Genome Survey Sequencing of Betula platyphylla

Abstract

Research Highlights: A rigorous genome survey helped us to estimate the genomic characteristics, remove the DNA contamination, and determine the sequencing scheme of Betula platyphylla. Background and Objectives: B. platyphylla is a common tree species in northern China that has high economic and medicinal value. However, there is a lack of complete genomic information for this species, which severely constrains the progress of relevant research. The objective of this study was to survey the genome of B. platyphylla and determine the large-scale sequencing scheme of this species. Materials and Methods: Next-generation sequencing was used to survey the genome. The genome size, heterozygosity rate, and repetitive sequences were estimated by k-mer analysis. After preliminary genome assembly, sequence contamination was identified and filtered by sequence alignment. Finally, we obtained sterilized plantlets of B. platyphylla by plant tissue culture, which can be used for third-generation sequencing. Results: We estimated the genome size to be 432.9 Mb and the heterozygosity rate to be 1.22%, with repetitive sequences accounting for 62.2%. Bacterial contamination was observed in the leaves taken from the field, and most of the contaminants may be from the genus Mycobacterium. A total of 249,784 simple sequence repeat (SSR) loci were also identified in the B. platyphylla genome. Among the SSRs, only 11,326 can be used as candidates to distinguish the three Betula species. Conclusions: The B. platyphylla genome is complex and highly heterozygous and repetitive. Higher-depth third-generation sequencing may yield better assembly results. Sterilized plantlets can be used for sequencing to avoid contamination.

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

“…The contaminants may also lead to 14.82 Mb (0.82% of the whole genome) overestimation of the genome size. Our results are in contrast to the genome survey sequencing of B. platyphylla [47], which showed that contaminants brought no interference to genomic characterization.…”

“…As plant genomes are generally giant, genome survey by next-generation sequencing offers an affordable way to characterize the genome before conducting costly long-read genome sequencing [46]. Similar strategies have been applied to Betula platyphylla [47], Pistacia vera [48], and Rhododendron micranthum [49]. Genome survey sequencing has been shown that it enables to provide a preliminary understanding of such genomic characteristics as genome size, heterozygosity, and repetitive rate.…”

Genome survey ofZanthoxylum bungeanumand development of genomic-SSR markers in congeneric species

“…In addition, a fat tail was observed in the K-mer analysis, and the repeat sequence rate was calculated to be 86.04% (Figure 2A). The heterozygosity and repeat sequence rates of the ZB genome are much higher than those reported from the genome survey data of other woody plants, such as Acer truncatum (1.06%; 48.80%) [8], Xanthoceras sorbifolium (0.89%; 62.00%) [17], and Betula platyphylla (1.22%; 62.20%) [22]. Because of the high values for heterozygosity and repeat sequence rates combined with the chromosome number of ZB (2n = 136) [23], we speculate that ZB has a very complex genome.…”

“…Although a large amount of clean data (197.16 Gb) were used for assembly, the assembly results were unsatisfactory. The N50 lengths of contigs and scaffolds are notably shorter than those calculated in other similar studies [8,17,22]. A likely reason for these findings is that the ZB genome contains 68 chromosomes (2n = 136), has a high heterozygosity rate, and has a The x-axis is depth; the y-axis represents the frequency at a particular depth divided by the total frequency of all depths.…”

“…After excluding the effects of erroneous K-mers, the revised genome size is 3971.92 Mb (Table 3). Furthermore, based on the K-mer map, a high peak (22) was observed at half the K-mer depth (44), which indicates that the ZB genome has high heterozygosity, and the heterozygosity rate is estimated to be 1.73%. In addition, a fat tail was observed in the K-mer analysis, and the repeat sequence rate was calculated to be 86.04% (Figure 2A).…”