The Experts below are selected from a list of 789 Experts worldwide ranked by ideXlab platform
Douglas E. Soltis - One of the best experts on this subject based on the ideXlab platform.
-
diversification in the arctic biogeography and systematics of the north american micranthes Saxifragaceae
Systematic Botany, 2020Co-Authors: Rebecca L Stubbs, Douglas E. Soltis, Ryan A Folk, Nico CellineseAbstract:Flora endemic to the cold habitats of the Northern Hemisphere provide important models for investigating diversification and disjunctions, given both the intense climatic fluctuations of these areas in the recent past and the fascinating biogeographic patterns of today's Arctic-alpine plant communities. Micranthes Haw. (Saxifragaceae), a clade of small-flowered herbaceous flowering plants comprising ∼80 species, is an ideal group for investigating the evolution and diversification of plants in montane and Arctic ecosystems. Micranthes has proven to be a particularly challenging clade to unravel taxonomically due in part to rampant auto- and allopolyploidy, hybridization, and cryptic speciation. With the goal of providing an updated conspectus for this group, we build upon a recent large phylogenomic analysis to help elucidate the evolution of Micranthes. Here, we present new downstream analyses including diversification analyses, biogeographical reconstructions, and a comparison of methods for dating phylogenomic data sets. To complement these new analyses, we also synthesize chromosomal variation, new observations regarding morphology and species identification, comprehensive field studies, and an extensive review of the literature for Saxifragaceae and Micranthes. A new perspective on the systematics and taxonomy of Micranthes is provided.
-
plastome evolution in Saxifragaceae and multiple plastid capture events involving heuchera and tiarella
Frontiers in Plant Science, 2020Co-Authors: Luxian Liu, Douglas E. Soltis, Ryan A Folk, Shenyi Wang, Fude ShangAbstract:Saxifragaceae, a family of over 600 species and approximately 30 genera of herbaceous perennials, is well-known for intergeneric hybridization. Of the main lineages in this family, the Heuchera group represents a valuable model for the analysis of plastid capture and its impact on phylogeny reconstruction. In this study, we investigated plastome evolution across the family, reconstructed the phylogeny of the Heuchera group and examined putative plastid capture between Heuchera and Tiarella. Seven species (11 individuals) representing Tiarella, as well as Mitella and Heuchera, were selected for genome skimming. We assembled the plastomes, and then compared these to six others published for Saxifragaceae; the plastomes were found to be highly similar in overall size, structure, gene order and content. Moreover, ycf15 was lost due to pseudogenization and rpl2 lost its only intron for all the analyzed plastomes. Comparative plastome analysis revealed that size variations of the plastomes are purely ascribed to the length differences of LSC, SSC, and IRs regions. Using nuclear ITS + ETS and the complete plastome, we fully resolved the species relationships of Tiarella, finding that the genus is monophyletic and the Asian species is most closely related to the western North American species. However, the position of the Heuchera species was highly incongruent between nuclear and plastid data. Comparisons of nuclear and plastid phylogenies revealed that multiple plastid capture events have occurred between Heuchera and Tiarella, through putative ancient hybridization. Moreover, we developed numerous molecular markers for Tiarella (e.g., plastid hotspot and polymorphic nuclear SSRs), which will be useful for future studies on the population genetics and phylogeography of this disjunct genus.
