Single-Molecule Real-Time Sequencing of the Madhuca pasquieri (Dubard) Lam. Transcriptome Reveals the Diversity of Full-Length Transcripts

Lei Kan,Shuyu Wang,Zhiyao Su,Qicong Liao,Yushan Tan,Lu Zhang

doi:10.3390/f11080866

Lei Kan, Shuyu Wang + Show 4 more

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https://doi.org/10.3390/f11080866

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Journal: Forests	Publication Date: Aug 8, 2020
Citations: 6	License type: CC BY 4.0

Affiliation: South China Agricultural University

Abstract

Madhuca pasquieri (Dubard) Lam. is a tree on the International Union for Conservation of Nature Red List and a national key protected wild plant (II) of China, known for its seed oil and timber. However, lacking of genomic and transcriptome data for this species hampers study of its reproduction, utilization, and conservation. Here, single-molecule long-read sequencing (PacBio) and next-generation sequencing (Illumina) were combined to obtain the transcriptome from five developmental stages of M. pasquieri. Overall, 25,339 transcript isoforms were detected by PacBio, including 24,492 coding sequences (CDSs), 9440 simple sequence repeats (SSRs), 149 long non-coding RNAs (lncRNAs), and 182 alternative splicing (AS) events, a majority was retained intron (RI). A further 1058 transcripts were identified as transcriptional factors (TFs) from 51 TF families. PacBio recovered more full-length transcript isoforms with a longer length, and a higher expression level, whereas larger number of transcripts (124,405) was captured in de novo from Illumina. Using Nr, Swissprot, KOG, and KEGG databases, 24,405 transcripts (96.31%) were annotated by PacBio. Functional annotation revealed a role for the auxin, abscisic acid, gibberellin, and cytokinine metabolic pathways in seed germination and post-germination. These findings support further studies on seed germination mechanism and genome of M. pasquieri, and better protection of this endangered species.

Highlights

IntroductionMadhuca pasquieri (Dubard) Lam., a member of the Sapotaceae family, is considered a vulnerable (VU) species on the International Union for Conservation of Nature (IUCN) Red List, and in
Madhuca pasquieri (Dubard) Lam., a member of the Sapotaceae family, is considered a vulnerable (VU) species on the International Union for Conservation of Nature (IUCN) Red List, and inChina, is listed as a national key protected wild plant (II) and wild plant of extremely small population
We identified 25,339 transcript isoforms by PacBio, including 24,492 coding sequences (CDSs), 9440 simple sequence repeats (SSRs), and 149 long non-coding RNAs (lncRNAs)

Summary

Introduction

Madhuca pasquieri (Dubard) Lam., a member of the Sapotaceae family, is considered a vulnerable (VU) species on the International Union for Conservation of Nature (IUCN) Red List, and in. China, is listed as a national key protected wild plant (II) and wild plant of extremely small population. This tree is endemic to southwest Guangdong, southern Guangxi, and southeast. The oil content of M. pasquieri seeds can reach approximately 30%. It is a precious timber species, with a basic density of 0.711 and an air-dry density of 0.893, which is often used for its strength, wear resistance, when used for equipment or furniture, and in veneer manufacturing.

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