| Saxifragaceae,a family of over 600 species and approximately 30 genera of herbaceous perennials,is found mostly in the Northern Hemisphere.The diversity center of Saxifragaceae is located in the Himalayas,East Asia and Western North America.The family comprises two main lineages: Saxifragoids and Heucheroids.In Heucheroids,nine genera of herbaceous perennials comprise the Heuchera group,which is a particularly valuable model for the analysis of plastid capture and its impact on phylogeny reconstruction due to evidence of numerous hybridization events among and within those genera.Tiarella is a small genus within the Heuchera group and contains only three species: T.polyphylla D.Don,T.cordifolia L.and T.trifoliata L..The genus shows an interesting eastern Asia(T.polyphylla)-western North America(T.trifoliata)-eastern North America(T.cordifolia)disjunct distribution pattern,with one species each in these three areas.Previous studies have proved the ancestral area of this genus is in western North American.However,the phylogenetic relationships within the genus are not yet well resolved.In this study,we used a genome skimming approach to investigate the phylogeny of Tiarella and test the hypothesis of plastid capture between Tiarella and Heuchera.Seven species with a total of 11 individuals,were selected for genome skimming.We specifically aimed to reveal the chloroplast genome evolutionary pattern of Saxifragaceae,the phylogenetic relationship of Tiarella and the direction of plastid capture between Tiarella and Heuchera.The main results are as follows:(1)The sequencing and analyses of chloroplast genomesWe generated 15,431,294 to 49,735,470 paired-end clean reads with the length was 150 bp.After filtering by quality with average Phred score < 30,the percentage of the remaining reads was more than 80% and the average length was 124 bp.All the plastomes sequenced in this study had a standard angiosperm structure comprising two copies of the IR region separated by the LSC region and SSC region.For all the species,the complete plastomes ranged from 154,717 bp to 155,400 bp.The plastomes of all 11 accessions encoded an identical set of 132 genes,of which 113 were unique and 19 were duplicated in the IR regions.Among the 113 unique genes,there were 79 protein-coding genes,30 t RNA genes and four r RNA genes.Six t RNA genes and eight protein-coding genes contained single intron,and three genes including rps12,clp P and ycf3 contained two introns.(2)The evolutionary pattern of chloroplast genomes in SaxifragaceaeCombing with the published chloroplast genomes of four genera(Bergenia,Mukdenia,Oresitrophe,Saxifraga)in Saxifragaceae,we investigated the plastid genome evolutionary pattern of the family.The results showed that the plastomes exhibited high levels of sequence similarity and structural conservation,and no rearrangement occurred in gene organization after verification.IR regions were more conservative than the LSC and SSC regions.Among the 12 Saxifragaceae species,the plastome size ranged from 150,752 bp to 156,960 bp in length and size variations of the plastomes are purely ascribed to the length differences of LSC,SSC,and IRs regions.Moreover,we found the loss of ycf15 and rpl2 intron may represent a synapomorphy of Saxifragaceae.(3)Phylogeny and plastid capture of TiarellaFor the nuclear dataset,we obtained the nr ITS and nr ETS regions of the fourteen Heucheroid species from genome skimming data based on BLAST search.The phylogenetic relationship of Tiarella was well resolved used the matrix of ITS and ETS.The result revealed that T.cordifolia was located the basal position of this genus,and T.trifolia was sister to T.polyphylla.However,the tree topologies based on plastid data are incongruent with those based on nr DNA data.Comparisons of nuclear and plastid phylogenies revealed that plastid capture events have occurred multiple times(at least two times)among species and genera of the Heuchera group through ancient hybridization.(4)Genomic resources development for TiarellaIn Tiarella,T.polyphylla has a wide distribution from the Himalayas all the way east to Hokkaido.It occupies two subkingdoms in East Asia,the Sino-Japanese subkingdom and the Sino-Himalayan subkingdom.The unique geographical distribution pattern makes it an ideal model to test the boundary of these two floristic regions and to reveal the cause of its formation.However,the studies relating to the phylogeography and species formation of Tiarella are scarce.In present study,nine of plastid regions including psb I-trn S,trn R-atp A,pet N-psb M,psb C-trn S,trn T-trn L,trn L-trn F,pet G-trn W,rpl32-trn L,and ndh D-psa C showed relative high levels of intergeneric variation and may be used as effective phylogenetic markers for the genus Tiarella.Besides,1,800 polymorphic nuclear n SSR were obtained based on Candi SSR software. |
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