Dataset Information

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 166,151?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 A. podophylla is sister to A. spinulosa. This work provides a solid molecular resource for surveying phylogeny and chloroplast genomics of ferns.

SUBMITTER: Liu S

PROVIDER: S-EPMC7800846 | biostudies-literature | 2017 Dec

REPOSITORIES: biostudies-literature

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

Liu Shanshan S Ping Jingyao J Wang Zhen Z Wang Ting T Su Yingjuan Y

Mitochondrial DNA. Part B, Resources 20171222 1

The chloroplast genome of the tree fern Alsophila podophylla 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 A. podophylla is sister ...[more]

PMID: 33474061

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Project description:BACKGROUND: 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). RESULTS: 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. CONCLUSION: 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.

Dataset Information

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

Publications

Complete chloroplast genome of the tree fern <i>Alsophila podophylla</i> (Cyatheaceae).

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