Loading content, please wait..
loading..
Logo
Version 3.22
or
Publication Type J
Authors Yao, P. C., H. Y. Gao, Y. N. Wei, J. H. Zhang, X. Y. Chen and H. Q. Li
Title Evaluating sampling strategy for DNA barcoding study of coastal and inland halotolerant Poaceae and Chenopodiaceae: A case study for increased sample size
Source Plos One
Author Keywords phylogenetic-relationships species identification biogeography distance plants conservation diversity evolution taxonomy moraceae
Abstract Environmental conditions in coastal salt marsh habitats have led to the development of specialist genetic adaptations. We evaluated six DNA barcode loci of the 53 species of Poaceae and 15 species of Chenopodiaceae from China's coastal salt marsh area and inland area. Our results indicate that the optimum DNA barcode was ITS for coastal salt-tolerant Poaceae and matK for the Chenopodiaceae. Sampling strategies for ten common species of Poaceae and Chenopodiaceae were analyzed according to optimum barcode. We found that by increasing the number of samples collected from the coastal salt marsh area on the basis of inland samples, the number of haplotypes of Arundinella hirta, Digitaria ciliaris, Eleusine indica, Imperata cylindrica, Setaria viridis, and Chenopodium glaucum increased, with a principal coordinate plot clearly showing increased distribution points. The results of a Mann- Whitney test showed that for Digitaria ciliaris, Eleusine indica, Imperata cylindrica, and Setaria viridis, the distribution of intraspecific genetic distances was significantly different when samples from the coastal salt marsh area were included (P < 0.01). These results suggest that increasing the sample size in specialist habitats can improve measurements of intraspecific genetic diversity, and will have a positive effect on the application of the DNA barcodes in widely distributed species. The results of random sampling showed that when sample size reached 11 for Chloris virgata, Chenopodium glaucum, and Dysphania ambrosioides, 13 for Setaria viridis, and 15 for Eleusine indica, Imperata cylindrica and Chenopodium album, average intraspecific distance tended to reach stability. These results indicate that the sample size for DNA barcode of globally distributed species should be increased to 11-15.
Author Address [Yao, Peng-Cheng; Gao, Hai-Yan; Wei, Ya-Nan; Zhang, Jian-Hang; Li, Hong-Qing] East China Normal Univ, Sch Life Sci, Shanghai, Peoples R China. [Chen, Xiao-Yong] East China Normal Univ, Sch Ecol & Environm Sci, Tiantong Natl Stn Forest Ecosyst, Shanghai, Peoples R China. Li, HQ (reprint author), East China Normal Univ, Sch Life Sci, Shanghai, Peoples R China.; Chen, XY (reprint author), East China Normal Univ, Sch Ecol & Environm Sci, Tiantong Natl Stn Forest Ecosyst, Shanghai, Peoples R China. xychen@des.ecnu.edu.cn; hqli@bio.ecnu.edu.cn
ISSN 1932-6203
ISBN 1932-6203
29-Character Source Abbreviation PLoS One
Publication Date Sep
Year Published 2017
Volume 12
Issue 9
Digital Object Identifier (DOI) 10.1371/journal.pone.0185311
Unique Article Identifier WOS:000411339900143
Plants associated with this reference

LEGAL NOTICES — This website is protected by Copyright © The University of Sussex, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021. The eHALOPH database is protected by Database Right and Copyright © The University of Sussex and other contributors, 2006, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021. This database is based on an earlier work by James Aronson.
THIS WEBSITE AND THIS DATABASE ARE PROVIDED ON AN "AS IS" BASIS, AND YOU USE THEM AND RELY ON THEM AT YOUR OWN RISK.

Contact email: halophytes@sussex.ac.uk
Credits – Tim Flowers, Joaquim Santos, Moritz Jahns, Brian Warburton, Peter Reed