Abstract Detail

Phylogenomics

Kim, Young-kee [1], Jo, Sangjin [1], Kwak, Myounghai [2], Kim, Ki-Joong [1].

Two contrasting modes of plastome evolution from photosynthetic and mycoheterotrophic vanilloid orchids (Vanilloideae, Orchidaceae).

Vanilloideae is one of five subfamilies of Orchidaceae and composed of fourteen genera and 245 species. Some of these species are mycoheterotrophic species. In order to understand the evolutionary dynamics of vanilloid orchids, six new plastomes (two Lecanorchis, two Pogonia, and two Vanilla species) were completely decoded and compared to available data. Pogonia japonica has the longest plastome, 158,200 bp in length. And Lecanorchis japonica has the shortest plastome, 70,498 bp in length. First, the drastic contraction of small single copy (SSC) regions occurred in the vanilloid orchid plastomes. While related subfamily Apostasioideae has a normal size of SSC region, the vanilloid plastomes have substantially shortened SSC region. The two recognized tribes (Pogonieae and Vanilleae) of Vanilloideae show different levels of SSC contraction. Second, the other special feature of Vanilloideae plastome is the gene losses. Photosynthetic vanilloid species such as Pogonia and Vanilla only lost ndh gene class, which show the degradation stage 1 of plastome. Mycoheterotrophic vanilloid species such as Cyrotsia and Lecanorchis, however, lost almost all photosynthesis related genes, which show degradation stage 3 or 4 of plastome. Third, a total of ten genome rearrangements were found among fourteen vanilloid plastomes compare to four apostasioid plastomes. These genome rearrangements are related to the gene loss events. Eight regions of vanilloid plastomes shifted their position between SC and IR. Synonymous substitution rates of IR in-cooperated regions substantially decreased compare to reference taxa. Majority gene regions (16 of 24) of mycoheterotrophic species show elevated levels of base substitution rates compare to photosynthetic species. Among them, six regions are statistically significant in the result of RELAX analysis. Therefore, several plastome regions of mycoheterotrophic species are under relaxation selection pressure. In contrast, rpl2 gene is under the intensification selection pressure. Finally, the maximum likelihood tree supports the previous phylogenetic position of Vanilloideae that locates between Apostasioideae and Cypripedioideae.

1 - Korea University, Department of Life Sciences, 145, Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
2 - Biological and Genetic Resources Utilization Division, National Institute of Biological Resources, Hwangyeong-ro, Seo-gu, Incheon, 22689, Republic of Korea

Keywords:
Orchidaceae
Vanilloideae
phylogenomics
Plastome
gene loss
substitution rates.

Presentation Type: Poster
Session: P3, Phylogenomics Posters
Location: Virtual/Virtual
Date: Wednesday, July 21st, 2021
Time: 5:00 PM(EDT)
Number: P3PL002
Abstract ID:266
Candidate for Awards:None