DOI: 10.5061/dryad.70rxwdc7h
title: Data from: A new species in Iris section Pseudoregelia (Iridaceae) from Gansu, China

description: Iris longnanensis Z.F. Bai, Y.E. Xiao, F.Y. Yu (Iridaceae: subgenus Iris
 section Pseudoregelia), a novel herbaceous species native to the arid and
 thermal valleys of Longnan city, Gansu province, China, is herein
 described and illustrated. Morphologically akin to I. leptophylla
 Lingelsheim, I. longnanensis is distinguished by its dense, persistent
 foliage and strikingly short new leaves (6.6–15.1 cm) during the blooming
 season, along with its distinctive purplish-brown flowering stem.
 Phylogenetic analyses based on chloroplast DNA sequences corroborate the
 classification of I. longnanensis within section Pseudoregelia,
 highlighting the significance of this new species discovery for
 understanding the evolution and diversity within the genus.
description: Living specimens and vouchers were examined from mid-March to
 mid-June in 2023. Ten randomly selected individuals of the new species
 were used for the morphometric surveys (Table 1). Additionally, the new
 species was compared with herbarium sheets at the herbaria E, BNU, CAS,
 NAS, CDBI, EE, HNWP, IATM, IBSC, IFP, KUN, NAS, PE and SG, and with the
 original descriptions of <em>I. dolichosiphon</em>,
 <em>I.</em> <em>dolichosiphon</em> subsp.
 <em>orientalis</em>, <em>I. cuniculiformis</em>,
 <em>I. goniocarpa</em>, <em>I.
 goniocarpa</em> var. <em>tenella</em>, <em>I.
 hookeriana</em>, <em>I. leptophylla</em>,<em> I.
 narcissiflora</em>, <em>I. pandurata</em>, <em>I.
 sichuanensis</em>, <em>I. kemaonensis</em>, <em>I.
 pandurata</em>,<em> </em>and <em>I.
 tigridia</em>. (No specimen<em> </em>of <em>I.
 sikkimensis</em> was available.) <em>Taxon
 sampling for the phylogenetic analysis</em> The
 Longnan species and 11 species/varieties in
 <em>Iris</em> subg. <em>Iris</em> (<em>I.
 bloudowii</em>, <em>I. cuniculiformis</em>, <em>I.
 goniocarpa</em>, <em>I. goniocarpa</em> var.
 <em>tenella</em>, <em>I. leptophylla</em>,
 <em>I. mandshurica</em>, <em>I. sichuanensis</em>,
 <em>I. pandurata</em>, <em>I. tigridia</em>,
 <em>I. mandshurica</em>, and <em>I.
 bloudowii</em>), two sister species to <em>I.
 </em>subgen.<em> Iris</em> (<em>I.
 domestica</em> and<em> I. dichotoma</em>, Wilson, 2017),
 and one species in <em>I. </em>subgen.
 <em>Limniris</em> (<em>I. ensata</em>) were used
 to construct phylogenetic trees based on complete chloroplast genome data.
 <em>Iris domestica</em>,<em> I. dichotoma</em>,
 and <em>I. ensata</em> were selected as the outgroup for the
 phylogenetic analysis. All samples were obtained from the conservation
 nursery of Shanghai Botanical Garden. <em>Iris
 kemaonensis</em>, <em>I. dolichosiphon</em>,
 <em>I.</em> <em>dolichosiphon</em> subsp.
 <em>orientalis</em>, <em>I.
 hookeriana</em><em>, I. narcissiflora</em>, and
 <em>I. sikkimensis </em>was not available for
 phylogenetic study. <em>Iris sikkimensis </em>is not known
 from the wild so it is ignored here. Genomic DNA was
 extracted from silica-dried leaf materials of the Longnan species (two
 individuals) and the other species using a commercial plant genomic DNA
 extraction kit (CW0531; CWBIO, Jiangsu, China). We constructed a library
 with an average length of 350 bp using the Illumina DNA Library
 Preparation Kit (E7370L; NEB, USA), which was then sequenced on the
 NovaSeq 6000 platform (Illumina, San Diego, CA). Low-quality reads and
 adapters were trimmed using FastQC v.0.11.9 (Andews, 2010). The raw data
 of the 10 species was &gt;3.30G, and the clean data was &gt;3.28G
 after quality control processing, resulting in a &gt;496-fold depth of
 coverage of the chloroplast genome. The GC content of the cleaned data
 from the 11 species was 43.34% (<em>I. bloudowii</em>), 41.96%
 (<em>I. cuniculiformis</em>), 42.68% (<em>I.
 goniocarpa</em>), 42.59% (<em>I. goniocarpa</em> var.
