Abstract Detail

Pteridology

Wickell, David [1], Li, Fay-Wei [2], Kuo, Li-Yaung [3], Huang, Xiong [4], Li, Quanzi [4].

Gene fractionation and differential expression of homoeologues following whole genome duplication in the tree fern, Alsophila spinulosa.

Ferns are known for having high base chromosome counts as well as exceptionally large genomes. While several outliers exist among the heterosporous Salviniales, the average chromosome number in homosporous ferns is nearly four times that of angiosperms. One of the primary forces driving increases in genome size in plants and especially in ferns is whole genome duplication (WGD). While recent WGD has been thoroughly researched in a wide range of polyploid fern taxa, the genomic consequences of ancient WGD remain elusive owing largely to a lack of high quality genome assemblies for homosporous ferns. Here we focus on the tree fern Alsophila spinulosa (Cyatheaceae), combining a chromosome-level assembly with extensive RNA-seq data in order to assess the history and effects of WGD. We find that A. spinulosa has a rich history of WGD experiencing at least two duplication events. Furthermore, A. spinulosa appears to have retained an unprecedented degree of synteny among homoeologous gene pairs resulting from the most recent WGD common to all members of Cyatheaceae. We identify functional biases in gene retention following WGD and utilize RNA-seq data to characterize divergent expression of homoeologues across a wide range of tissue types. As one of the first chromosome-level genome assemblies for any fern, this project represents a crucial component of our understanding of the processes governing genomic rearrangement following WGD in seed-free plants. Additionally, it has broad implications on the forces that drive the incredible diversity in genome size across the plant tree of life.

1 - Cornell University, Plant Biology, 533 Tower Rd, Ithaca, NY, 14853, USA
2 - Boyce Thompson Institute, 533 Tower Rd, Ithaca, NY, 14853, United States
3 - National Tsing Hua University, Institute of Molecular & Cellular Biology, Hsinchu, Taiwan
4 - Chinese Academy of Forestry, Beijing, China

Keywords:
ferns
Pteridology
WGD
genomics
RNA-seq
Cyatheaceae
genome size.

Presentation Type: Oral Paper
Session: PTR2, Pteridology II
Location: /
Date: Monday, July 19th, 2021
Time: 1:30 PM(EDT)
Number: PTR2001
Abstract ID:552
Candidate for Awards:Edgar T. Wherry award