Genome Survey Sequencing of In Vivo Mother Plant and In Vitro Plantlets of Mikania cordata

Abstract

Mikania cordata, the only native congener of the invasive weed Mikania micrantha in China, is an ideal species for comparative study to reveal the invasion mechanism. However, its genome resources are lagging far behind its congener, which limits the comparative genomic analysis. Our goal is to characterize the genome of M. cordata by next-generation sequencing and propose a scheme for long-read genome sequencing. Previous studies have shown that the genomic resources of the host plant would be affected by the endophytic microbial DNA. An aseptic sample of M. cordata will ensure the proper genome in downstream analysis. Because endophytes are ubiquitous in the greenhouse-grown M. cordata, the in vitro culture with cefotaxime or timentin treatment was undertaken to obtain the aseptic plantlets. The in vivo mother plant and in vitro plantlets were used to survey the genome. The microbial contamination in M. cordata was recognized by blast search and eliminated from the raw reads. The decontaminated sequencing reads were used to predict the genome size, heterozygosity, and repetitive rate. The in vivo plant was so contaminated that microbes occupied substantial sequencing resources and misled the scaffold assembly. Compared with cefotaxime, treatment with timentin performed better in cultivating robust in vitro plantlets. The survey result from the in vitro plantlets was more accurate due to low levels of contamination. The genome size was estimated to be 1.80 Gb with 0.50% heterozygosity and 78.35% repetitive rate. Additionally, 289,831 SSRs were identified in the genome. The genome is heavily contaminated and repetitive; therefore, the in vitro culture technique and long-read sequencing technology are recommended to generate a high-quality and highly contiguous genome.

Draft Genome of the Medicinal Tea Tree Melaleuca Alternifolia (Maiden & Betche) Cheel (Myrtaceae)

“…May be related to its short-read assembly method. However, it is much higher than that of Mikania cordata (312∼352 bp) which used the same SOAPdenovo software [10]. Genome completeness, estimated by BUSCO using the viridiplantae dataset, was 88.7%, indicating a relatively high geonome completeness.…”

“…Next-generation sequencing (NGS) can be used to generate and assemble high-quality genomes, based on its high throughput, high resolution, high precision, and low cost. Short-read sequencing is usually performed to estimate genome size, heterozygosity, repetitive rate, and evaluate the simple sequencing repeat (SSR) markers at the genome level, in advance of long-read sequencing due to its cost-effective [10]. M. alternifolia genome had been sequenced recently [11], as well as several other Myrtaceae trees such as Eucalyptus pauci ora [12], Eucalyptus grandis [13], Metrosideros polymorpha [14], and Leptospermum scoparium [15].…”