4.7 Article

Sampling Strategy and Potential Utility of Indels for DNA Barcoding of Closely Related Plant Species: A Case Study in Taxus

Journal

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
Volume 13, Issue 7, Pages 8740-8751

Publisher

MDPI
DOI: 10.3390/ijms13078740

Keywords

DNA barcoding; indel (gap) coding; sampling strategy; noncoding chloroplast regions; Taxus

Funding

  1. Chinese Academy of Sciences [2009-LSF-GBOWS-01, 9223111W1]
  2. National Natural Science Foundation of China [30700042]
  3. talent project of Yunnan province [2008YP064]

Ask authors/readers for more resources

Although DNA barcoding has become a useful tool for species identification and biodiversity surveys in plant sciences, there remains little consensus concerning appropriate sampling strategies and the treatment of indels. To address these two issues, we sampled 39 populations for nine Taxus species across their entire ranges, with two to three individuals per population randomly sampled. We sequenced one core DNA barcode (matK) and three supplementary regions (trnH-psbA, trnL-trnF and ITS) for all samples to test the effects of sampling design and the utility of indels. Our results suggested that increasing sampling within-population did not change the clustering of individuals, and that meant within-population P-distances were zero for most populations in all regions. Based on the markers tested here, comparison of methods either including or excluding indels indicated that discrimination and nodal support of monophyletic groups were significantly increased when indels were included. Thus we concluded that one individual per population was adequate to represent the within-population variation in these species for DNA barcoding, and that intra-specific sampling was best focused on representing the entire ranges of certain taxa. We also found that indels occurring in the chloroplast trnL-trnF and trnH-psbA regions were informative to differentiate among for closely related taxa barcoding, and we proposed that indel-coding methods should be considered for use in future for closed related plant species DNA barcoding projects on or below generic level.

Authors

I am an author on this paper
Click your name to claim this paper and add it to your profile.

Reviews

Primary Rating

4.7
Not enough ratings

Secondary Ratings

Novelty
-
Significance
-
Scientific rigor
-
Rate this paper

Recommended

Article Biochemistry & Molecular Biology

DNA barcoding of Cymbidium by genome skimming: Call for next-generation nuclear barcodes

Le Zhang, Yi-Wei Huang, Jia-Lin Huang, Ji-Dong Ya, Meng-Qing Zhe, Chun-Xia Zeng, Zhi-Rong Zhang, Shi-Bao Zhang, De-Zhu Li, Hong-Tao Li, Jun-Bo Yang

Summary: In this study, DNA barcoding was conducted for species identification of Cymbidium using plastomes. A comprehensive DNA barcode reference library for Cymbidium species identification was established. The plastome showed improved species identification rates compared to standard DNA barcodes, but still had limitations. Nuclear genome data were also explored for species identification and showed potential as next-generation nuclear barcodes.

MOLECULAR ECOLOGY RESOURCES (2023)

Article Ecology

The diversity of mycorrhiza-associated fungi and trees shapes subtropical mountain forest ecosystem functioning

Ya-Huang Luo, Liang-Liang Ma, Sebastian Seibold, Marc W. W. Cadotte, Kevin S. S. Burgess, Shao-Lin Tan, Lin-Jiang Ye, Wei Zheng, Jia-Yun Zou, Zhi-Fa Chen, De-Tuan Liu, Guang-Fu Zhu, Xiao-Chun Shi, Wei Zhao, De-Zhu Li, Jie Liu, Lian-Ming Gao

Summary: This study assessed the effects of different mycorrhizal types on forest carbon storage and the biodiversity-ecosystem functioning (BEF) relationships in the Gaoligong Mountains, Southwest China. It was found that different mycorrhizal types have significant impacts on forest carbon storage and species diversity. Furthermore, future global changes could potentially alter the mycorrhizal-mediated BEF relationships in mountain forests.

