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Ginkgo biloba  is a pharmaceutical resource for terpenes and flavonoids. However, few insights discussed endophytes’ role in  Ginkgo , and whether genetic exchange happens between  Ginkgo  and endophytes remains unclear. Herein, functional gene profiles and repetitive sequences were analyzed to focus on these issues. A total of 25 endophyte strains were isolated from the  Ginkgo  root and distributed in 16 genera of 6 phyla. Significant morphological diversities lead to the diversity in the COG functional classification. KEGG mapping revealed that endophytic bacteria and fungi potentially synthesize chalcone, while endophytic fungi might also promote flavonoid derivatization. Both bacteria and fungi may facilitate the lignin synthesis.  Aspergillus  sp. Gbtc_1 exhibited the feasibility of regulating alcohols to lignans. Although  Ginkgo  and the endophytes have not observed the critical levopimaradiene synthase in ginkgolides synthesis, the upstream pathways of terpenoid precursors are likely intact. The MVK genes in  Ginkgo  may have alternative non-homologous copies or be compensated by endophytes in long-term symbiosis.  Cellulomonas  sp. Gbtc_1 became the only bacteria to harbor both MEP and MVA pathways. Endophytes may perform the mutual transformation of IPP and DMAPP in the root.  Ginkgo  and bacteria may lead to the synthesis and derivatization of the carotenoid pathway. The isoquinoline alkaloid biosynthesis seemed lost in the  Ginkgo  root community, but  L -dopa is more probably converted into dopamine as an essential signal-transduction substance. So, endophytes may participate in the secondary metabolism of the  Ginkgo  in a shared or complementary manner. Moreover, a few endophytic sequences predicted as  Ty3/Gypsy  and  Ty1/Copia  superfamilies exhibited extremely high similarity to those of  Ginkgo . CDSs in such endophytic LTR-RT sequences were also highly homologous to one  Ginkgo  CDS. Therefore, LTR-RTs may be a rare unit flowing between the  Ginkgo  host and endophytes to exchange genetic information. Collectively, this research effectively expanded the insight on the symbiotic relationship between the  Ginkgo  host and the endophytes in the root.

frontiers in plant science

Root Endophytes and Ginkgo biloba Are Likely to Share and Compensate Secondary Metabolic Processes, and Potentially Exchange Genetic Information by LTR-RTs