Deciphering the Taxonomic Delimitation of Ottelia acuminata (Hydrocharitaceae) Using Complete Plastomes as Super-Barcodes

Abstract

Accurate species delimitation and identification, which is a challenging task in traditional morphology-based taxonomy, is crucial to species conservation. Ottelia acuminata (Hydrocharitaceae) is a severely threatened submerged macrophyte endemic to southwestern China. The taxonomy of O. acuminata, which has long been in dispute, remains unresolved, impeding effective conservation and management practices. Here, we aim to address the long-standing issues concerning species boundary and intraspecific subdivision of O. acuminata using complete plastome sequences as super-barcodes. The taxonomic delimitation of O. acuminata was explored using phylogenetic inference and two independent sequence-based species delimitation schemes: automatic barcode gap discovery (ABGD) and multi-rate Poisson tree processes (mPTP). The reciprocally reinforcing results support the reduction of the closely related congeneric species, O. balansae and O. guanyangensis, as two conspecific varieties of O. acuminata. Within the newly defined O. acuminata, accurate varietal identification can be achieved using plastome super-barcodes. These findings will help inform future decisions regarding conservation, management and restoration of O. acuminata. This case study suggests that the use of plastome super-barcodes can provide a solution for species delimitation and identification in taxonomically difficult plant taxa, thus providing great potential to lessen the challenges of inventorying biodiversity, as well as biologically monitoring and assessing threatened species.

The Complete Chloroplast Genomes of Primula obconica Provide Insight That Neither Species nor Natural Section Represent Monophyletic Taxa in Primula (Primulaceae)

“…Due to the rapid development of next-generation sequencing technologies, chloroplast genomes have become easier to obtain. As "super-barcodes", chloroplast genomes have been successful in solving taxonomic issues of closely related plant taxonomy [3], such as in Ottelia acuminata, which consists of six phenotypic varieties, of which the chloroplast genome was successfully divided it into two conspecific varieties [4], thus providing new insight into the use of the chloroplast genome as a super-barcode for species delimitation in taxonomically difficult plant taxa.…”

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

“…With next-generation DNA sequencing (NGS) technologies, genome-wide sequence variation has begun to replace one or a few sequence loci for the identification and delimitation of plant species ( Li et al, 2015 ; Coissac et al, 2016 ; Hollingsworth et al, 2016 ). The genome skimming approach, which uses NGS technologies to generate multi-copy and highly repetitive genome components, such as whole plastid genomes (plastomes) and nuclear ribosomal DNA (nrDNA) clusters via relatively low coverage genome sequencing ( Straub et al, 2012 ), has been increasingly used for species identification and delimitation in recent years ( Nock et al, 2011 ; Kane et al, 2012 ; Dodsworth, 2015 ; Li et al, 2015 ; Ruhsam et al, 2015 ; Firetti et al, 2017 ; Fu et al, 2019 , 2021 ; Ji et al, 2019a , 2020 , 2021 ; Knope et al, 2020 ; Ślipiko et al, 2020 ; Su et al, 2021 ). Compared with restriction-site associated DNA sequencing (RAD-seq; Miller et al, 2007 ; Baird et al, 2008 ), another NSG-based technique that is extensively used to generate genomic data for plant species identification and delimitation (e.g., Wu et al, 2018 ; Donkpegan et al, 2020 ; Ma et al, 2020 ; Zhou et al, 2020 ; Li et al, 2021 ), the promising advantage of using genome skimming for species identification and delimitation is the avoidance of problems encountered with RAD-seq ( Kane et al, 2012 ; Hollingsworth et al, 2016 ), such as only applying to diploids and generating asymmetric data between distinctly related taxa.…”

An integrated study of Violae Herba (Viola philippica) and five adulterants by morphology, chemical compositions and chloroplast genomes: insights into its certified plant origin

“…With the rapid development of NGS, cp genome sequences can be obtained efficiently and economically [ 90 ]. It is possible to develop new barcodes derived from the cp genomes or use the whole cp genome as a superbarcode to authenticate species-rich genera [ 25 – 27 ]. cp DNA markers were more commonly used in phylogenetic studies of Viola rather than species authentication studies [ 15 , 16 , 74 , 76 ].…”