Plant Genomics Data

Green Biome Institute

The GBI is striving to publish our draft genomic profiles in as transparent a manner as possible.
We will therefore compose a White Papers for every plant dataset created illustrating our data quality and the details of analysis methodology. These will be available shortly. If you have questions or inquiries, please contact Dr. Chris Baysdorfer.

The table below contains links to all available sequencing data we have assembled on endangered California plants to date.The first accession number link will take you to the bioproject page of Genbank and from there you can access raw datasets and other information. The second link under Calflora takes you to the appropriate CalFlora page for each plant type. The in-depth Calflora reviews of each of California's plants are a great resource for plant information. Lastly, several plants are listed as unavailable. Data for these plants exists and if you are interested in a not-yet-released plant, please reach out to our PIs in charge of the plant species. Dr. Ana Almeida is in charge of the Manzanita program. All other plants including; the Fritillaria, Scoliopus, and Prosartes programs are managed by Dr. Chris Baysdorfer. We hope you find the information useful and encourage you to reach out to us if you have any questions!

RARE PLANT GENOMIC DATA AND REPORTS

Sequence and Plant Data

The table contains links to all available sequencing data we have assembled on endangered California plants to date.
Name	Common Name(s)	CNPS classification	BioProject Accession Number(s)	Calflora	Data Released
Abronia alpina	Ramshaw meadows abronia	1B.1			Yes
Agrostis hooveri	Hoover's bent grass, Hoover's bentgrass	1B.2			Yes
Astragalus pycnostachyus var. lanosissimus	Marsh milk vetch, Marsh milkvetch	1B.1			Yes
Baccharis plummerae ssp. glabrata	San simeon baccharis	1B.2			Yes
Baccharis vanessae	Encinitas baccharis	1B.1			Yes
Balsamorhiza macrolepis	Big scale balsam root, California balsamroot	1B.2			Yes
Bensoniella oregona	Bensoniella	1B.1			Yes
Berberis nevinii	Nevin's barberry	1B.1			Yes
Berberis pinnata ssp. insularis	Island barberry	1B.2			Yes
Brodiaea filifolia	Thread leaved brodiaea, Threadleaf brodiaea	1B.1			Yes
Brodiaea orcutti	Orcutt's brodiaea	1B.1			Yes
Brodiaea pallida	Chinese camp brodiaea	1B.1	PRJNA1083552		Yes
Calystegia purpurata ssp. saxicola	Bodega morning glory, Pacific false bindweed	1B.2			Yes
Calystegia stebbinsii	Cutleaf morning glory, El dorado morningglory, Stebbins's morning glory	1B.1			Yes
Campanula californica	Swamp harebell	1B.2			Yes
Carex klamathensis		1B.2			Yes
Carex xerophila	chaparral sedge	1B.2			Yes
Castilleja ambigua var. humboldtiensis	Humboldt bay owl's-clover	1B.2			Yes
Castilleja hololeuca	Island white-felted paintbrush	1B.2			Yes
Castilleja mendocinensis	Mendocino coast paintbrush	1B.2			Yes
Castilleja mollis	Soft leaved indian paintbrush	1B.1			Yes
Ceanothus confusus	Rincon ridge ceanothus	1B.1			Yes
Ceanothus divergens	Calistoga ceanothus	1B.2			Yes
Ceanothus foliosus var. vineatus	Vine hill ceanothus	1B.1			Yes