 <em>Tenella</em>), 40.49% (<em>I.
 leptophylla)</em>, 40.77% (<em>I. mandshurica</em>),
 40.29% (<em>I. sichuanensis</em>), 41.46% (<em>I.
 pandurata</em>), 41.46% (<em>I. tigridia</em>), 41.40%
 and 40.80% (<em>I. longnanensis</em>), the Q20-value was
 &gt;95.77%, and the Q30 value was &gt;89.77%, indicating that the
 quality of the chloroplast genome sequencing and assembly results was very
 high. <em>De novo</em> assembly was performed on the clean
 data using SPAdes v.3.14.1, and k-mer values of 105 were set to obtain the
 graph file. Then, the redundant contigs were removed visually using the
 Bandage software and edited into a circular form. The circular sequence
 thus obtained is the complete chloroplast genome sequence. Finally, it was
 annotated by PGA (Qu et al., 2019) with <em>Iris dichotoma
 </em>(OK448492) as the reference genome. IR regions were identified
 with IRscope (Amiryousefi et al. 2018), which detected the IRa and IRb
 regions along with single-copy regions (LSC and SSC). The identified IRs
 were manually validated by aligning IRa and IRb to confirm sequence
 similarity. Boundaries of the IR regions were annotated by locating
 conserved genes, such as ycf1 and rps19. Finally, the complete plastome
 map, including IR, LSC, and SSC regions, was visualized using OGDraw to
 confirm IR boundaries and genome structure. We used a
 dataset including the 115 coding-genes sequence to construct the
 phylogenetic tree. A maximum likelihood (ML) tree was constructed using
 RAxML-HPC v.8 (Stamatakis 2014) with 1000 bootstrap replicates under the
 best substitution model (GTR+GAMMA). The Bayesian inference of the
 phylogeny was performed using MrBayes v.3.7.2a (Ronquist et al. 2012). The
 Markov chain Monte Carlo chain length was set to 20 million and the sample
 frequency was set to 2,000 (two independent operations). The final average
 standard deviation of split frequencies was less than 0.01.
 <em>Distribution and mapping</em>
 The survey sites for the new species were located on a GPS map
 (GARMIN GPSMAP 639csx). Maps were produced using QGIS v.3.32 based on the
 free vector and raster map data available online (https://www.naturalearthdata.com).
description: # A new species in Iris section Pseudoregelia (Iridaceae) from Gansu,
 China
 [https://doi.org/10.5061/dryad.70rxwdc7h](https://doi.org/10.5061/dryad.70rxwdc7h) ## Description of the data and file structure Genomic DNA was extracted from silica-dried leaf materials of the Longnan species (two individuals) and the other species using a commercial plant genomic DNA extraction kit (CW0531; CWBIO, Jiangsu, China). We constructed a library with an average length of 350 bp using the Illumina DNA Library Preparation Kit (E7370L; NEB, USA), which was then sequenced on the NovaSeq 6000 platform (Illumina, San Diego, CA). *De novo* assembly was performed on the clean data using SPAdes v.3.14.1, and k-mer values of 105 were set to obtain the graph file. Then, the redundant contigs were removed visually using the Bandage software and edited into a circular form. The circular sequence thus obtained is the complete chloroplast genome sequence. ### Files and variables #### File: sequence\_data.zip **Description:** This file contains all the complete chloroplast genome sequence datas. The sequences of Longnan species and 12 species/varieties in *Iris* subg. *Iris* (*I. bloudowii*, *I. cuniculiformis*, *I. goniocarpa*, *I. goniocarpa* var. *tenella*, *I. leptophylla*, *I. mandshurica*, *I. sichuanensis*, *I. pandurata*, *I. tigridia*, *I. mandshurica*, and *I. bloudowii*)  were obtained by our sequencing. *I. domestica* , *I. dichotoma* and *I. ensata* were downloaded from GenBank. ## Code/software #### Genomic Data Analysis: * **Software Options**: NCBI's BLAST, Artemis, and GBRAP (GenBank Retrieving, Analyzing, and Parsing software) for handling .gbk/.gb files. A maximum likelihood (ML) tree was constructed using RAxML-HPC v.8 (Stamatakis 2014) with 1000 bootstrap replicates under the best substitution model (GTR+GAMMA). The Bayesian inference of the phylogeny was performed using MrBayes v.3.7.2a (Ronquist et al. 2012). Data was derived from the following sources: * The sequences data of  *I. domestica*, *I. dichotoma* and *I. ensata* were downloaded from Genbank, the Genbank accession numbers were NC_050833.1(*I. domestica*) , NC_056172.1( *I.dichotoma*) and NC_056173.1(*I. ensata*).