-
chloroplast genome analyses and genomic resource development for epilithic sister genera oresitrophe and mukdenia Saxifragaceae using genome skimming data
BMC Genomics, 2018Co-Authors: Luxian Liu, Yuewen Wang, Joongku Lee, Douglas E. SoltisAbstract:Epilithic sister genera Oresitrophe and Mukdenia (Saxifragaceae) have an epilithic habitat (rocky slopes) and a parapatric distribution in East Asia, which makes them an ideal model for a more comprehensive understanding of the demographic and divergence history and the influence of climate changes in East Asia. However, the genetic background and resources for these two genera are scarce. The complete chloroplast (cp) genomes of two Oresitrophe rupifraga and one Mukdenia rossii individuals were reconstructed and comparative analyses were conducted to examine the evolutionary pattern of chloroplast genomes in Saxifragaceae. The cp genomes ranged from 156,738 bp to 156,960 bp in length and had a typical quadripartite structure with a conserved genome arrangement. Comparative analysis revealed the intron of rpl2 has been lost in Heuchera parviflora, Tiarella polyphylla, M. rossii and O. rupifraga but presents in the reference genome of Penthorum chinense. Seven cp hotspot regions (trnH-psbA, trnR-atpA, atpI-rps2, rps2-rpoC2, petN-psbM, rps4-trnT and rpl33-rps18) were identified between Oresitrophe and Mukdenia, while four hotspots (trnQ-psbK, trnR-atpA, trnS-psbZ and rpl33-rps18) were identified within Oresitrophe. In addition, 24 polymorphic cpSSR loci were found between Oresitrophe and Mukdenia. Most importantly, we successfully developed 126 intergeneric polymorphic gSSR markers between Oresitrophe and Mukdenia, as well as 452 intrageneric ones within Oresitrophe. Twelve randomly selected intergeneric gSSRs have shown that these two genera exhibit a significant genetic structure. In this study, we conducted genome skimming for Oresitrophe rupifraga and Mukdenia rossii. Using these data, we were able to not only assemble their complete chloroplast genomes, but also develop abundant genetic resources (cp hotspots, cpSSRs, polymorphic gSSRs). The genomic patterns and genetic resources presented here will contribute to further studies on population genetics, phylogeny and conservation biology in Saxifragaceae.
-
Chloroplast genome analyses and genomic resource development for epilithic sister genera Oresitrophe and Mukdenia (Saxifragaceae), using genome skimming data
'Springer Science and Business Media LLC', 2018Co-Authors: Luxian Liu, Yuewen Wang, Joongku Lee, Douglas E. SoltisAbstract:Abstract Background Epilithic sister genera Oresitrophe and Mukdenia (Saxifragaceae) have an epilithic habitat (rocky slopes) and a parapatric distribution in East Asia, which makes them an ideal model for a more comprehensive understanding of the demographic and divergence history and the influence of climate changes in East Asia. However, the genetic background and resources for these two genera are scarce. Results The complete chloroplast (cp) genomes of two Oresitrophe rupifraga and one Mukdenia rossii individuals were reconstructed and comparative analyses were conducted to examine the evolutionary pattern of chloroplast genomes in Saxifragaceae. The cp genomes ranged from 156,738 bp to 156,960 bp in length and had a typical quadripartite structure with a conserved genome arrangement. Comparative analysis revealed the intron of rpl2 has been lost in Heuchera parviflora, Tiarella polyphylla, M. rossii and O. rupifraga but presents in the reference genome of Penthorum chinense. Seven cp hotspot regions (trnH-psbA, trnR-atpA, atpI-rps2, rps2-rpoC2, petN-psbM, rps4-trnT and rpl33-rps18) were identified between Oresitrophe and Mukdenia, while four hotspots (trnQ-psbK, trnR-atpA, trnS-psbZ and rpl33-rps18) were identified within Oresitrophe. In addition, 24 polymorphic cpSSR loci were found between Oresitrophe and Mukdenia. Most importantly, we successfully developed 126 intergeneric polymorphic gSSR markers between Oresitrophe and Mukdenia, as well as 452 intrageneric ones within Oresitrophe. Twelve randomly selected intergeneric gSSRs have shown that these two genera exhibit a significant genetic structure. Conclusions In this study, we conducted genome skimming for Oresitrophe rupifraga and Mukdenia rossii. Using these data, we were able to not only assemble their complete chloroplast genomes, but also develop abundant genetic resources (cp hotspots, cpSSRs, polymorphic gSSRs). The genomic patterns and genetic resources presented here will contribute to further studies on population genetics, phylogeny and conservation biology in Saxifragaceae
