Expanded Understanding of Eleusine Diversity and Evolution

Abstract

Eleusine, including 9 to 12 species, is a small genus of annual and perennial grass species within the Eragrosteae tribe and Chloridoideae subfamily. There are very few genomic information about this genus. The primary goal of this dissertation research is to expand understanding of Eleusine diversity and evolution. The dissertation opens with a brief literature review regarding the motivation for this research. In chapter 2 we report a draft assembly of approximately 498 Mb whole-genome sequences of goosegrass obtained by de novo assembly of paired-end and mate-paired reads generated by Illumina sequencing of total genomic DNA. From around 88 GB of the clean data, the genome was assembled into 24,063 scaffolds with N50 = 233,823 bp. The nuclear genome assembly contains 25,467 predicted unique protein-coding genes. Sixteen target herbicide resistant genes and four non-target herbicide resistant gene families were obtained from this draft genome. Chapter 3 presents a complete plastid genome sequence of goosegrass obtained by de novo assembly of paired-end and mate-paired reads obtained in chapter 2. The goosegrass plastome is a circular molecule of 135,151 bp in length, consisting of two single-copy regions separated by a pair of inverted repeats (IRs) of 20,919 bases. The large (LSC) and the small (SSC) single-copy regions span 80,667 bases and 12,646 bases, respectively. The plastome of goosegrass has 38.19% GC content and includes 108 unique genes, of which 76 are protein-coding, 28 are transfer RNA, and 4 are ribosomal RNA. Finally, Chapter 4 presents a study utilizing transcriptome to resolve E. coracana heritage problem. We developed transcriptomes for six Eleusine species from fully developed seedlings using Illumina technology and three de novo assemblers (Trinity, Velvet, and SOAPdenovo2) with the redundancy-reducing EvidentialGene pipeline. E. coracana reads filtered for only nuclear-encoded genes were mapped to E. indica transcriptome and the unmapped reads were extracted and assembled to create a E. coracana Synthetic B transcriptome. The other five Eleusine species’ transcriptome reads were mapped to the E. coracana Synthetic B transcriptome, however, no mapped percentage exceeded 54.5%. By comparison, the reads of E. indica mapping to the E. coracana Synthetic A transcriptome is 72.9%. Variants and phylogenetic analyses found that no diploid Eleusine species close to the E. coracana Synthetic B transcriptome branch. The utilization of our synthetic B transcriptome is openly available as a resource to aid in the future identification of the paternal genome donor of E. coracana.