Plant Genomics Data

Green Biome Institute

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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

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

Coming soon.
Coming soon.

 

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