Ceanothus hearstiorum	Hearst ranch buckbrush, Hearst's ceanothus	1B.2			Yes
Ceanothus maritimus	Maritime ceanothus, San luis obispo ceanothus	1B.2			Yes
Ceanothus roderickii	Pine hill buckbrush, Pine hill ceanothus	1B.1			Yes
Centromadia parryi ssp. parryi	Pappose tarplant	1B.2			Yes
Centromadia pungens ssp. laevis	Smooth tarplant	1B.1			Yes
Chlorogalum grandiflorum	Red hills soap plant, Red hills soaproot	1B.2			Yes
Chlorogalum purpureum var. purpureum	Purple amole	1B.1			Yes
Chloropyron palmatum	Palmate-bracted bird's-beak	1B.1			Yes
Chorizanthe robusta var. hartwegii	Robust spineflower, Scott's valley spineflower	1B.1			Yes
Clarkia franciscana	Presidio clarkia	1B.1			Yes
Clarkia imbricata	Vine hill clarkia	1B.1			Yes
Clarkia jolonensis	Jolon clarkia	1B.2			Yes
Clarkia mildrediae ssp. mildrediae	Mildred's clarkia	1B.3			Yes
Crocanthemum greenei	Island rush-rose	1B.2			Yes
Deinandra bacigalupii	Livermore moonshine, Livermore tarplant	1B.1			Yes
Delphinium bakeri	Baker's delphinium, Baker's larkspur	1B.1			Yes
Delphinium luteum	Golden larkspur, Yellow larkspur	1B.1			Yes
Dirca occidentalis	Western leatherwood	1B.2			Yes
Dudleya densiflora	San gabriel mountains liveforever, San gabriel mtns. dudleya	1B.1			Yes
Dudleya gnoma	Munchkin liveforever	1B.1			Yes
dudleya setchellii	Santa clara valley dudleya	1B.1			Yes
Erigeron maniopotamicus	Mad river fleabane daisy	1B.2			Yes
Eriodictyon altissimum	Indian knob mountainbalm	1B.1			Yes
Eriogonum crocatum	Conejo buckwheat	1B.2			Yes
Eriogonum giganteum var. compactum	Santa barbara island buckwheat	1B.3			Yes
Eriogonum grande var. rubescens	Red flowered buckwheat, Redflower buckwheat	1B.2			Yes
Eriogonum grande var. timorum	San nicolas island buckwheat	1B.1			Yes
Eriogonum luteolum var. saltuarium	Goldencarpet buckwheat	1B.2			Yes
Eriogonum ovalifolium var. vineum	Cushenbury buckwheat	1B.1			Yes
Eriogonum truncatum	Mt. Diablo buckwheat	1B.1			Yes
Eriogonum umbellatum var. lautum	Scott valley buckwheat	1B.1			Yes
Eryngium jepsonii	Jepson's eryngo	1B.2			Yes
Eryngium pinnatisectum	Tuolumne button celery, Tuolumne eryngo	1B.2			Yes
Erysimum concinnum	Bluff wallflower, Headland wallflower	1B.2			Yes
Frangula purshiana ssp. ultramafica	Caribou coffeeberry	1B.2			Yes
Fremontodendron decumbens	Pine hill flannelbush	1B.2			Yes
Fremontodendron mexicanum	Mexican flannelbush	1B.1			Yes
Galium buxifolium	Box bedstraw	1B.2			Yes
Galium californicum ssp. luciense	Cone Peak bedstraw	1B.3			Yes
Galium californicum ssp. sierrae	El dorado bedstraw	1B.2			Yes
Gambelia speciosa	Showy island snapdragon	1B.2			Yes
Gambelia speciosa	Showy island snapdragon	1B.2			Yes
Helianthella castanea	Mt. diablo helianthella	1B.2			Yes
Heuchera brevistaminea	Laguna mountain alumroot, Mt. laguna alumroot	1B.3			Yes
Heuchera maxima	Island alum root, Island alumroot, Jill of the rocks	1B.2			Yes
Hoita strobilina	Loma Prieta hoita, Loma prieta psoralea	1B.1			Yes
Horkelia marinensis	Point reyes horkelia	1B.2			Yes
Horkelia parryi	Parry horkelia, Parry's horkelia	1B.2			Yes
Lasthenia conjugens	Contra costa goldfields	1B.1			Yes
