Insights into the phylogenetic relationships and species boundaries of the Myricaria squamosa complex (Tamaricaceae) based on the complete chloroplast genome

Abstract

Myricaria plants are widely distributed in Eurasia and are helpful for windbreak and embankment protection. Current molecular evidence has led to controversy regarding species boundaries within the Myricaria genus and interspecific phylogenetic relationships between three specific species—M. bracteata, M. paniculata and M. squamosa—which have remained unresolved. This study treated these three unresolved taxa as a species complex, named the M. squamosa complex. The genome skimming approach was used to determine 35 complete plastome sequences and nuclear ribosomal DNA sequences for the said complex and other closely related species, followed by de novo assembly. Comparative analyses were conducted across Myricaria to identify the genome size, gene content, repeat type and number, SSR (simple sequence repeat) abundance, and codon usage bias of chloroplast genomes. Tree-based species delimitation results indicated that M. bracteata, M. paniculata and M. squamosa could not be distinguished and formed two monophyletic lineages (P1 and P2) that were clustered together. Compared to plastome-based species delimitation, the standard nuclear DNA barcode had the lowest species resolution, and the standard chloroplast DNA barcode and group-specific barcodes delimitated a maximum of four out of the five species. Plastid phylogenomics analyses indicated that the monophyletic M. squamosa complex is comprised of two evolutionarily significant units: one in the western Tarim Basin and the other in the eastern Qinghai-Tibet Plateau. This finding contradicts previous species discrimination and promotes the urgent need for taxonomic revision of the threatened genus Myricaria. Dense sampling and plastid genomes will be essential in this effort. The super-barcodes and specific barcode candidates outlined in this study will aid in further studies of evolutionary history.

Mitogenome Assembly Reveals Gene Migration and RNA Editing Events in Plateau Hongliu (Myricaria elegans Royle.)

“…P. Y. Zhang & Y. J. Zhang. Most are critical ecological and pharmaceutical resources [3]. By contrast, the M. elegans species is an ethnobotanical herb and grows at the riverside and arid areas of the highest altitude mountains (>3500 m), exhibiting superior qualities in extreme climate tolerance and tangible economic benefits to indigenous communities in poverty [4].…”

“…It is a xylophyta that grows at high altitudes (3500-4800 m) and is predominantly in the China Tibet (Ngari Prefecture) and arid areas of western Himalaya (e.g., Ladakh and Kashmir) [2]. They thrive in extreme climates and saline-alkaline lands, prompting them to be the origin of the genus Myricaria to study genetic evolution and ecological adaptation to harsh environments, particularly in high-altitude mountains [3]. During the ancient and current ages, M. elegans was used by indigenous people in western Tibet as an ethnological herb to alleviate injuries, including bruises, wounds, and burns [4].…”