Genome assembly of the bearded iris Iris pallida Lam
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Curated by GigaByte
**Editors Assessment: **
Irises on top of being a popular and beautiful ornamental plant, have wider commercial interest due to the many interesting secondary metabolites present in their rhizomes that have value to the fragrance and pharmaceutical industries. Many of these have large and difficult to assemble genomes, and to fill that gap the Dalmatian Iris (Iris pallida Lam.) is sequenced here. Using PacBio long-read sequencing and bionano optical mapping to produce a giant 10Gbp assembly with a scaffold N50 of 14.34 Mbp. The authors didn’t manage to handle the haplotigs separately or to study the ploidy, but as all of the data is available for reuse others can explore these questions further. This reference genome should also allow researchers to study the biosynthesis of these secondary metabolites in much greater detail, opening new avenues of investigation for drug discovery and fragrance formulations.
This evaluation refers to version 1 of the preprint
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Abstract
Irises are perennial plants, representing a large genus with hundreds of species. While cultivated extensively for their ornamental value, commercial interest in irises lies in the secondary metabolites present in their rhizomes. The Dalmatian Iris ( Iris pallida Lam.) is an ornamental plant that also produces secondary metabolites with potential value to the fragrance and pharmaceutical industries. In addition to providing base notes for the fragrance industry, iris tissues and extracts possess anti-oxidant, anti- inflammatory, and immunomodulatory effects. However, study of these secondary metabolites has been hampered by a lack of genomic information, instead requiring difficult extraction and analysis techniques. Here, we report the genome sequence of Iris pallida Lam., generated with Pacific Bioscience long-read sequencing, resulting in a 10.04 Gbp assembly with a scaffold N50 of 14.34 Mbp and 91.8% complete BUSCOs. This reference genome will allow researchers to study the biosynthesis of these secondary metabolites in much greater detail, opening new avenues of investigation for drug discovery and fragrance formulations.
Research area: Genetics and Genomics; Botany; Plant Genetics
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**Editors Assessment: **
Irises on top of being a popular and beautiful ornamental plant, have wider commercial interest due to the many interesting secondary metabolites present in their rhizomes that have value to the fragrance and pharmaceutical industries. Many of these have large and difficult to assemble genomes, and to fill that gap the Dalmatian Iris (Iris pallida Lam.) is sequenced here. Using PacBio long-read sequencing and bionano optical mapping to produce a giant 10Gbp assembly with a scaffold N50 of 14.34 Mbp. The authors didn’t manage to handle the haplotigs separately or to study the ploidy, but as all of the data is available for reuse others can explore these questions further. This reference genome should also allow researchers to study the biosynthesis of these secondary metabolites in much greater detail, opening …
**Editors Assessment: **
Irises on top of being a popular and beautiful ornamental plant, have wider commercial interest due to the many interesting secondary metabolites present in their rhizomes that have value to the fragrance and pharmaceutical industries. Many of these have large and difficult to assemble genomes, and to fill that gap the Dalmatian Iris (Iris pallida Lam.) is sequenced here. Using PacBio long-read sequencing and bionano optical mapping to produce a giant 10Gbp assembly with a scaffold N50 of 14.34 Mbp. The authors didn’t manage to handle the haplotigs separately or to study the ploidy, but as all of the data is available for reuse others can explore these questions further. This reference genome should also allow researchers to study the biosynthesis of these secondary metabolites in much greater detail, opening new avenues of investigation for drug discovery and fragrance formulations.