JOURNAL OF BIOGEOGRAPHY (2023)

Review Biochemistry & Molecular Biology

Phylogenomics and the flowering plant tree of life

Cen Guo, Yang Luo, Lian-Ming Gao, Ting-Shuang Yi, Hong-Tao Li, Jun-Bo Yang, De-Zhu Li

Summary: The advancement of next-generation sequencing and long-read sequencing technologies has greatly influenced plant phylogenetic studies. Numerous phylogenetic studies using hundreds to thousands of genes across various clades have emerged in the past decade, bringing plant phylogenetics and evolution into a new era. This review focuses on the application of genomic data in phylogenetic and evolutionary investigations, describes the methodology of experimental and analytical procedures, and summarizes recent progress in flowering plant phylogenomics at different taxonomic levels. Challenges, such as systematic errors and underlying biological factors, are discussed, suggesting that a bifurcating tree may not be the most suitable model for the tree of life. Finally, promising avenues for future plant phylogenomic studies are discussed.

JOURNAL OF INTEGRATIVE PLANT BIOLOGY (2023)

Article Plant Sciences

Functional consequences of temporal reversal of height dimorphism for pollen and seed dispersal in a dioecious plant

Zhi-Hua Zeng, Qian Yu, Qing-Hong Feng, Xin-Jia Wang, Li Zhong, Hua-Ying Sun, Hong Wang, De-Zhu Li, Spencer C. H. Barrett, Wei Zhou

Summary: This study demonstrates the functional consequences of height dimorphism reversal in dioecious plants, shedding light on the reproductive strategies of males and females in terms of pollen and seed dispersal.

JOURNAL OF SYSTEMATICS AND EVOLUTION (2023)

Article Biochemistry & Molecular Biology

Phylogenomic insights into the origin and evolutionary history of evergreen broadleaved forests in East Asia under Cenozoic climate change

Sheng-Yuan Qin, Zheng-Yu Zuo, Cen Guo, Xin-Yu Du, Shui-Yin Liu, Xiang-Qin Yu, Xiao-Guo Xiang, Jun Rong, Bing Liu, Zhi-Fang Liu, Peng-Fei Ma, De-Zhu Li

Summary: This study focuses on the Litsea complex, which is a key lineage of evergreen broadleaved forests (EBLFs) in East Asia, aiming to explore the shift of evergreen versus deciduous trait and understand the origin and historical dynamics of EBLFs under Cenozoic climate change. The results show that the prototype of EBLFs in East Asia probably appeared in the Early Eocene period (about 55-50 million years ago) facilitated by greenhouse warming. With the cooling and drying climate in the Middle to Late Eocene period (48-38 million years ago), deciduous habits evolved. The development of East Asian monsoon in the Early Miocene period (23 million years ago) increased the extreme seasonal precipitation and promoted the emergence of evergreen habits.

MOLECULAR ECOLOGY (2023)

Editorial Material Plant Sciences

Burning lignin: overlooked cues for post-fire seed germination

Dechang Cao, Jerry M. Baskin, Carol C. Baskin, De-Zhu Li

Summary: Smoke cues released from decaying leaves after drying are crucial for seed germination.

TRENDS IN PLANT SCIENCE (2023)

Article Plant Sciences

Variation in gene expression along an elevation gradient of Rhododendron sanguineum var. haemaleum assessed in a comparative transcriptomic analysis

Lin-Jiang Ye, Michael Moller, Ya-Huang Luo, Jia-Yun Zou, Wei Zheng, Jie Liu, De-Zhu Li, Lian-Ming Gao

Summary: Selection along environmental gradients in alpine ecosystems can drive adaptive evolution in plants. However, the genetic variation and adaptation in plants along environmental gradients remain poorly understood. To address this gap, we studied the transcriptomic profiles of Rhododendron sanguineum var. haemaleum at different elevations in the Gaoligong Mountains. We found that gene expression patterns in flower and leaf organs showed parallel shifts but with different functionality, indicating flexibility in response strategies to the heterogeneous environments.

FRONTIERS IN PLANT SCIENCE (2023)

Article Plant Sciences

Amentotaxus x hybridia (Taxaceae), a new natural Amentotaxus hybrid from southeast Yunnan province, China

Lian-Ming Gao, Gui-Liang Zhang, Zhi-Qiong Mo, Philip Thomas

Summary: During a floristic survey in Hekou County, Yunnan Province, China, a putative natural hybrid of A. yunnanensis and A. hekouensis was discovered. Morphological and molecular evidence confirms its status as a natural hybrid. Named Amentotaxus x hybridia, it has linear or linear-lanceolate leaves, white stomatal bands, and 3-6 seeds at the base of each branchlet.

