The complete mitochondrial genome of <i>Dryopteris crassirhizoma</i> Nakai (Dryopteridaceae, <i>Dryopteris</i> Adanson)

Song, Yueyue; Cui, Xusheng; Xu, Liang; Xing, Yanping; Bian, Che; Qiao, Yang; Yang, Yongqiang; Kang, Ting-Guo

doi:10.1080/23802359.2021.1966344

Cited by 11 publications

(3 citation statements)

References 5 publications

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“…However, mitogenomes remain understudied across fern diversity. To date, complete or near complete mitogenomic sequences have been described in less than six fern genera (Guo et al, 2017;Song et al, 2021;Feng and Wicke, 2022;Hao et al, 2022b;Zumkeller et al, 2023), and this number is even less than those published for nuclear genomes. This lack of fern mitogenomic data is in part due to the complexity of these genomes in most species, which is rich in long repetitive sequences and even IGT from plastomes.…”

Section: Conclusion and Future Perspectivesmentioning

confidence: 95%

Organellar phylogenomics of Ophioglossaceae fern genera

Kuo,

Su,

Koubínová

et al. 2024

Front. Plant Sci.

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Previous phylogenies showed conflicting relationships among the subfamilies and genera within the fern family Ophioglossaceae. However, their classification remains unsettled where contrasting classifications recognize four to 15 genera. Since these treatments are mostly based on phylogenetic evidence using limited, plastid-only loci, a phylogenomic understanding is actually necessary to provide conclusive insight into the systematics of the genera. In this study, we have therefore compiled datasets with the broadest sampling of Ophioglossaceae genera to date, including all fifteen currently recognized genera, especially for the first time the South African endemic genus Rhizoglossum. Notably, our comprehensive phylogenomic matrix is based on both plastome and mitogenome genes. Inferred from the coding sequences of 83 plastid and 37 mitochondrial genes, a strongly supported topology for these subfamilies is presented, and is established by analyses using different partitioning approaches and substitution models. At the generic level, most relationships are well resolved except for few within the subfamily Ophioglossoideae. With this new phylogenomic scheme, key morphological and genomic changes were further identified along this backbone. In addition, we confirmed numerous horizontally transferred (HGT) genes in the genera Botrypus, Helminthostachys, Mankyua, Sahashia, and Sceptridium. These HGT genes are most likely located in mitogenomes and are predominately donated from angiosperm Santalales or non-Ophioglossaceae ferns. By our in-depth searches of the organellar genomes, we also provided phylogenetic overviews for the plastid and mitochondrial MORFFO genes found in these Ophioglossaceae ferns.

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Section: Conclusion and Future Perspectivesmentioning

confidence: 95%

Organellar phylogenomics of Ophioglossaceae fern genera

Kuo,

Su,

Koubínová

et al. 2024

Front. Plant Sci.

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“…A Perl script (get_longest_isoform_seq_per_trinity_gene.pl) was used to retain the longest isoform from each gene. Minimap2 v2.17-r941 (Li, 2018) and Samtools v1.11 (Danecek et al, 2021) were chosen to filter out the organelle transcripts using the closest publicly available reference organelle genomes (chloroplast: Microsorum punctatum [MW876342; Wei et al, 2021]; mitochondrion: Dryopteris crassirhizomaNakai [MW732172; Song et al, 2021]). CD-HIT-EST v4.8.1 (Li and Godzik, 2006) was implemented on the transcripts with a clustering threshold of 99%.…”

Section: Rna Extraction Sequencing De Novo Assembly and Orthologs Ide...mentioning

confidence: 99%

Deciphering the reticulate evolution and phylo-biogeography of Ant-Ferns Lecanopteris s.s.

He,

Jiang,

Zhao

et al. 2024

Preprint

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Southeast Asia is a biodiversity hotspot characterized by a complex paleogeography, and its Polypodiopsida flora is particularly diverse. While hybridization is recognized as common in ferns, investigations into the relationship between hybridization events and fern diversity are notably lacking. Lecanopteris s.s., an ant-associated fern, has been subject to debate regarding species delimitations primarily due to limited DNA markers and species sampling. Our study integrates 22 newly generated plastomes, 22 transcriptomes, and flow cytometry of all native species along with two cultivated hybrids. Our objective is to elucidate the reticulate evolutionary history within Lecanopteris through the integration of phylo-biogeography reconstruction, gene flow inference, and genome size estimation. Key findings of our study include: (1) An enlarged plastome size in Lecanopteris, attributed to extreme expansion of the Inverted Repeat (IR) regions; (2) The traditional ‘pumila’ and ‘crustacea’ groups are paraphyletic; (3) Significant cytonuclear discordance attributed to gene flow; (4) Natural hybridization and introgression in the ‘pumila’ and ‘darnaedii’ groups; (5) L. luzonensis is the maternal parent of L. ‘Yellow Tip’, with L. pumila suggested as a possible paternal parent; (6) L. ‘Tatsuta’ is a hybrid between L. luzonensis and L. crustacea; (7) Lecanopteris first diverged during the Neogene and then during the middle Miocene climatic optimum in Indochina and Sundaic regions. In conclusion, the biogeographic history and speciation of Lecanopteris have been profoundly shaped by past climate changes and geodynamics of Southeast Asia. Dispersals, hybridization and introgression between species act as pivotal factors in the evolutionary trajectory of Lecanopteris.

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“…To our knowledge the only study that has so far applied broad mitogenomic data in fern systematics focused on Marattiales and used plastome data together with 39 mitochondrial markers to resolve congruent trees between the two genomes (Lehtonen et al 2020). So far, only five complete fern mitogenomes have been reported (Guo et al 2017, Song et al 2021, Feng & Wicke 2022.…”

Section: Introductionmentioning

confidence: 99%

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2023

Phytotaxa

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The current understanding of fern phylogeny is primarily based on plastid and nuclear sequences, but the third genome-the mitogenome-has remained practically unstudied. We inferred the first broad scale fern phylogeny based on mitogenomic data, obtained from the One Thousand Plant Transcriptomes Initiative project, and compared it with the plastid phylogeny. The trees were mostly congruent and corresponded to the current understanding of the fern phylogeny, but we observed different evolutionary patterns between the two genomes. Protein-coding markers located in the plastome had, on average, over two times higher substitution rate than the markers from the mitogenome. The similar rate variation pattern between the genomes in different fern lineages supports the idea that a common mechanism, like life history traits, drives the rates of molecular evolution. The few conflicting nodes we observed have also been difficult to resolve in other studies, suggesting that even genomic data may not suffice to resolve them.

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The complete mitochondrial genome of Dryopteris crassirhizoma Nakai (Dryopteridaceae, Dryopteris Adanson)

Cited by 11 publications

References 5 publications

Organellar phylogenomics of Ophioglossaceae fern genera

Organellar phylogenomics of Ophioglossaceae fern genera

Deciphering the reticulate evolution and phylo-biogeography of Ant-Ferns Lecanopteris s.s.

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