Genome skimming and exploration of DNA barcodes for Taiwan endemic cypresses

Chung-Shien Wu,Chi-Tsong Chen,Chiun-Jr Huang,Bo-Cyun Wang,Shu-Miaw Chaw,Edi Sudianto,Yu-Mei Hung

doi:10.1038/s41598-020-77492-2

Chung-Shien Wu, Chi-Tsong Chen + Show 5 more

Open Access

https://doi.org/10.1038/s41598-020-77492-2

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Abstract

Cypresses are characterized by their longevity and valuable timber. In Taiwan, two endemic cypress species, Chamaecyparis formosensis and C. obtusa var. formosana, are threatened by prevalent illegal logging. A DNA barcode system is urgently needed for reforestation and conservation of these two cypresses. In this study, both plastomes and 35S rDNAs from 16, 10, and 6 individuals of C. formosensis, C. obtusa var. formosana, and C. obtusa var. obtusa were sequenced, respectively. We show that the loss of plastid trnT-GGU readily distinguishes C. formosensis from its congeneric species. We demonstrate that entire sequences of plastomes or 35S rDNAs are capable of correctly identifying cypress species and varieties, suggesting that they are effective super-barcodes. We also discover three short hypervariable loci (i.e., 3′ETS, ITS1, and trnH-psbA) that are promising barcodes for identifying cypress species and varieties. Moreover, nine species-specific indels of > 100 bp were detected in the cypress plastomes. These indels, together with the three aforementioned short barcodes, constitute an alternative and powerful barcode system crucial for identifying specimens that are fragmentary or contain degraded/poor DNA. Our sequenced data and barcode systems not only enrich the genetic reference for cypresses, but also contribute to future reforestation, conservation, and forensic investigations.

Highlights

Cypresses are characterized by their longevity and valuable timber
We address two questions: (1) Can we use whole plastomes and 35S rDNA as effective super-barcodes for identifying cypress species and varieties? and (2) If yes, do they contain hypervariable loci that can be used as promising barcodes? To address these questions, we sampled 16 C. formosensis individuals and 10 C. obtusa var. formosana individuals from natural populations scattered across the cloud forests of Taiwan
Our results reveal that the entire sequences of plastomes or 35S rDNAs serve as an effective super-barcode, and contain short hypervariable loci and long lineagespecific indels that together constitute an alternative and powerful barcode system for cypress identification at both interspecies and inter-variety levels

Summary

Introduction

Cypresses are characterized by their longevity and valuable timber. In Taiwan, two endemic cypress species, Chamaecyparis formosensis and C. obtusa var. formosana, are threatened by prevalent illegal logging. In Taiwan, two endemic cypress species, Chamaecyparis formosensis and C. obtusa var. A DNA barcode system is urgently needed for reforestation and conservation of these two cypresses. In this study, both plastomes and 35S rDNAs from 16, 10, and 6 individuals of C. formosensis, C. obtusa var. We demonstrate that entire sequences of plastomes or 35S rDNAs are capable of correctly identifying cypress species and varieties, suggesting that they are effective super-barcodes. We discover three short hypervariable loci (i.e., 3′ETS, ITS1, and trnH-psbA) that are promising barcodes for identifying cypress species and varieties. In Taiwan, two endemic cypress taxa, Chamaecyparis formosensis and C. obtusa var. None of the above-mentioned loci has ever been used to identify cypress species

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