Full-length SMRT transcriptome sequencing and microsatellite characterization in Paulownia catalpifolia

Abstract

Paulownia catalpifolia is an important, fast-growing timber species known for its high density, color and texture. However, few transcriptomic and genetic studies have been conducted in P. catalpifolia. In this study, single-molecule real-time sequencing technology was applied to obtain the full-length transcriptome of P. catalpifolia leaves treated with varying degrees of drought stress. The sequencing data were then used to search for microsatellites, or simple sequence repeats (SSRs). A total of 28.83 Gb data were generated, 25,969 high-quality (HQ) transcripts with an average length of 1624 bp were acquired after removing the redundant reads, and 25,602 HQ transcripts (98.59%) were annotated using public databases. Among the HQ transcripts, 16,722 intact coding sequences, 149 long non-coding RNAs and 179 alternative splicing events were predicted, respectively. A total of 7367 SSR loci were distributed throughout 6293 HQ transcripts, of which 763 complex SSRs and 6604 complete SSRs. The SSR appearance frequency was 28.37%, and the average distribution distance was 5.59 kb. Among the 6604 complete SSR loci, 1–3 nucleotide repeats were dominant, occupying 97.85% of the total SSR loci, of which mono-, di- and tri-nucleotide repeats were 44.68%, 33.86% and 19.31%, respectively. We detected 112 repeat motifs, of which A/T (42.64%), AG/CT (12.22%), GA/TC (9.63%), GAA/TTC (1.57%) and CCA/TGG (1.54%) were most common in mono-, di- and tri-nucleotide repeats, respectively. The length of the repeat SSR motifs was 10–88 bp, and 4997 (75.67%) were ≤ 20 bp. This study provides a novel full-length transcriptome reference for P. catalpifolia and will facilitate the identification of germplasm resources and breeding of new drought-resistant P. catalpifolia varieties.

Full-length transcriptome analysis of the bloom-forming dinoflagellate Akashiwo sanguinea by single-molecule real-time sequencing

“…A total number of 514 TFs were obtained and categorized into 23 families, with C3H (137) ranked the highest, followed by SNF2 (72), SET (63), CSD (63), and Others (41). Since all eukaryotic TF families were historically identified and SSR polymorphic genetic markers, also known as microsatellites, show significant species-specific differences and have been widely used for genetic map construction, functional gene mining, genetic diversity analyses, and molecular markerrelated studies (Shen et al, 2014;Feng et al, 2021). A total of 4,397 SSRs identified in A. sanguinea, exceeding the SSRs detected in T. weissflogii (3,295 SSRs) and P. tricornutum (1,390 SSRs) on numbers (Rastogi et al, 2018;Cheng et al, 2021).…”

“…SSR polymorphic genetic markers, also known as microsatellites, show significant species-specific differences and have been widely used for genetic map construction, functional gene mining, genetic diversity analyses, and molecular marker-related studies ( Shen et al, 2014 ; Feng et al, 2021 ). A total of 4,397 SSRs identified in A. sanguinea , exceeding the SSRs detected in T. weissflogii (3,295 SSRs) and P. tricornutum (1,390 SSRs) on numbers ( Rastogi et al, 2018 ; Cheng et al, 2021 ).…”

Microsatellite analysis and polymorphic marker development based on the full-length transcriptome of Camellia chekiangoleosa

“…This result was also consistent with the results found for other species, such as Persea americana Mill. 33 , Styrax japonicus 34 , and Paulownia catalpifolia 35 . The differences in the transcriptomic information and basic SSR characteristics between C. chekiangoleosa and other species might be due to species specificity, sequencing technology, reference genome quality and other factors.…”

“…This result was also consistent with the results found for other species, such as Persea americana Mill. 33 , Styrax japonicus 34 , and Paulownia catalpifolia 35 . The differences in the transcriptomic and tetranucleotide repeat types 18 .…”

Microsatellite analysis and polymorphic marker development based on the full-length transcriptome of Camellia chekiangoleosa

“…This result was also consistent with the results found for other species, such as Persea americana Mill. 33 , Styrax japonicus 34 , and Paulownia catalpifolia 35 . The differences in the transcriptomic information and basic SSR characteristics between C. chekiangoleosa and other species might be due to species speci city, sequencing technology, reference genome quality and other factors.…”