A high-quality genome provides insights into the new taxonomic status and genomic characteristics of Cladopus chinensis (Podostemaceae).

Horticulture Research
Ting XueYouqiang Chen

Abstract

The Podostemaceae are ecologically and morphologically unusual aquatic angiosperms that survive only in rivers with pristine hydrology and high water quality and are at a relatively high risk of extinction. The taxonomic status of Podostemaceae has always been controversial. Here, we report the first high-quality genome assembly for Cladopus chinensis of Podostemaceae, obtained by incorporating Hi-C, Illumina and PacBio sequencing. We generated an 827.92 Mb genome with a contig N50 of 1.42 Mb and 27,370 annotated protein-coding genes. The assembled genome size was close to the estimated size, and 659.42 Mb of the assembly was assigned to 29 superscaffolds (scaffold N50 21.22 Mb). A total of 59.20% repetitive sequences were identified, among which long terminal repeats (LTRs) were the most abundant class (28.97% of the genome). Genome evolution analysis suggested that the divergence time of Cladopus chinensis (106 Mya) was earlier than that of Malpighiales (82 Mya) and that this taxon diverged into an independent branch of Podestemales. A recent whole-genome duplication (WGD) event occurred 4.43 million years ago. Comparative genomic analysis revealed that the expansion and contraction of oxidative phosphorylation, photosynthesi...Continue Reading

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Citations

Apr 2, 2021·Horticulture Research·Guodong RaoChenhe Wang
Nov 26, 2020·Plant Biotechnology Journal·Yiyang LiuShubo Wan

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Datasets Mentioned

BETA
FNU0039809

Methods Mentioned

BETA
Hi-C
flow cytometry
Illumina sequencing
RNA-seq
environmental stresses
laser capture microdissection
electrophoresis
cDNA library construction
PCR

Software Mentioned

SE
Primer Premier
MEGA7
Bowtie2
LACHESIS
Cufflinks
tRNAscan
LTR
RepeatMasker
Pilon

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