-
phylogenetic placement of the enigmatic and critically endangered genus saniculiphyllum Saxifragaceae inferred from combined analysis of plastid and nuclear dna sequences
Molecular Phylogenetics and Evolution, 2012Co-Authors: Chunlei Xiang, Douglas E. Soltis, Matthew A Gitzendanner, Hua Peng, Ligong LeiAbstract:Saniculiphyllum, a monotypic genus distributed in Southwest China, was thought to be extinct before our recent rediscovery. The taxonomic position of this genus has been enigmatic ever since its publication. It was originally treated as the only member of a distinct tribe Saniculiphylleae in the family Saxifragaceae. Some proposed a new family, Saniculophyllaceae, to accommodate this genus, although its affinities are clearly with members of Saxifragaceae. Here we analyzed six DNA regions, the nuclear ribosomal ITS and 26S rDNA and the plastid rbcL, matK, trnL-trnF, psbA-trnH genes, spacers, and intron to explore the phylogenetic position of Saniculiphyllum within Saxifragaceae. The combined nuclear and chloroplast dataset includes 63 ingroup species, representing all genera but Hieronymusia in the family. Results from likelihood, parsimony and Bayesian phylogenetic methods corroborate earlier results. Two clades of Saxifragaceae, the Heucheroid and Saxifragoid clades, were recovered. The topologies obtained from different analyses confirm the placement of Saniculiphyllum in Saxifragaceae, but our analyses reveal that Saniculiphyllum is embedded within the large Heucheroid clade. However, the closest relatives of Saniculiphyllum within the Heucheroid clade remain unclear. Combined with morphological data, our results suggest that Saniculiphyllum should best be regarded as a highly distinctive lineage within the Heucheroid clade of Saxifragaceae. Morphological novelties and conservation status of Saniculiphyllum are also presented.
Pamela S. Soltis - One of the best experts on this subject based on the ideXlab platform.
-
phylogeny divergence times and historical biogeography of the angiosperm family Saxifragaceae
Molecular Phylogenetics and Evolution, 2015Co-Authors: Jiabin Deng, Matthew A Gitzendanner, Bryan T Drew, Evgeny V Mavrodiev, Pamela S. SoltisAbstract:Abstract Saxifragaceae (Saxifragales) contain approximately 640 species and 33 genera, about half of which are monotypic. Due to factors such as morphological stasis, convergent morphological evolution, and disjunct distributions, relationships within Saxifragaceae have historically been troublesome. The family occurs primarily in mountainous regions of the Northern Hemisphere, with the highest generic and species diversity in western North America, but disjunct taxa are known from southern South America. Here, we integrate broad gene (56 loci) and taxon (223 species) sampling strategies, both the most comprehensive to date within Saxifragaceae, with fossil calibrations and geographical distribution data to address relationships, divergence times, and historical biogeography among major lineages of Saxifragaceae. Two previously recognized main clades, the heucheroids (eight groups + Saniculiphyllum) and saxifragoids (Saxifraga s.s.), were re-affirmed by our phylogenetic analyses. Relationships among the eight heucheroid groups, as well as the phylogenetic position of Saniculiphyllum within the heucheroids, were resolved with mostly high support. Divergence time estimates indicate that Saxifragaceae began to diversify ca. 38.37 million years ago (Mya; 95% HPD = 30.99–46.11 Mya) in the Mid-Late Eocene, and that the two major lineages, the heucheroids and saxifragoids, began to diversify approximately 30.04 Mya (95% HPD = 23.87–37.15 Mya) and 30.85 Mya (95% HPD = 23.47–39.33 Mya), respectively. We reconstructed ancestral geographic areas using statistical dispersal-vicariance (S-DIVA). These analyses indicate several radiations within Saxifragaceae: one in eastern Asia and multiple radiations in western North America. Our results also demonstrate that large amounts of sequence data coupled with broad taxon sampling can help resolve clade relationships that have thus far seemed intractable.
