Shanshan Liu

The first complete chloroplast genome of a traditional Chinese medicinal herb Odontosoria chinensis (Lindsaeaceae)

Abstract It is the first report on complete chloroplast genome of Odontosoria chinensis, a traditional Chinese medicinal herb. The genome size is 156,293u2009bp, containing a pair of inverted repeats (IRs) (25,198u2009bp) separated by a small single-copy (SSC) region (20,649u2009bp) and a large single-copy (LSC) region (85,248u2009bp), respectively. The plastome has 128 genes, including 87 protein-coding genes, 32 tRNA genes, eight rRNA genes, and one pseudogene. The overall GC content is 40.43%. Maximum likelihood tree reveals that O. chinensis is basal lineages of polypods. The study will provide powerful molecular information for further phylogenetic analysis.

The complete chloroplast genome sequence of Cyrtomium fortunei (Dryopteridaceae), an important medical fern

Abstract The complete chloroplast genome of an important medical fern Cyrtomium fortunei has been sequenced. Its genome is 151,699u2009bp in length with a pair of inverted repeats (IRs, 23,875u2009bp), separated by a small single copy region (SSC, 21,625u2009bp) and a large single copy region (LSC, 82,324u2009bp). It contains 132 genes, covering 88 protein coding genes, 35 tRNA genes, eight rRNA genes, and one pseudogene. Maximum likelihood analysis indicates that the phylogenetic tree is monophyletic with three clades. Cyrtomium fortunei is closely related to C. devexiscapulae, which further forms a sister clade to C. falcatum.

The complete chloroplast genome sequence of medicinal fern Polypodiodes niponica (Polypodiaceae)

Abstract The complete chloroplast genome of Polypodiodes niponica has been determined. It is a double stranded circular DNA of 152,551u2009bp length, containing two inverted repeat (IR, 24,643u2009bp each) regions, separated by large single-copy (LSC, 81,506u2009bp) and small single-copy (SSC, 21,759u2009bp) regions, respectively. The genome contains 131 genes, including 88 protein-coding genes, 35 tRNA genes, and eight rRNA genes. The total GC content of the chloroplast genome is 42.4%. ML phylogenetic analysis revealed that P. niponica was most closely related to Lepisorus clathratus.

The complete chloroplast genome of Leptochilus hemionitideus, a traditional Chinese medical fern

Abstract The complete chloroplast genome of Leptochilus hemionitideus was sequenced. Its length is 156,083u2009bp with 44.2% GC content. The genome exhibits typical quadripartite with two inverted repeat regions (24,594u2009bp, each) separated by a large single-copy (LSC, 81,403u2009bp) region and a small single-copy (SSC, 25,492u2009bp) region. It has 131 genes, including 87 protein-coding genes, 34 tRNA genes, eight rRNA genes and two pseudogenes. Maximum-likelihood phylogenetic tree indicated that L. hemionitideus was closely related to Lepisorus clathratus. The complete chloroplast genome of L. hemionitideus would provide very valuable molecular information for further inferring the relationships of the microsoroid ferns.

The complete chloroplast genome of Cibotium barometz (Cibotiaceae), an endangered CITES medicinal fern

Abstract The complete chloroplast (cp) genome sequence of Cibotium barometz, an endangered CITES medicinal fern, was determined by Illumina sequencing. Its genome is a circular molecule of 166,027u2009bp in length, including a pair of inverted repeats (IRs) of 29,158u2009bp, a large single-copy (LSC) region of 85,665u2009bp, and a small single-copy (SSC) region of 22,046u2009bp. The genome encodes 118 unique genes, involving 84 protein-coding genes, 28 tRNA genes, four rRNA genes, and two pseudogenes. Maximum likelihood tree showed that C. barometz was closely related to Alsophila spinulosa. This investigation lays solid foundations for endangered medicinal resource conservation and fern phylogenetic studies.

