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

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

Liu S ，Ping J ，Wang Z ，Wang T ，Su Y ... -  《Mitochondrial DNA Part B-Resources》

Complete chloroplast genome sequence of a tree fern Alsophila spinulosa: insights into evolutionary changes in fern chloroplast genomes.

Ferns have generally been neglected in studies of chloroplast genomics. Before this study, only one polypod and two basal ferns had their complete chloroplast (cp) genome reported. Tree ferns represent an ancient fern lineage that first occurred in the Late Triassic. In recent phylogenetic analyses, tree ferns were shown to be the sister group of polypods, the most diverse group of living ferns. Availability of cp genome sequence from a tree fern will facilitate interpretation of the evolutionary changes of fern cp genomes. Here we have sequenced the complete cp genome of a scaly tree fern Alsophila spinulosa (Cyatheaceae). The Alsophila cp genome is 156,661 base pairs (bp) in size, and has a typical quadripartite structure with the large (LSC, 86,308 bp) and small single copy (SSC, 21,623 bp) regions separated by two copies of an inverted repeat (IRs, 24,365 bp each). This genome contains 117 different genes encoding 85 proteins, 4 rRNAs and 28 tRNAs. Pseudogenes of ycf66 and trnT-UGU are also detected in this genome. A unique trnR-UCG gene (derived from trnR-CCG) is found between rbcL and accD. The Alsophila cp genome shares some unusual characteristics with the previously sequenced cp genome of the polypod fern Adiantum capillus-veneris, including the absence of 5 tRNA genes that exist in most other cp genomes. The genome shows a high degree of synteny with that of Adiantum, but differs considerably from two basal ferns (Angiopteris evecta and Psilotum nudum). At one endpoint of an ancient inversion we detected a highly repeated 565-bp-region that is absent from the Adiantum cp genome. An additional minor inversion of the trnD-GUC, which is possibly shared by all ferns, was identified by comparison between the fern and other land plant cp genomes. By comparing four fern cp genome sequences it was confirmed that two major rearrangements distinguish higher leptosporangiate ferns from basal fern lineages. The Alsophila cp genome is very similar to that of the polypod fern Adiantum in terms of gene content, gene order and GC content. However, there exist some striking differences between them: the trnR-UCG gene represents a putative molecular apomorphy of tree ferns; and the repeats observed at one inversion endpoint may be a vestige of some unknown rearrangement(s). This work provided fresh insights into the fern cp genome evolution as well as useful data for future phylogenetic studies.

Gao L ，Yi X ，Yang YX ，Su YJ ，Wang T ... -  《BMC EVOLUTIONARY BIOLOGY》

The complete chloroplast genome of Alsophila latebrosa, a common and widespread tree fern (Cyatheaceae).

Alsophila latebrosa is a common and widespread tree fern of Cyatheaceae. Its complete chloroplast genome is first assembled and reported with 155,724 bp in length, including a large single copy (LSC) region of 85,800 bp, a small single copy (SSC) region of 21,620 bp, and a pair of inverted repeats (IRs) of 24,152 bp. The genome has 133 genes, including 89 protein-coding genes, 33 tRNA genes, eight rRNA genes and three pseudogenes. Maximum likelihood approach was employed to construct the phylogenetic relationship among ten ferns including A. latebrosa. The result showed that A. latebrosa was most related to A. costularis as a sister group with 100% bootstrap support. The complete chloroplast genome sequences of A. latebrosa will provide valuable genomic information to further illuminate phylogenetic classification of Cyatheacea.

Wang Z ，Wang R ，Lin L ，Liu R ，Ma S ，Hong Y ，He Z ，Su Y ，Wang T ... -  《Mitochondrial DNA Part B-Resources》

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

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 166,027 bp in length, including a pair of inverted repeats (IRs) of 29,158 bp, a large single-copy (LSC) region of 85,665 bp, and a small single-copy (SSC) region of 22,046 bp. 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.

Liu S ，Wang Z ，Wang T ，Su Y ... -  《Mitochondrial DNA Part B-Resources》

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

The complete chloroplast genome of an important medical fern Cyrtomium fortunei has been sequenced. Its genome is 151,699 bp in length with a pair of inverted repeats (IRs, 23,875 bp), separated by a small single copy region (SSC, 21,625 bp) and a large single copy region (LSC, 82,324 bp). 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.

Li S ，Liu S ，Wang Z ，Wang T ，Su Y ... -  《Mitochondrial DNA Part B-Resources》