Plastomes of limestone karst gesneriad genera Petrocodon and Primulina, and the comparative plastid phylogenomics of Gesneriaceae

Abstract

Petrocodon and Primulina are two characteristic genera of Gesneriaceae that exhibit remarkable species and floral diversity, and high endemism across the Sino-Vietnamese Limestone Karsts. To better understand the evolution of limestone gesneriad plastomes, we report nine complete plastomes of seven Primulina and two Petrocodon which have never been assembled before. The newly generated plastomes range from 152,323 to 153,786 bp in size and display a typical quadripartite structure. To further explore the plastome evolution across Gesneriaceae, we assembled five additional plastomes from public reads data and incorporated 38 complete Gesneriaceae plastomes available online into comparative and phylogenomic analyses. The comparison of 52 Gesneriaceae plastomes reveals that not only Primulina and Petrocodon but all gesneriad genera analyzed are highly conserved in genome size, genome structure, gene contents, IR boundary configurations, and codon usage bias. Additionally, sliding window analyses were implemented across alignments of Primulina and Petrocodon for identifying highly variable regions, providing informative markers for future studies. Meanwhile, the SSRs and long repeats of Gesneriaceae plastomes were characterized, serving as useful data in studying population and repetitive sequence evolutions. The results of plastome phylogenetics represent a preliminary but highly resolved maternal backbone genealogy of Primulina and the Old World subtribes of Gesneriaceae.

Plastome evolution and phylogenomics of Trichosporeae (Gesneriaceae) with its morphological characters appraisal

“…For example, both Roalson and Roberts (2016) and Li et al. (2022) indicated that Hemiboea was close to Lysionotus with weak supporting values, while Hsieh et al. (2022) supported that Oreocharis was a sister group of Hemiboea based on plastomes with one IR excluded.…”

Langbiangia, a new genus of Gesneriaceae endemic to Langbiang Plateau, southern Vietnam and a taxonomic endeavor to achieve key targets of the post-2020 global biodiversity framework

“…As shown in previous phylogenetic studies of Didymocarpinae using ITS and trnL-F sequences, relationships within the ‘core’ Didymocarpinae remained poorly resolved [ 75 , 77 , 79 , 86 , 87 , 90 ]. The employment of genomic data such as whole plastome sequences [ 96 ] and target capture [ 101 ] will be essential to clarify and understand this apparent radiation of Asian gesneriad clade.…”

“…Based on the most updated classification of Gesneriaceae, Primulina and Deinostigma are both placed in subtribe Didymocarpinae, tribe Trichosporeae, subfamily Didymocarpoideae [ 63 , 77 , 96 , 101 ]. To maximize taxon sampling while exploiting DNA sequences available in the GenBank, we sequenced the internal transcribed spacer (ITS) of the nuclear ribosomal DNA (including the 5.8S gene) and the plastid trnL-trnF intergenic spacer ( trnL-F ), which have been the most widely used molecular markers in reconstructing phylogenetic relationships of Asian Gesneriaceae and delimitating new gesneriad genera [ 74 – 76 , 86 – 88 , 90 , 102 , 103 ].…”

“…Biogeographically, Primulina annamensis, P. poilanei, and P. scutellifolia are all restricted to the Langbiang Plateau, representing the southernmost and disjunctively distributed species of Primulina (Fig 2). Ecologically, while a majority of Primulina are calciphilous plants on limestone karsts (Fig 2 ) of lower elevations [64,[94][95][96], P. annamensis, P. poilanei, and P. scutellifolia grow on humid fertile soils of the evergreen broad-leaved forest at elevation of 1,450-2,000 m [58,78,92,93,97]. Morphologically, P. annamensis, P. poilanei, and P. scutellifolia also differ from the typical Primulina by their alternate and spirally arranged phyllotaxy [58,78], while a majority of Primulina are characterized by decussate or whorled leaves (Fig 4).…”

“…scutellifolia are all restricted to the Langbiang Plateau, representing the southernmost and disjunctively distributed species of Primulina ( Fig 2 ). Ecologically, while a majority of Primulina are calciphilous plants on limestone karsts ( Fig 2 ) of lower elevations [ 64 , 94 – 96 ], P . annamensis , P .…”