Abstract Detail

Comparative Genomics/Transcriptomics

Silva, AndersoN [1], Fisher, Kirsten [2], Bei, Gao [3], Stark, Lloyd [4], Mishler, Brent [5], Zhang, Daoyuan [6], Oliver, Melvin [7].

The genome of the desiccation tolerant moss Syntrichia caninervisand its response to abiotic stress.

Using Dovetail’s proprietary proximity ligation technologies, we sequenced the genome of a single Syntrcihia caninervisfemale derived from Mojave Desert of the United States. The final reference genome assembly is at chromosome scale with 13 assembled scaffolds (chromosomes) ranging from 14.9 Mb to 37.3 Mb in length. The genome annotation revealed 16,545 nuclear encoded protein-coding genes with an average coding-sequence length of 1,513 kb. Our genome annotation recovered 403 complete BUSCOs of the 430 highly conserved core proteins in the Viridiplantae. Among the 16,545 genes predicted in S. caninervis, a total of 15,793 (95.4%) demonstrated at least partial sequence similarities (BLASTP E-value < 1e-5) toPhyscomitrella patensproteins and all 16,545 genes could be annotated with InterProScan domain/family information. The intra-genomic synteny detected between the genomes S. caninervisand P. patensidentifies a total of 1003 syntenic blocks with 5,412 gene pairs. In addition, we detected in each S. caninervisgene a maximum of four syntenic genes in P. patensgenome. This might relate to the two successive whole genome duplication events (Pp-WGD2) reported for P. patensand suggests chromosomal or segmental losses in the evolutionary history of S. caninervis. We generated a complete transcriptome for S. caninervis, and identified 3.972 transcripts that were differentially accumulated in response to environmental stress: heat, cold, dehydration/desiccation, and rehydration. A dominant pattern (DP) analysis script, used to analyze the patterns of changes in transcript abundance for each stress, identified 11 DPs. These patterns in transcript abundance suggested the occurrence of processes related to the plasticity of the stress responses of the moss exposed to altered environments. Functional analysis of each DP gave insight into processes important in each stress response. For example, DP2 transcripts, a possible signature transcript set for dehydration tolerance, revealed a significant enrichment of transcripts involved in membrane function and stability, responses to desiccation, and cysteine biosynthesis. DP2 contained over 240 transcripts that are involved in the response to desiccation, and we are currently investigating the control process that leads to the change in transcript abundance: transcription or sequestration (demonstrated to be of major importance in the response of the moss to desiccation). Assessed transcriptomal changes during dehydration of S. caninerviswill greatly facilitate map-based cloning of important genes for crop improvement, particularly those involved in abiotic stress tolerance.

Related Links:
Desiccation & Diversity in Dryland Mosses

1 - University of Missouri, Plant Sciences, 214 Curtis Hall, Columbia, Missouri, 65211, USA
2 - California State University, Los Angeles, 2362 Tanoble Dr., Altadena, CA, 91001.0, United States
3 - Chinese University of Hong Kong, School of Life Sciences and the State Key Laboratory of Agrobiotechnology, Hong Kong, Hong Kong, China
4 - University Of Nevada, Las Vegas, School Of Life Sciences, Las Vegas, NV, 89154, United States
5 - University Of California, Berkeley, Department Of Integrative Biology, University And Jepson Herbaria, 1001 Valley Life Sciences Building, # 2465, Berkeley, CA, 94720, United States
6 - Xinjiang Institute of Ecology and Geography, Key Laboratory of Biogeography and Bioresources, Urumqi, Xinjiang , 830011, China
7 - USDA-ARS, Plant Genetics Research Unit, 206 Curtis Hall, Columbia, MIssouri, 65211, USA

Keywords:
syntrichia caninervis
genome
Desiccation
Transcriptomics.

Presentation Type: Oral Paper
Session: CG1, Comparative Genetics/Genomics I
Location: Tucson I/Starr Pass
Date: Tuesday, July 30th, 2019
Time: 11:00 AM
Number: CG1010
Abstract ID:681
Candidate for Awards:Margaret Menzel Award