DOI: 10.5061/dryad.7pvmcvf1n
title: Microsatellite exploration in the climbing hydrangea (Hydrangea petiolaris Siebold & Zucc.) transcriptome: A resource for population genetics and functional genomics

description: Background Hydrangea petiolaris Siebold & Zucc., also known as
 climbing hydrangea, is a vine native to the woodlands of Korea, Japan, and
 Sakhalin Island. It is an economically important ornamental plant with
 fertile and sterile flowers. Despite the recent increase in Hydrangea
 breeding and interest in germplasm conservation, relatively little is
 known about the relationships between Hydrangea species. Results We
 employed Illumina NovaSeq 6000 sequencing technology to generate a total
 of 39,945,480 reads, which were assembled into 137,715 contigs. A total of
 109,092 filtered transcripts were used to identify microsatellites, and
 54,587 microsatellite repeat motifs were revealed within 33,556 contigs.
 Among these, 4,510 transcripts harboring microsatellites had Gene Ontology
 annotations, and numerous microsatellite-containing transcripts exhibited
 associations with genes, including those encoding PPR proteins, aldehyde
 dehydrogenases, and bHLH transcription factors, related to the restorer of
 fertility (Rf) genes, which play a critical role in restoring fertility in
 plants with cytoplasmic male sterility. Validation of transcriptomic SSR
 markers demonstrated high levels of polymorphism, revealing significant
 genetic diversity within populations. However, null alleles and deviations
 from Hardy‒Weinberg equilibrium at specific loci suggested caution in
 genotyping accuracy. Population-level analysis disclosed high genetic
 differentiation and distinct clustering of populations. Conclusions The H.
 petiolaris transcriptomic SSR markers offer valuable insight for gaining
 insights into the population genetics, evolutionary background, and
 practical strategies for conserving this species. Moreover, the
 microsatellite loci we have identified and their associations with
 annotated genes hold promise for creating functional markers specifically
 tailored for H. petiolaris. These markers include valuable resources of
 transcriptomic SSR markers suitable for population genetic investigations
 and have a reasonable degree of applicability across different taxa.
description: # Microsatellite exploration in the climbing hydrangea (Hydrangea
 petiolaris Siebold & Zucc.) transcriptome: A resource for population
 genetics and functional genomics
 ## Description of the data
 and file structure There are two datasets for this article. Dataset 1
 (filename: c320hanIDssrReads.fa) is a fasta file of 33,556 transcripts,
 which contain microsatellites, from Hydrangea petiolaris (Hydrangeaceae).
 \# The transcripts were generated using Trinity v2.15.1 program using
 RNA-seq raw reads. \# Final transcripts were filtered by TransRate v1.0.3
 and RSEM v1.2.15 programs. \# The final transcript were utilized to
 identify microsatellite loci using the MIcroSAtellite identification tool
 (MISA). Dataset 2 (filename: c320hanID.p2top6AA.fa) is a fasta file of
 27,006 ORFs from the 33,556 transcripts. \# These best ORF generated by
 TransDecoder v.5.5.0 programs.