Lavatera assurgentiflora ssp. glabra	Southern island mallow	1B.1			Yes
Lilium maritimum	Coast lily	1B.1			Yes
Lilium occidentale	Western lily	1B.1			Yes
Lilium pardalinum ssp. pitkinense	Pitkin marsh lily	1B.1			Yes
Limnanthes douglasii ssp. sulphurea	Douglas' meadowfoam, Meadow foam, Point Reyes meadowfoam	1B.2			Yes
Lonicera subspicata var. subspicata	Santa Barbara honeysuckle, Southern honeysuckle	1B.2			Yes
Lyonothamnus floribundus ssp. aspleniifolius	Santa cruz island ironwood	1B.2			Yes
Malacothamnus abbottii	Abbott's bushmallow	1B.1			Yes
Malacothamnus fasciculatus var. nesioticus	Santa Cruz Island bushmallow	1B.1			Yes
Malacothrix indecora	Santa cruz island cliff aster, Santa cruz island desertdandelion, Santa cruz island malacothrix	1B.1			Yes
Monardella australis ssp. jokerstii	Jokerst's monardella	1B.1			Yes
Monardella palmeri	Palmer's monardella	1B.2			Yes
Munzothamnus blairii	Blair's wirelettuce	1B.2			Yes
Neviusia cliftonii	Shasta snow wreath	1B.2			Yes
Noccaea fendleri ssp. californica	Kneeland prairie pennycress	1B.1			Yes
Nolina interrata	Dehesa beargrass, Dehesa nolina	1B.1			Yes
Oenothera wolfii	Wolf's evening primrose	1B.1			Yes
Packera layneae	Layne's ragwort	1B.2			Yes
Panicum acuminatum var. thermale	Geysers panicum	1B.2			Yes
Penstemon newberryi var. sonomensis	Sonoma beardtongue	1B.3			Yes
Pinus contorta ssp. bolanderi	Bolander pine, Bolander's beach pine	1B.2			Yes
Plagiobothrys chorisianus var. chorisianus	Artist's popcornflower, Choris's popcorn flower	1B.2			Yes
Polygonum hickmanii	Hickman's knotweed, Scotts Valley polygonum	1B.1			Yes
Quercus dumosa	Coastal sage scrub oak, Nuttall's scrub oak	1B.1			Yes
Ribes viburnifolium	Catalina currant, Island gooseberry, Santa catalina island currant	1B.2			Yes
Rosa woodsii var. glabrata	Woods' rose	1B.1			Yes
Salvia brandegeei	Brandegee's sage, Santa rosa island sage	1B.2			Yes
Sidalcea calycosa ssp. rhizomata	Point reyes checkerbloom, Pt. reyes checkerbloom, Pt. reyes sidalcea	1B.2			Yes
Sidalcea oregana ssp. valida	Kenwood marsh checkerbloom	1B.1			Yes
Silene verecunda ssp. verecunda	Dolores campion, San francisco campion	1B.2			Yes
Streptanthus albidus ssp. albidus	Metcalf canyon jewel flower, Metcalf canyon jewelflower	1B.1			Yes
Streptanthus albidus ssp. peramoenus	Most beautiful jewel flower, Most beautiful jewelflower	1B.2			Yes
Streptanthus hispidus	Mt. diablo jewel flower, Mt. diablo jewelflower	1B.3			Yes
Streptanthus tortuosus ssp. truei	True's mountain jewelflower	1B.1			Yes
Suaeda esteroa	Estuary seablite	1B.2			Yes
Tracyina rostrata	Beaked tracyina, Indian headdress	1B.2			Yes
Wyethia reticulata	El dorado county mule ears, El dorado mule ears, Eldorado wyethia	1B.2			Yes
Arctostaphylos andersonii	Heartleaf manzanita, Santa cruz manzanita	1B.2			No
Arctostaphylos auriculata	Mount Diablo manzanita	1B.3			No
Arctostaphylos bakeri ssp. bakeri	Baker's manzanita	1B.1			No
Arctostaphylos bakeri ssp. sublaevis	The cedars manzanita	1B.2			No
Arctostaphylos confertiflora	Santa rosa island manzanita	1B.2			No
