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To begin, read this attached article that appeared in the Philadelphia Inquirer in February 2021.(or read the online version here).  The reporter interviewed local seed experts who cite names of plants with strong Philadelphia or Philadelphia-area connections and provides seed sources both from 

Roughwood Seeds   operated by food historian William Woys Weaver and 

Truelove Seeds Philadelphia Collection  click on each variety to get the seed's history and Philadelphia connection

Other Plants With Philadelphia Connections

Franklinia alatamaha: In 1765 Franklinia tree was discovered by John and William Bartram on the Altamaha River, Georgia.Years later, William returned to Georgia to collect seeds and grow the plant in Bartram’s Garden. The tree was last seen in the wild in 1803. All Franklinia are descended from those grown by the Bartrams.

The following list of plants with Philadelphia connections comes from garden historian and writer Nicole Juday:

Seckel Pear—discovered as a seedling on a farm in the early 1800s, at what’s now 21st and Pattinson Avenue (in South Philadelphia) .

Pink Flowering dogwood—discovered in the Wissahickon by Thomas Meehan. See Nicole's article on this discovery: ,

First red rose, Rosa chinensis—Imported from India, grown by William Hamilton at The Woodlands  in West Philadelphia

First female fruiting Gingko—William Hamilton, Woodlands

Several extinct roses rediscovered at Wyck Historic House and Garden, in Philadelphia's Germantown neighborhood

Lady Petre Pear—sent to Bartram from Lord Petre in England. A very old one exists in Germantown.
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Selected Eponyms

Franklinia - named for Benjamin Franklin, who had obvious Philadelphia connections

Bartonia – named for Benjamin Smith Barton (1766-1815) wrote first textbook in America on botany; taught at University of Pennsylvania

Mahonia -  named for  Philadelphia seed merchant Bernard McMahon (sometimes spelled "M'Mahon")  an Irish-born American nurseryman and horticulturist. Thomas Nuttall, a British botanist, named the genus Mahonia in 1818 to honor McMahon, who was also a friend of Thomas Jefferson. McMahon was a prominent figure in the development of American horticulture and served as a steward of plant collections from the Lewis and Clark Expedition. 

Lilium philadelphicum - honors Philadelphia. 

Hymenocallis henryae –  a daylily named for botanist Mary Gibson Henry  - she lived in Lower Merion, a suburb close to Philadelphia (and was a long-time member of PHS Council)

Itea virginica ‘Henry’s Garnet’ -  Mary Gibson Henry

Phlox – ‘Chattahoochee’ – Mary Gibson Henry  (Henry Source)

Here are related FAQs in askPHS

https://pennhort.libanswers.com/faq/282721

https://pennhort.libanswers.com/faq/251296

https://pennhort.libanswers.com/faq/251328

                                                                          -------   Janet Evans, PHS McLean Library Associate Director