Complete chloroplast genome of the tree fern Alsophila podophylla (Cyatheaceae)

Abstract The chloroplast genome of the tree fern Alsophila podophylla has been completely sequenced. The genome is 166,151u2009bp in size and features a typical quadripartite structure with the large (LSC, 86,762u2009bp) and small single copy (SSC, 21,641u2009bp) regions separated by a pair of inverted repeats (IRs, 28,874u2009bp each). It encodes 133 genes including 91 protein-coding genes, 33 tRNA genes, eight rRNA genes, and one pseudogene. Maximum-likelihood tree indicates that A. podophylla is sister to A. spinulosa. This work provides a solid molecular resource for surveying phylogeny and chloroplast genomics of ferns.

The complete chloroplast genome of Pyrrosia bonii (Polypodiaceae), an important ornamental and medical fern

Abstract Pyrrosia bonii is an important ornamental and medical fern from Polypodiaceae. Its complete chloroplast genome sequence was characterized through de novo assembly with Illumina sequencing data. The genome size is 158,174u2009bp, with large single copy (LSC, 82,479u2009bp) and small single copy (SSC, 21,723u2009bp) regions separated by a pair of inverted repeats (IR, 26,986u2009bp). A total of 132 genes were identified, including 88 protein coding genes, 35 tRNA genes, eight rRNA genes, and one pseudogene. Maximum-likelihood phylogenetic tree revealed that P. bonii was most closely related to Lepisorus clathratus. The study will greatly facilitate the chloroplast phylogenomics of Polypodiaceae.

The complete chloroplast genome of monotypic fern, Mesopteris tonkinensis (Thelypteridaceae)

Abstract Mesopteris tonkinensis is monotypic species in the genus Mesopteris (Thelypteridaceae). We characterized its complete chloroplast genome sequences by Illumina sequencing and de novo assembly. The genome size is 161,380u2009bp in length with a GC content of 43.6%, containing a large single-copy (LSC) region of 82,678u2009bp, a small single-copy (SSC) region of 21,786u2009bp and a pair of inverted repeat (IR) of 28,458u2009bp. In total, 131 genes are identified, including 88 protein-coding genes, 34 tRNA genes with absent trnV-UAC, eight rRNA genes and one pseudogene. ML tree revealed that M. tonkinensis and Christella appendiculata were closely related.

The complete chloroplast genome of Macrothelypteris torresiana, a reputed medicinal fern (Thelypteridaceae)

Abstract Macrothelypteris torresiana is a reputed medicinal fern. Its complete chloroplast genome was determined by Illumina paired-end sequencing. The genome is 151,150u2009bp in length with 43.1% overall Guanine+Cytosine (GC) content, which is divided into four distinct parts such as a small single copy (SSC, 21,772u2009bp), a large single copy (LSC, 82,422u2009bp), and two inverted repeats (IRs, 23,478u2009bp each). It contains 132 genes, including 86 protein-coding genes, eight ribosomal RNA genes, 35 tRNA genes, and three pseudogenes. Maximum likelihood (ML) tree revealed that M. torresiana was closely grouped with Christella appendiculata with 100% bootstrap value.

The first complete chloroplast genome of Pteris vittata (Pteridaceae), an arsenic hyperaccumulating fern

Abstract It is the first report on complete chloroplast genome of Pteris vittata, an arsenic hyperaccumulating fern. Its genome size is 154,130u2009bp, with a typical circular structure including a large single-copy (LSC) (82,623u2009bp) and a small single-copy (SSC) (20,957u2009bp) regions separated by a pair of inverted repeats (25,275u2009bp each). The plastome encodes 132 genes, including 87 protein-coding genes, 35 tRNA genes, eight rRNA genes, and two pseudogenes. The overall Guanine+Cytosine (GC) content is 41.7% and GC content in the IR regions is higher than in the LSC and SSC regions. Maximum likelihood (ML) tree indicated that P. vittata was clustered with Ceratopteris richardii.