-
phylogenetic relationships within lithophragma Saxifragaceae hybridization allopolyploidy and ovary diversification
Systematic Botany, 1999Co-Authors: Robert K. Kuzoff, Pamela S. Soltis, Douglas E. Soltis, Larry Hufford, Shields Ave, Alan T WhittemoreAbstract:We explore phylogenetic relationships in Lithophragma through parsimony and maximum like- lihood estimation analyses of internal transcribed spacer sequences of 18S-26S ribosomal DNA. Results based on internal transcribed spacer sequences are compared with those from previous studies based on chloroplast DNA restriction site, morphological, and flavonoid variation. Phylogenetic analysis of internal transcribed spacer sequences produces a highly resolved topology with six main clades. These results suggest that three previously described species of Lithophragma are not monophyletic. Based on this topology and previous findings, two species not recognized in the most recent monograph, L. thompsonii and tetraploid L. bolanderi, are hypothesized to have arisen through hybridization and allopolyploidy, respectively. Flowers of Lithophrag- ma exhibit a diverse array of ovary positions ranging from what has been described as superior to deeply inferior. Analysis of ovary position in light of our phylogenetic results reveals a complex pattern of diversi- fication in Lithophragma. This pattern is explored through character mapping and correlation analyses and is found to be inconsistent with either an active or a passive trend toward greater inferiority. A weak relation- ship between variation in ovary position and the topological position of each taxon suggests homoplastic
-
phylogenetic relationships in Saxifragaceae sensu lato a comparison of topologies based on 18s rdna and rbcl sequences
American Journal of Botany, 1997Co-Authors: Douglas E. Soltis, Pamela S. SoltisAbstract:Relationships among the morphologically diverse members of Saxifragaceae sensu lato were inferred using 130 18S rDNA sequences. Phylogenetic analyses were conducted using representatives of all 17 subfamilies of Saxifragaceae sensu lato, as well as numerous additional taxa traditionally assigned to subclasses Magnoliidae, Caryophyllidae, Hamamelidae, Dilleniidae, Rosidae, and Asteridae. This analysis indicates that Saxifragaceae should be narrowly defined (Saxifragaceae sensu stricto) to consist of ~30 herbaceous genera. Furthermore, Saxifragaceae s. s. are part of a well-supported clade (referred to herein as Saxifragales) that also comprises lteoideae, Pterostemonoideae, Ribesioideae, Penthoroideae, and Tetracarpaeoideae, all traditional subfamilies of Saxifragaceae sensu lato, as well as Crassulaceae and Haloragaceae (both of subclass Rosidae). Paeoniaceae (Dilleniideae), and Hamamelidaceae, Cercidiphyllaceae, and Daphniphyllaceae (all of Hamamelidae). The remaining subfamilies of Saxifragaceae sensu lato fall outside this clade. Francoa (Francooideae) and Bauera (Baueroideae) are allied, respectively, with the rosid families Greyiaceae and Cunoniaceae. Brexia (Brexioideae), Parnassia (Parnassioideae), and Lepuropetolon (Lepuropetaloideae) appear in a clade with Celastraceae. Representatives of Phyllonomoideae, Eremosynoideae, Hydrangeoideae, Escallonioideae, Montinioideae, and Vahlioideae are related to taxa belonging to an expanded asterid clade (Asteridae sensu lato). The relationships suggested by analysis of 18S rDNA sequences are highly concordant with those suggested by analysis of rbcL sequences. Furthermore, these relationships are also supported in large part by other lines of evidence, including embryology. serology, and iridoid chemistry.
-
geographic structuring of chloroplast dna genotypes in tiarella trifoliata Saxifragaceae
Plant Systematics and Evolution, 1992Co-Authors: Douglas E. Soltis, Pamela S. Soltis, Robert K. Kuzoff, T L TuckerAbstract:Tiarella trifoliata comprises varietieslaciniata, trifoliata, andunifoliata, and is distributed from southeastern Alaska to northern California. We analyzed restriction site variation of chloroplast DNA (cpDNA) using 23 endonucleases in 76 populations representing the entire geographic range of the species and the three recognized varieties. We also employed comparative restriction site mapping of PCR-amplified chloroplast DNA fragments using 16 restriction endonucleases. This species exhibits low cpDNA restriction site variation. No differentiation is evident among varieties of this species based on cpDNA data; some plants of each variety were characterized by each of the two major cpDNA types detected. The two major cpDNA clades, which differ by only a single restriction site mutation, are geographically structured. A northern clade comprises populations from Alaska to central Oregon; most populations analyzed from southern Oregon and California form a southern clade. Populations that possess the typical northern cpDNA type also occur disjunctly to the south at high elevations in the Siskiyou—Klamath Mountain area of southern Oregon and northern California. Conversely, the southern cpDNA type is found disjunctly to the north in the Olympic Peninsula of Washington. Both geographic areas characterized by disjunct cytoplasms are considered glacial refugia.Tiarella trifoliata joins two other species,Tolmiea menziesii andTellima grandiflora, in having well-demarcated northern and southern cpDNA lineages. All three species have similar life-history traits and geographic distributions. We suggest that glaciation may have played a major role in the formation of the cpDNA discontinuities present in these three taxa. The pronounced relationship between cpDNA variation and geographic distribution suggests the potential applicability of “intraspecific phylogeography” to plants via the analysis of intraspecific cpDNA variation. These three examples also join a rapidly growing data base which indicates that cytoplasms are often geographically structured within species and species complexes.