This evaluation refers to version 1 of the preprint
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Irises are perennial plants, representing a large genus with hundreds of species. While cultivated extensively for their ornamental value, commercial interest in irises lies in the secondary metabolites present in their rhizomes. The Dalmatian Iris (Iris pallida Lam.) is an ornamental plant that also produces secondary metabolites with potential value to the fragrance and pharmaceutical industries. In addition to providing base notes for the fragrance industry, iris tissues and extracts possess anti-oxidant, anti- inflammatory, and immunomodulatory effects. However, study of these secondary metabolites has been hampered by a lack of genomic information, instead requiring difficult extraction and analysis techniques. Here, we report the genome sequence of Iris pallida Lam., generated with Pacific Bioscience long-read sequencing, …
Irises are perennial plants, representing a large genus with hundreds of species. While cultivated extensively for their ornamental value, commercial interest in irises lies in the secondary metabolites present in their rhizomes. The Dalmatian Iris (Iris pallida Lam.) is an ornamental plant that also produces secondary metabolites with potential value to the fragrance and pharmaceutical industries. In addition to providing base notes for the fragrance industry, iris tissues and extracts possess anti-oxidant, anti- inflammatory, and immunomodulatory effects. However, study of these secondary metabolites has been hampered by a lack of genomic information, instead requiring difficult extraction and analysis techniques. Here, we report the genome sequence of Iris pallida Lam., generated with Pacific Bioscience long-read sequencing, resulting in a 10.04 Gbp assembly with a scaffold N50 of 14.34 Mbp and 91.8% complete BUSCOs. This reference genome will allow researchers to study the biosynthesis of these secondary metabolites in much greater detail, opening new avenues of investigation for drug discovery and fragrance formulations.
This work has been published in GigaByte Journal under a CC-BY 4.0 license (https://doi.org/10.46471/gigabyte.94), and has published the reviews under the same license. These are as follows.
**Reviewer 1. Baocai Han **
Iris pallida Lam., an ornamental plant, produces secondary metabolites with potential value to the fragrance and pharmaceutical industries, while also possessing anti-oxidant, anti-inflammatory, and immunomodulatory effects. The genome assembly of this species could be more helpful in investigation for drug discovery and fragrance formulations.
I have a number of comments that follow:
Line 10 (page 2): “resulting in a 10.04 Gbp assembly with a scaffold N50 of 14.34 Mbp”. I found the genome size is 13.49 Gb in Table 2 and line 18 (page 7) due to differing haplotigs in the phased assembly. While I can not find how to deal with this problem. I suggest to purge the duplicates from the genome using the Purge_Dups pipeline. (Guan D, McCarthy SA, Wood J et al. Identifying and removing haplotypic duplication in primary genome assemblies. Bioinformatics, 2020; 36(9): 2896–2898.)
Line 5 (page 8): why is the gene number of the Complete and duplicated BUSCOs so high. Is it due to issues with genome assembly or the presence of a particularly high number of repetitive sequences in the species?
there is no reference or website for many softwares and pipelines, eg. HybridScaffolding pipeline (line 22, page 5), lima (line 2, page 6) and Exonerate (line 11, page 6)
I suggest upload the genome annotation file, given that genome annotation has already been performed.
**Reviewer 2. Kang Zhang **
Is the language of sufficient quality?
Yes. Though I found several sentences confusing: P2L8 (Is the DNA/RNA extraction particularly difficult for iries?), and P9L5 (wording).
Is there sufficient information for others to reuse this dataset or integrate it with other data?
Yes. With the following comments.
1. P7L20. The basic stats of the subreads should be introduced before the assembling process.- The authors should provide more methodological details about the BUSCO assessment, such as the database version, the mode (genome or protein), etc.
- I am curious about the genome size enlargement introduced by the scaffolding. Were different haplotigs (from different haplotypes) were used for scaffolding, and why? I suppose that only the primary haplotigs should be used.
- Considering the high proportion of duplicated BUSCO genes, I wonder whether the iris sequenced is a polyploid or not? Please clarify it in the Background.
Additional Comments: Dr. Wong and her colleagues reported a genome assembly of iris using the PacBio technology. Due to the huge genome size, the generated data volume is impressive. Although the quality of the assembly is not so satisfying, it is reasonable considering the genome size and the high heterozygosity, which is commonly found in many flowers. Overall, the methods used in this work are well described, and the data could be accessed. I only get several minor points regarding the details during the assembling process.
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