key: cord-0857044-o3a696mq
authors: Jin, Lei; Yang, Jin; Liu, Changkun; He, Mengling; Yan, Hanjing
title: Complete plastome of Houttuynia cordata (Saururaceae), a medicinal and edible plant
date: 2019-09-24
journal: Mitochondrial DNA. Part B, Resources
DOI: 10.1080/23802359.2019.1667910
sha: 78f9390c74492765444e446c1b6e307a871a05c1
doc_id: 857044
cord_uid: o3a696mq

The complete plastome of Houttuynia cordata, an important medicinal and edible plant, was identified and sequenced in this study. The circular plastome is 160,217 bp in length and consists of a pair of inverted repeats (IRs 26,854 bp each), which is separated by a large single-copy region (LSC, 88,189 bp) and a small single-copy region (SSC, 18,320 bp). It encodes 132 genes, of which 114 are unique genes (80 protein-coding genes, 30 tRNAs, and 4 rRNAs). The phylogenetic analysis strongly reveals the sister group between H. cordata and the clade including Piper kadsura, Piper cenocladum, Saruma henryi, and Asarum sieboldii.

Houttuynia cordata; complete plastome; phylogenetic analysis Houttuynia cordata Thunb., a perennial herb belonging to the family Saururaceae, grows in moist and shady places (Shingnaisui et al. 2018) . The species is a medicinal plant traditionally used in China, Japan, Korea, and India for the treatment of pneumonia, severe acute respiratory syndrome, muscular sprain, as well as stomach ulcer (Lou et al. 2019 ). Furthermore, the species is popularly consumed as a healthy vegetable in East Asia (Toda 2005) . With the increase of demand and irregular collection, wild H. cordata resource has greatly damaged. It is necessary to establish a strategy to conserve for this medicinally and commercially important plant as soon as possible. However, the available genomic resource of H. cordata is limited. Here, we report the complete plastome of H. cordata using high throughput Illumina sequencing technology.

Samples of H. cordata were collected from Tengchong, Yunnan, China (25 25 0 35 00 N, 98 39 0 07 00 E). Voucher specimen (Y. Ji 2017131) was deposited in the Herbarium of Kunming Institute of Botany, Chinese Academy of Sciences (KUN). We used the modified CTAB method (Yang et al. 2014 ) to extract genomic DNA from silica gel dried leaf tissues at first. Subsequently, the purified DNA was shared by sonication so that fragments of 500 bp length was obtained for constructing a paired-end library. Then the paired-end sequencing was performed using Illumina HiSeq 2000 system at BGI (Wuhan, Hubei, China). Plastome of Asarum sieboldii (GenBank Accession No. MG551543) was used as reference sequence and we assembled the plastome following the method described by Jin et al (2018) . Finally, the annotation of the plastome was performed in Geneious 10.2.3 (Kearse et al. 2012 ). The plastome was manually checked for start and stop codons and intron/exon boundaries. The validated complete plastome of H. cordata was deposited in the NCBI GenBank database under the accession number MN263890.

The H. cordata plastome is 160,217 bp in length and consists of a pair of inverted repeats (IRs, 26,854 bp each), which is separated by a large single-copy region (LSC, 88,189 bp) and a small single-copy region (SSC, 18,320 bp). It encodes 132 genes, of which 114 are unique genes (80 protein-coding genes, 30 tRNAs, and 4 rRNAs). Among unique genes, 9 protein-coding genes (atpF, ndhA, ndhB, petB, petD, rpl16, rpl2, rpoC1, and rps12) , and 6 tRNAs (trnA-UGC, trnG-UCC, trnI-GAU, trnK-UUU, trnL-UAA, and trnV-UAC) contain one intron, while three protein-coding genes (ycf3, clpP and rps12) have two introns.

To identify the phylogenetic position of H. cordata, a maximum-likelihood (ML) (Stamatakis 2014) tree was generated using species within the order Piperales. Drimys granadensis was used to root the tree. The phylogenetic analysis reveals the sister group between H. cordata and the clade including Piper kadsura, Piper cenocladum, Saruma henryi, Asarum sieboldii ( Figure 1 ). Our findings will provide a foundation for further investigation of genetic inheritance and evolution of H.cordata.

GetOrganelle: a simple and fast pipeline for de novo assembly of a complete circular chloroplast genome using genome skimming data

Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data

Houttuynia cordata thunb. and its bioactive compound 2-undecanone significantly suppress benzo(a)pyrene-induced lung tumorigenesis by activating the nrf2-ho-1/nqo-1 signaling pathway

Therapeutic potentials of Houttuynia cordata Thunb. against inflammation and oxidative stress: a review

Raxml version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

Antioxidative effects of polyphenols in leaves of Houttuynia cordata on protein fragmentation by copper-hydrogen peroxide in vitro

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Figure 1. Phylogenetic relationships among Piperales species, based on complete plastomes

The authors declare no potential conflict of interests.

This study was supported by Scientific and Technological Project of Guangdong Province [2017A020213023].