Arctostaphylos cruzensis	Arroyo de la cruz manzanita, La cruz manzanita	1B.2			No
Arctostaphylos densiflora	Vine hill manzanita	1B.1			No
Arctostaphylos edmundsii	Little sur manzanita	1B.2			No
Arctostaphylos franciscana	Franciscan manzanita	1B.1			No
Arctostaphylos gabilanensis	Gabilan mountains manzanita	1B.2			No
Arctostaphylos glandulosa ssp. crassifolia	Costa baja manzanita, Del mar manzanita	1B.1			No
Arctostaphylos hookeri ssp. hearstiorum	Hearst's manzanita	1B.2			No
Arctostaphylos hookeri ssp. hookeri	Hooker's manzanita, Monterey manzanita	1B.2			No
Arctostaphylos imbricata	San bruno mountain manzanita, San bruno mtn. manzanita	1B.1			No
Arctostaphylos manzanita ssp. laevigata	Contra costa manzanita	1B.2			No
Arctostaphylos montana ssp. ravenii	Presidio manzanita	1B.1			No
Arctostaphylos montereyensis	Monterey manzanita, Toro manzanita	1B.2			No
Arctostaphylos morroensis	Morro manzanita	1B.1			No
Arctostaphylos nummularia ssp. mendocinoensis	Pygmy manzanita	1B.2			No
Arctostaphylos ohloneana	Ohlone manzanita	1B.1			No
Arctostaphylos osoensis	Oso manzanita	1B.2			No
Arctostaphylos Otayensis	Otay manzanita	1B.2			No
Arctostaphylos pacifica	Pacific manzanita	1B.1			No
Arctostaphylos pajaroensis	Pajaro manzanita	1B.1			No
Arctostaphylos pallida	Alameda manzanita, Oakland hills manzanita, Pallid manzanita	1B.1			No
Arctostaphylos pechoensis	Pecho manzanita	1B.2			No
Arctostaphylos pumila	Dune manzanita, Sandmat manzanita	1B.2			No
Arctostaphylos purissima	La purisima manzanita, La purissima manzanita	1B.1			No
Arctostaphylos rainbowensis	Rainbow manzanita	1B.1			No
Arctostaphylos refugioensis	Refugio manzanita	1B.2			No
Arctostaphylos regismontana	Kings mountain manzanita, Kings mtn. manzanita	1B.2			No
Arctostaphylos rudis	Sand mesa manzanita, Shagbark manzanita	1B.2			No
Arctostaphylos silvicola	Bonny doon manzanita, Silverleaf manzanita	1B.2			No
Arctostaphylos stanfordiana ssp. decumbens	Rincon manzanita	1B.1			No
Arctostaphylos stanfordiana ssp. raichei	Rincon manzanita	1B.1			No
Arctostaphylos tomentosa ssp. daciticola	Dacite manzanita	1B.1			No
Arctostaphylos virgata	Bolinas manzanita, Marin manzanita	1B.2			No
Cercocarpus traskiae	Catalina Island Mountain Mahogany	1B.1			No
Fritillaria affinis var. tristulis	Coast checker lily, Mission bells	1B.1			No
Fritillaria agrestis	Stinkbells	4.2			No
Fritillaria agrestis	Stinkbells	4.2			No
Fritillaria biflora	Chocolate lily	CBR			No
Fritillaria biflora var. ineziana	Hillsborough chocolate lily	1B.1			No
Fritillaria falcata	Talus fritillary	1B.2			No
Fritillaria liliacea	Fragrant fritillary	1B.2			No
Fritillaria liliacea	Fragrant fritillary	1B.2			No
Fritillaria liliacea	Fragrant fritillary	1B.2			No
Fritillaria pluriflora	Adobe lily	1B.2			No
Fritillaria roderickii	Roderick's fritillary	1B.1			No
Fritillaria striata	Striped adobe lily	1B.1			No
Scoliopus bigelovii	California fetid adderstongue, Fetid adder's tongue, Slink pod	S1			No
Scoliopus hallii	Oregon Fetid Adder's Tongue	S4			No
Prosartes parvifolia	Siskiyou bells	1B.2			No

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