In the present study, fresh leaf material was obtained from the collection sites of Andaihou Village, Songyang County, Lishui City, China (119.273422 E, 28.271808 N) (Figure 1 ) and dried with silica. Specimens (voucher no.: Yufeng Gu Fern08748) were deposited at the Herbarium of the National Orchid Conservation Center (NOCC). Silica-dried material was sent to Shanghai Majorbio Bio-pharm Technology Co., Ltd. (Shanghai, China) for DNA extraction and sequencing, performed on an Illumina HiSeq X Ten platform (Illumina, San Diego, CA). The plastid genome was assembled using GetOrganelle v1.7.5 (Jin et al. 2018 ) using default parameters, and the results viewed and edited by Bandage v0.8.1 (Wick et al. 2015 (link)). The assembled chloroplast genome was annotated by Geneious Prime 2021.0.3 (https://www.geneious.com ) (Kearse et al. 2012 (link)) with I. nuttallii as a reference at 90% similarity.
We drew the chloroplast complete genome map of this quillwort species (Figure 2 ) in OGDRAW – Draw Organelle Genome Maps (https://chlorobox.mpimp-golm.mpg.de/OGDraw.html ). To find the phylogenetic position of I. orientalis, molecular phylogenetic analysis was carried out with 15 published, complete chloroplast genomes of Isoetes downloaded from GenBank.
Coding sequences (CDS) were extracted from the annotated sequences, then they were aligned using mauveAligner in Geneious Prime 2021.0.3. By employing a progressive algorithm and assuming collinearity, poorly aligned regions were excluded from the complete plastome dataset using Gblocks v0.91b in PhyloSuite v1.2.2 (Zhang et al. 2020 (link)). Using nucleotide as the type of sequence, up to half gap positions were allowed, and other parameters were set as default settings. For phylogenomic analysis, the resulting alignment was subjected to ML analyses performed using IQ-TREE v. 1.6.12 (Lam-Tung et al. 2015 (link)) with 10,000 bootstrap replicates. The best-fitting model was selected by ModelFinder (Kalyaanamoorthy et al. 2017 (link)) and implemented in IQ-TREE.
We drew the chloroplast complete genome map of this quillwort species (
Coding sequences (CDS) were extracted from the annotated sequences, then they were aligned using mauveAligner in Geneious Prime 2021.0.3. By employing a progressive algorithm and assuming collinearity, poorly aligned regions were excluded from the complete plastome dataset using Gblocks v0.91b in PhyloSuite v1.2.2 (Zhang et al. 2020 (link)). Using nucleotide as the type of sequence, up to half gap positions were allowed, and other parameters were set as default settings. For phylogenomic analysis, the resulting alignment was subjected to ML analyses performed using IQ-TREE v. 1.6.12 (Lam-Tung et al. 2015 (link)) with 10,000 bootstrap replicates. The best-fitting model was selected by ModelFinder (Kalyaanamoorthy et al. 2017 (link)) and implemented in IQ-TREE.
Free full text: Click here
