Identifying Candidate Genes for Flowering Time and Floral Development in Genome and Transcriptome Assemblies of the Non-Model Plant Lythrum salicaria.

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Fuentes-Vergara, Mabel S.
Keyword
Lythrum salicaria , Genomics , Transcriptomics , Invasive species , Non model plant , Flowering time , Adaptive traits , Purple loosestrife , Climate change , Rapid adaptation , Heterostyly , Polyploidy
Abstract
Climate change is leading to environmental shifts, challenging the survival of many organisms. Some invasive species like Lythrum salicaria (purple loosestrife) can rapidly adapt to new conditions and thrive in human-altered habitats, offering a valuable model for studying the ecological and genetic factors that enable species survival under global change. While the ecological factors promoting the invasion and spread of L. salicaria are well-studied, the genetic basis for ecologically important traits is less understood. The aim of this thesis was to develop an annotated genome and transcriptome to investigate the genetic architecture of L. salicaria and the genetic basis of adaptive traits. A draft genome of a diploid ancestor from the native range was assembled using paired-end and mate-pair libraries sequenced on the Illumina HiSeq and MiSeq platforms. Ten transcriptomes were sequenced, representing four tetraploid individuals from the introduced range, and included different samples from the stem, floral meristem, flowers, and fruits of early and late-flowering phenotypes. Additionally, the genome assembly was annotated using the transcriptome as well as sequence-based predictions. The genome assembly was approximately 0.8 Gb in size across 648 scaffolds with 60,656 potential genes. A re-assembly of the transcriptome using the annotated genome resulted in 120,565 transcripts derived from 66,445 potential genes, including isoforms. An enrichment analysis identified 1,946 genes potentially involved in flowering processes, with 1,399 showing protein matches to 124 reviewed flowering-related proteins in the UniProtKB database. Additionally, matches were identified for genes related to stress response and defense metabolites. A key focus was the differential expression analysis of transcripts related to flowering time and floral tissues, providing insights into the genetic factors influencing these traits in L. salicaria. This research enhances the understanding of the genetic architecture of L. salicaria and identifies candidate genes for future investigations into plant genomics and adaptation strategies in changing environments.
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