PHYTOKEYS (2023)

Article Plant Sciences

Diversity, Distribution, Systematics and Conservation Status of Podocarpaceae

Raees Khan, Robert S. S. Hill, Jie Liu, Ed Biffin

Summary: Podocarpaceae is the second largest conifer family with diverse and functional traits, dominating the Southern Hemisphere. However, comprehensive studies on its diversity, distribution, systematics, and ecophysiological aspects are lacking. This study aims to outline and evaluate the current and past diversity, distribution, systematics, ecophysiological adaptations, endemism, and conservation status of podocarps. Through analyzing data on living and extinct macrofossil taxa and combining it with genetic data, an updated phylogeny is reconstructed and historical biogeography is understood. Podocarpaceae includes 20 genera and approximately 219 taxa, distributed in three clades, and shows remarkable adaptations from leaves to seeds, dispersal methods, and plant types, as well as a complex pattern of seed and leaf functional trait evolution.

PLANTS-BASEL (2023)

Article Biochemistry & Molecular Biology

High-quality Cymbidium mannii genome and multifaceted regulation of crassulacean acid metabolism in epiphytes

Weishu Fan, Zheng-Shan He, Mengqing Zhe, Jing-Qiu Feng, Le Zhang, Yiwei Huang, Fang Liu, Jia-Lin Huang, Ji-Dong Ya, Shi-Bao Zhang, Jun-Bo Yang, Andan Zhu, De-Zhu Li

Summary: This study reports a high-quality chromosome-level genome assembly of a CAM epiphyte, Cymbidium mannii, and provides insights into the molecular regulation of CAM photosynthesis in epiphytes. The study also reveals the rhythmic changes in metabolism and gene expression during the CAM diel cycle. The findings of this study are valuable for investigating post-transcription and translation scenarios in epiphytes.

PLANT COMMUNICATIONS (2023)

Article Plant Sciences

Dynamics of imprinted genes and their epigenetic mechanisms in castor bean seed with persistent endosperm

Bing Han, Yelan Li, Di Wu, De-Zhu Li, Aizhong Liu, Wei Xu

Summary: Genomic imprinting plays a significant role in the endosperm development, storage compound accumulation, and seed germination in castor bean. The study reveals that DNA methylation has a limited role in controlling genomic imprinting, while histone modifications play a more significant role in regulating the expression of most imprinted genes.

NEW PHYTOLOGIST (2023)

Article Plant Sciences

A comparative full-length transcriptomic resource provides insight into the perennial monocarpic mass flowering

Jiu-Xia Zhao, Shu Wang, Jiazhi Liu, Xiao-Dong Jiang, Jing Wen, Zhi-Quan Suo, Jie Liu, Mi-Cai Zhong, Qin Wang, Zhirong Gu, Changning Liu, Yunfei Deng, Jin-Yong Hu, De-Zhu Li

Summary: This study generated a transcriptome resource for two Strobilanthes species, providing valuable information for understanding the molecular mechanisms of perennial monocarpic mass flowering. The differential expression of transcription factors potentially involved in the photoperiod and circadian-clock pathway suggests their role in regulating flowering time diversity.

PLANT JOURNAL (2023)

Article Biochemistry & Molecular Biology

Multiple paternally inherited chloroplast capture events associated with Taxus speciation in the Hengduan Mountains

Han-Tao Qin, Michael Moller, Richard Milne, Ya-Huang Luo, Guang-Fu Zhu, De-Zhu Li, Jie Liu, Lian-Ming Gao

Summary: Mountainous regions provide diverse habitats for speciation. In the Hengduan Mountains of southwest China, four Taxus lineages were studied. Conflicting phylogenetic relationships were found between nuclear and chloroplast sequences. Limited gene flow was observed between species. Based on the data, it was determined that two Taxus species originated through hybridization and chloroplast capture events.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2023)

No Data Available