DOI: 10.5061/dryad.4f4qrfjd9
title: Data from: Establishing community-wide DNA barcode references for conserving mangrove forests in China

description: Background: Mangrove ecosystems have been the focus of global attention
 for their crucial role in sheltering coastal communities and retarding
 global climate change by sequestering ‘blue carbon’. China is relatively
 rich in mangrove diversity, with one-third of the ca. 70 true mangrove
 species and a number of mangrove associate species occurring naturally
 along the country’s coasts. Mangrove ecosystems, however, are widely
 threatened by intensifying human disturbances and rising sea levels. The
 urgent need to protect mangrove ecosystems could be assisted by using
 barcoding technology, which provides rapid species identification.
 Results: To investigate this potential, 898 plant specimens were collected
 from 33 of the major mangrove sites in China. Based on the morphologic
 diagnosis, the specimens were assigned to 72 species, including all 28
 true mangrove species and all 12 mangrove associate species recorded in
 China. Three chloroplast DNA markers rbcL, trnH-psbA, matK, and one
 nuclear marker ITS2 were chosen to investigate the utility of using
 barcoding to identify these species. According to the criteria of
 barcoding gaps in genetic distance, sequence similarity and phylogenetic
 monophyly, we propose that a single marker, ITS2, is sufficient to barcode
 the species of mangroves and their associates in China. Furthermore, rbcL
 or trnH-psbA can also be used to gather supplement confirming data. In
 using these barcodes, we revealed a very low level of genetic variation
 among geographic locations in the mangrove species, which is an alert to
 their vulnerability to climate and anthropogenic disturbances. Conclusion:
 We suggest to use ITS2 to barcode mangrove species and terrestrial coastal
 plants in South China. The DNA barcode sequences we obtained would be
 valuable in monitoring biodiversity and the restoration of ecosystems,
 which are essential for mangrove conservation.
description: We collected 898 plant specimens from 33 mangrove sites along the
 coastlines of South China, from Hainan island to northernmost Zhejiang.
 Three plasmid barcoding regions rbcL, matK, trnHpsbA, and one nuclear
 barcoding gene ITS2 were amplified. Raw bidirectional sequences were
 assembled and manually checked by SeqMan (LASERGENE software package).
 Multiple sequences of each genomic region were aligned using MUSCLE in
 MEGA v7. We constructed neighbour-joining (NJ) trees, maximum likelihood
 (ML) trees for each candidate barcode, with supporting rates for nodes
 obtained from 1000 bootstrap replicates, and bayesian inference (BI) was
 performed to construct phylogeny trees for at most twelve orders. The NJ
 trees were generated in MEGA v7 based on the Kimura 2-parameter (K2P)
 genetic distance model. The ML trees were constructed using the RAxML
 program under the GTRCAT model. The BI trees were constructed by Markov
 chain Monte Carlo simulation under the GTR substitution model with
 gamma-distributed rate variation across sites and a proportion of
 invariable sites (“GTR + I + Γ”) in MrBayes v3.2.7a.