-
chloroplast dna variation in tellima grandiflora Saxifragaceae
American Journal of Botany, 1991Co-Authors: Douglas E. Soltis, Pamela S. Soltis, Michael S Mayer, Michael L EdgertonAbstract:Tellima grandiflora, a herbaceous, diploid (2n = 14) perennial, is distributed from the peninsula and panhandle of Alaska to central California. Restriction site variation of chloroplast DNA was surveyed in 51 populations representing the geographic range of T. grandiflora using 20 endonucleases. Two well-differentiated clades of populations differing by 19 restriction site mutations and several length mutations are geographically structured. A northern group comprises populations from Alaska to central Oregon; populations from central Oregon to San Francisco, California, form a southern group. The southern lineage of the monotypic Tellima appears to have obtained its chloroplast genome via ancient hybridization with a species of Mitella. Although northern and southern lineages have well-differentiated chloroplast genomes, populations of T. grandiflora show a high degree of genetic similarity of nuclear-encoded allozymes; furthermore, no apparent morphological differences characterize the lineages. Significantly, several populations of T. grandiflora that possess the typical southern chloroplast genome also occur disjunctly on Prince of Wales Island, Alaska, and the Olympic Peninsula, Washington. Because both areas are proposed glacial refugia, we suggest that past glaciation may have created discontinuities in the geographic distribution of T. grandiflora. Following glaciation, migration of once-isolated populations possessing different chloroplast genomes resulted in the formation of a continuous geographic distribution with a major organellar discontinuity. Additional support for this hypothesis is provided by the presence of welldifferentiated northern and southern chloroplast DNA lineages in Tolmiea menziesii, a species having a geographic distribution and life history traits similar to those of Tellima.
Michael L Edgerton - One of the best experts on this subject based on the ideXlab platform.
-
chloroplast dna variation in tellima grandiflora Saxifragaceae
American Journal of Botany, 1991Co-Authors: Douglas E. Soltis, Pamela S. Soltis, Michael S Mayer, Michael L EdgertonAbstract:Tellima grandiflora, a herbaceous, diploid (2n = 14) perennial, is distributed from the peninsula and panhandle of Alaska to central California. Restriction site variation of chloroplast DNA was surveyed in 51 populations representing the geographic range of T. grandiflora using 20 endonucleases. Two well-differentiated clades of populations differing by 19 restriction site mutations and several length mutations are geographically structured. A northern group comprises populations from Alaska to central Oregon; populations from central Oregon to San Francisco, California, form a southern group. The southern lineage of the monotypic Tellima appears to have obtained its chloroplast genome via ancient hybridization with a species of Mitella. Although northern and southern lineages have well-differentiated chloroplast genomes, populations of T. grandiflora show a high degree of genetic similarity of nuclear-encoded allozymes; furthermore, no apparent morphological differences characterize the lineages. Significantly, several populations of T. grandiflora that possess the typical southern chloroplast genome also occur disjunctly on Prince of Wales Island, Alaska, and the Olympic Peninsula, Washington. Because both areas are proposed glacial refugia, we suggest that past glaciation may have created discontinuities in the geographic distribution of T. grandiflora. Following glaciation, migration of once-isolated populations possessing different chloroplast genomes resulted in the formation of a continuous geographic distribution with a major organellar discontinuity. Additional support for this hypothesis is provided by the presence of welldifferentiated northern and southern chloroplast DNA lineages in Tolmiea menziesii, a species having a geographic distribution and life history traits similar to those of Tellima.
