TodoFirGene: Developing Transcriptome Resources for Genetic Analysis of Abies sachalinensis

Area of Science:

• Forestry science
• Genomics
• Plant biology

Background:

• Todo-matsu (Abies sachalinensis) is a key forestry species in Hokkaido, Japan, with a wide distribution.
• The species exhibits phenotypic adaptations to diverse environments, suggesting natural selection.
• Understanding its genetic basis is vital for conservation and sustainable forestry.

Purpose of the Study:

• To identify candidate genes under natural selection in Abies sachalinensis.
• To generate a comprehensive transcriptome resource for genetic analysis.
• To establish a foundation for comparative genomics.

Main Methods:

• Collected transcriptome data from female and male flowers, leaves, and inner bark.
• Performed de novo assembly of sequencing reads to generate transcripts.
• Conducted homology searches against public databases and identified genetic variants (SSRs and SNVs).

Main Results:

• Generated 158,542 transcripts from 69,618 loci with high coverage of conserved eukaryotic genes.
• Identified 28,944 simple sequence repeats (SSRs) and 80,758 single nucleotide variants (SNVs).
• Developed the TodoFirGene database for accessing annotations and facilitating comparative genomics.

Conclusions:

• The generated transcriptome data and identified genetic markers provide valuable resources for Abies sachalinensis genetic research.
• The TodoFirGene database enables comparative genomic studies across multiple plant species.
• This work supports future research into the adaptive evolution and genetic diversity of Todo-matsu.