Genome Skimming Contributes to Clarifying Species Limits in Paris Section Axiparis (Melanthiaceae)

Yunheng Ji; Jin Yang; Jacob B Landis; Shuying Wang; Lei Jin; Pingxuan Xie; Haiyang Liu; Jun-Bo Yang; Ting-Shuang Yi

doi:10.3389/fpls.2022.832034

Genome Skimming Contributes to Clarifying Species Limits in Paris Section Axiparis (Melanthiaceae)

Front Plant Sci. 2022 Apr 4:13:832034. doi: 10.3389/fpls.2022.832034. eCollection 2022.

Authors

Yunheng Ji^{1

2}, Jin Yang^{1

3}, Jacob B Landis^{4

5}, Shuying Wang^{1

3}, Lei Jin^{1

6}, Pingxuan Xie^{1

6}, Haiyang Liu⁷, Jun-Bo Yang⁸, Ting-Shuang Yi⁸

Affiliations

¹ CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.
² Yunnan Key Laboratory for Integrative Conservation of Plant Species With Extremely Small Population, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.
³ School of Life Sciences, Yunnan University, Kunming, China.
⁴ Section of Plant Biology and the L. H. Bailey Hortorium, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States.
⁵ BTI Computational Biology Center, Boyce Thompson Institute, Ithaca, NY, United States.
⁶ School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, China.
⁷ State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.
⁸ Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.

Abstract

Paris L. section Axiparis H. Li (Melanthiaceae) is a taxonomically perplexing taxon with considerable confusion regarding species delimitation. Based on the analyses of morphology and geographic distribution of each species currently recognized in the taxon, we propose a revision scheme that reduces the number of species in P. sect. Axiparis from nine to two. To verify this taxonomic proposal, we employed a genome skimming approach to recover the plastid genomes (plastomes) and nuclear ribosomal DNA (nrDNA) regions of 51 individual plants across the nine described species of P. sect. Axiparis by sampling multiple accessions per species. The species boundaries within P. sect. Axiparis were explored using phylogenetic inference and three different sequence-based species delimitation methods (ABGD, mPTP, and SDP). The mutually reinforcing results indicate that there are two species-level taxonomic units in P. sect. Axiparis (Paris forrestii s.l. and P. vaniotii s.l.) that exhibit morphological uniqueness, non-overlapping distribution, genetic distinctiveness, and potential reproductive isolation, providing strong support to the proposed species delimitation scheme. This study confirms that previous morphology-based taxonomy overemphasized intraspecific and minor morphological differences to delineate species boundaries, therefore resulting in an overestimation of the true species diversity of P. sect. Axiparis. The findings clarify species limits and will facilitate robust taxonomic revision in P. sect. Axiparis.

Keywords: Paris Linn.; plastome; ribosomal DNA; species delimitation; taxonomy.