera |
42345
|
2662206
|
3888448 |
Pholidota recurva |
|
|
3888452 |
Platanthera minor |
|
|
3888469 |
Pleione bulbocodioides |
141752
|
5760434
|
3888434 |
Plocoglottis bokorensis |
|
|
3888417 |
Pogonia yunnanensis |
|
|
3888459 |
Polystachya concreta |
38197
|
2663216
|
3888463 |
Risleya atropurpurea |
|
|
3888418 |
Shizhenia pingulata |
|
|
3888421 |
Sobralia macrantha |
78844
|
5855581
|
3888438 |
Spiranthes sinensis |
117406
|
3493712
|
3888480 |
Stanhopea graveolens |
|
|
3888411 |
Thaia saprophytica |
667022
|
9284545
|
3888477 |
Trichotosia pulvinata |
|
|
3888449 |
Tropidia angulosa |
|
|
3888464 |
Vanda brunnea |
536165
|
5759928
|
3888462 |
Vanilla planifolia |
51239
|
2663163
|