DOI: 10.5061/dryad.j6q573nm9
title: Assemblies, associated annotation files, and analysis source data of Platanus x acerifloia genome

description: Platanus × acerifolia (London plane; Platanaceae) is a major
 ornamental tree used worldwide. Platanaceae is one of the last
 early-diverging eudicot families without a complete nuclear genome
 assembly. Here, we assembled a high-quality, chromosome-level reference
 genome for P. × acerifolia.
description: <strong>Genome and transcriptome
 sequencing</strong> The extracted genomic DNA met the requirement
 for both Illumina (San Diego, CA, USA) sequencing and PacBio High Fidelity
 (HiFi; Covaris, Massachusetts, USA) sequencing (Supplementary Note 2.2).
 For Illumina sequencing of the <em>P</em>. ×
 <em>acerifolia</em> genome, a 350-bp library was constructed
 and sequenced on the Illumina NovaSeq platform. The approximately 10-kb
 SMRTbell<sup>TM</sup> libraries were constructed for
 single-molecule sequencing with PacBio; the data generated were used to
 assemble the highly heterogeneous <em>P</em>. ×
 <em>acerifolia</em> polyploid genome. The HiFi reads were
 sequenced using the PacBio Sequel II system following PacBio<sup>TM
 </sup>standard protocol. To anchor genome scaffolds onto
 chromosomes, we also constructed a Hi-C library and obtained sequence data
 via the MGI-SEQ 2000 platform (Wuhan, Hubei, China). In brief, fresh
 leaves were fixed with a nuclei isolation buffer containing 2%
 formaldehyde following previously reported methods. The DNA was digested
 with <em>Dpn</em>II. Biotin-14-dCTP was removed from unligated
 DNA ends due to the exonuclease activity of T4 DNA polymerase, and then
 the ligated DNA was sheared into 300−600-bp fragments. Finally, the raw
 cross-linked fragments were processed into paired-end sequencing
 libraries, and the obtained libraries were sequenced on the MGI-SEQ 2000
 platform. All the transcriptome libraries were also sequenced on the
 MGI-SEQ 2000 platform to obtain high-quality paired-end reads for
 subsequent analyses. <strong><em>De
 novo</em></strong><strong> assembly and chromosome
 anchoring</strong> Before the <em>de
 novo</em> assembly of the <em>P</em>. ×
 <em>acerifolia</em> genome, the genome size was estimated.
 After data trimming by fastp, 98 Gb of high-quality paired-end reads were
 obtained from NGS genome datasets. Then high-quality reads were split into
 <em>k</em>-mers from 17 bp to 31 bp by Jellyfish, and genome
 size was estimated using GenomeScope. The HiFi Circular Consensus Sequence
 (CCS) reads were generated by CCS software
 (github.com/PacificBiosciences/ccs) with parameters ‘--min-passes 1
 --min-rq 0.99 --min-length 100’. Hifiasm was employed to generate contigs
 and resolve segmental duplications. Afterward, contigs annotated to
 mitochondrial DNA, plasmids, and metazoa against the NT database by BLASTN
 were removed. Benchmarking Universal Single-Copy Ortholog
 (BUSCO) scores were used to assess the completeness of the assembled
 genome by comparison against embryophyta_odb10. This process can be done
 without genome annotation via "-m genome". We examined the
 sequence identity by aligning the Illumina NovaSeq-generated paired-end
 reads to the assembled genome using BWA. For chromosome
 anchoring, we first filtered low-quality sequences (quality scores
 &lt;20), adaptor sequences, and short sequences (&lt;30 bp) from
 Hi-C raw data by fastp software. The clean paired-end reads were mapped to
 the assembled contigs by Bowtie2 with the parameters ‘-end-to-end
 --very-sensitive -L 30’. Invalid read pairs including dangling-end,
 self-cycle, re-ligation, and dumped products were filtered by HiC-Pro.
