AUTHOR=Wang Shuaibin , Gao Junping , Li Zhaowu , Chen Kai , Pu Wenxuan , Feng Chen 

TITLE=Phylotranscriptomics supports numerous polyploidization events and phylogenetic relationships in Nicotiana

JOURNAL=Frontiers in Plant Science

VOLUME=14

YEAR=2023

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2023.1205683

DOI=10.3389/fpls.2023.1205683

ISSN=1664-462X

ABSTRACT=<sec><title>Introduction</title><p><italic>Nicotiana</italic> L. (Solanaceae) is of great scientific and economic importance, and polyploidization has been pivotal in shaping this genus. Despite many previous studies on the <italic>Nicotiana</italic> phylogenetic relationship and hybridization, evidence from whole genome data is still lacking.</p></sec><sec><title>Methods</title><p>In this study, we obtained 995 low-copy genes and plastid transcript fragments from the transcriptome datasets of 26 <italic>Nicotiana</italic> species, including all sections. We reconstructed the phylogenetic relationship and phylogenetic network of diploid species.</p></sec><sec><title>Results</title><p>The incongruence among gene trees showed that the formation of <italic>N. sylvestris</italic> involved incomplete lineage sorting. The nuclear–plastid discordance and nuclear introgression absence indicated that organelle capture from section <italic>Trigonophyllae</italic> was involved in forming section <italic>Petunioides</italic>. Furthermore, we analyzed the evolutionary origin of polyploid species and dated the time of hybridization events based on the analysis of PhyloNet, sequence similarity search, and phylogeny of subgenome approaches. Our results highly evidenced the hybrid origins of five polyploid sections, including sections <italic>Nicotiana, Repandae, Rusticae, Polydicliae</italic>, and <italic>Suaveolentes</italic>. Notably, we provide novel insights into the hybridization event of section <italic>Polydicliae</italic> and <italic>Suaveolentes</italic>. The section <italic>Polydicliae</italic> formed from a single hybridization event between maternal progenitor <italic>N. attenuata</italic> and paternal progenitor <italic>N. undulata</italic>; the <italic>N. sylvestris</italic> (paternal progenitor) and the <italic>N. glauca</italic> (maternal progenitor) were involved in the formation of section <italic>Suaveolentes</italic>.</p></sec><sec><title>Discussion</title><p>This study represents the first exploration of <italic>Nicotiana</italic> polyploidization events and phylogenetic relationships using the high-throughput RNA-seq approach. It will provide guidance for further studies in molecular systematics, population genetics, and ecological adaption studies in <italic>Nicotiana</italic> and other related species.</p></sec>