 After the valid interaction pairs were generated, the contigs were further
 clustered, ordered, and oriented onto chromosomes through valid
 interaction pairs by LACHESIS with the parameters ‘CLUSTER MIN RE
 SITES=100; CLUSTER MAX LINK DENSITY=2.5; CLUSTER NONINFORMATIVE RATIO
 =1.4; ORDER MIN N RES IN TRUNK=60; ORDER MIN N RES IN SHREDS=60’. Finally,
 we manually corrected the errors in the placement and orientation of the
 contigs exhibiting obvious discrete chromatin interaction
 patterns. <strong>Genome
 annotation</strong> We used <em>de
 novo</em> prediction and similarity mapping prediction strategies to
 identify repeat elements and gene boundaries. <em>De novo</em>
 predictions of repeat elements and family clustering were performed using
 RECON, RepeatScout, and RepeatModeler. For similarity-based repeat element
 prediction, RepeatMasker was used to identify the repeat elements from
 libraries of Repbase and Dfam. Long terminal repeats (LTRs) were detected
 by LTR_retriever and LTR_finder. INFERNAL was used to predict non-coding
 RNA based on the Rfam database, and tRNAscan-SE was employed to identify
 tRNAs. The gene structure of protein-coding genes
 was annotated by RNA-seq-based prediction, ab initio prediction, and
 similarity-based prediction. We used Trinity to generate <em>de
 novo</em> transcript assemblies. In addition, transcriptome reads
 also were aligned to the <em>P</em>. ×
 <em>acerifolia</em> genome by TopHat2 and assembled to
 transcripts via Cufflinks. CD-HIT was employed to filter the combined
 transcripts with the parameters ‘-aL -c 0.8’. Afterward, PASA (Program to
 Assemble Spliced Alignments) was used to align transcripts to the
 <em>P</em>. × <em>acerifolia </em>genome and
 predict complete structure with high confidence. Based on the resultant
 high-confidence complete structure, high-quality genic models were
 predicted using PASA, SNAP, GeneMark, and AUGUSTUS for ab initio
 annotation. Protein profiles from four species with the closest
 phylogenetic relationship to <em>P</em>. ×
 <em>acerifolia </em>according to APG IV were used for
 similarity-based prediction of gene structures (viz., <em>Nelumbo
 nucifera</em>, <em>Telopea speciosissima</em>,
 <em>Macadamia
 integrifolia</em>,<em> </em>and<em> Platanus
 occidentalis</em> (PRJNA79937)). Finally, gene structures were
 predicted using MAKER by integrating the above-mentioned prediction
 methods. The functions of protein-coding genes were identified by aligning
 protein sequences against the NR database, Gene Ontology, eggNOG,
 InterPro, Uniprot, TrEMBL, and KEGG databases. After that, the
 completeness of the annotation was assessed against the
 embryophyta_odb10 using BUSCO.
description: # Assemblies, associated annotation files, and analysis source data of
 Platanus x acerifloia genome
 [https://doi.org/10.5061/dryad.j6q573nm9](https://doi.org/10.5061/dryad.j6q573nm9) ## Description of the data and file structure This is the genome assembly, annotation, and source file of *Platanus* x *acerifloia* | File Name | Description | | ------------------------------------------ | ------------------------------------------------------------------ | | Platanus\_acerifolia\_Group1\_genome.fasta | Pseudo-haplotype genome sequence file | | Platanus\_acerifolia\_Group1.gff | Pseudo-haplotype genome annotation file | | Platanus\_acerifolia\_Group1\_prot.fasta | Pseudo-haplotype AA sequence file | | Platanus\_acerifolia\_Group1\_CDS.fasta | Pseudo-haplotype CDS sequence file | | Platanus\_acerifolia\_Group1\_function.xls | Pseudo-haplotype Function annotation | | Platanus\_hexaploid\_genome.fasta | Hexaploid genome sequence file | | Platanus\_hexaploid\_gene.gff3 | Hexaploid genome annotation file | | Platanus\_hexaploid\_prot.fasta | Hexaploid AA sequence file | | Platanus\_hexaploid\_CDS.fasta | Hexaploid CDS sequence file | | Platanus\_hexaploid\_function.xls | Hexaploid Function annotation | | Platanus\_source\_data.zip | Source analysis data of Pseudo-haplotype *Platanus* x *acerifolia* | The * Group1 * files contain the datasets from the Pseudo-haplotype genome of *Platanus* x *acerifolia*; The * hexaploid * files contain the datasets from the hexaploid genome of *Platanus* x *acerifolia*; The *.fasta files contain the nucleic acid sequences or peptide sequences represented by single letters with sequence names before the sequence in fasta format. The *.gff3 files contain the structural annotation of genes in gff3 format. The *function.xls contain the functional annotation of genes. The Platanus_source_data.zip file contains source analysis data for Platanus x acerifolia. The README files within this zip file provide descriptions of the data.