-
chloroplast dna variation within and among genera of the heuchera group Saxifragaceae evidence for chloroplast transfer and paraphyly
American Journal of Botany, 1991Co-Authors: Douglas E. Soltis, Pamela S. Soltis, Trace G Collier, Michael L EdgertonAbstract:The Heuchera group (Saxifragaceae) comprises Bensoniella, Conimitella, Elmera, Heuchera, Lithophragma, Mitella, Tellima, Tiarella, and Tolmiea. Earlier studies employing morphology, karyology, and flavonoid chemistry indicated that these genera form a natural group, but failed to resolve relationships among them. Restriction site analysis of chloroplast DNA (cpDNA) suggests that Bensoniella, Tolmiea, and Lithophragma are close allies and form the sister group of a large clade containing the remaining six genera. Mitella and Heuchera are both paraphyletic based on cpDNA data. cpDNA data, in conjunction with morphological and allozyme data, suggest at least four examples of intersectional hybridization and subsequent chloroplast capture in Heuchera. Several of these events may be explained via a stepping stone model in which the chloroplast genome of a species was captured by a second species, and then ultimately by a third taxon. Two well-differentiated groups of Tellima populations were detected: one group has a unique chloroplast genome characterized by nine autapomorphies, and the second group has a chloroplast genome identical to that found in M. trifida and M. diversifolia. cpDNA and allozyme data suggest that some Tellima populations probably obtained their chloroplast genome via intergeneric hybridization with M. trifida, M. diversifolia, or the ancestor of these taxa. The occurrence of intergeneric chloroplast transfer in some populations of Tellima, as well as extensive intersectional chloroplast capture in Heuchera, not only suggests caution in the use of cpDNA restriction site data in phylogenetic reconstruction, but also demonstrates again the importance of adequate sampling of conspecific populations. If the intergeneric relationships in the Heuchera group suggested by cpDNA analysis are accurate, fundamental questions arise regarding the validity of certain morphological traits as good taxonomic characters in Saxifragaceae. Furthermore, significant taxonomic changes at the generic level would be necessary.
Luxian Liu - One of the best experts on this subject based on the ideXlab platform.
-
plastome evolution in Saxifragaceae and multiple plastid capture events involving heuchera and tiarella
Frontiers in Plant Science, 2020Co-Authors: Luxian Liu, Douglas E. Soltis, Ryan A Folk, Shenyi Wang, Fude ShangAbstract:Saxifragaceae, a family of over 600 species and approximately 30 genera of herbaceous perennials, is well-known for intergeneric hybridization. Of the main lineages in this family, the Heuchera group represents a valuable model for the analysis of plastid capture and its impact on phylogeny reconstruction. In this study, we investigated plastome evolution across the family, reconstructed the phylogeny of the Heuchera group and examined putative plastid capture between Heuchera and Tiarella. Seven species (11 individuals) representing Tiarella, as well as Mitella and Heuchera, were selected for genome skimming. We assembled the plastomes, and then compared these to six others published for Saxifragaceae; the plastomes were found to be highly similar in overall size, structure, gene order and content. Moreover, ycf15 was lost due to pseudogenization and rpl2 lost its only intron for all the analyzed plastomes. Comparative plastome analysis revealed that size variations of the plastomes are purely ascribed to the length differences of LSC, SSC, and IRs regions. Using nuclear ITS + ETS and the complete plastome, we fully resolved the species relationships of Tiarella, finding that the genus is monophyletic and the Asian species is most closely related to the western North American species. However, the position of the Heuchera species was highly incongruent between nuclear and plastid data. Comparisons of nuclear and plastid phylogenies revealed that multiple plastid capture events have occurred between Heuchera and Tiarella, through putative ancient hybridization. Moreover, we developed numerous molecular markers for Tiarella (e.g., plastid hotspot and polymorphic nuclear SSRs), which will be useful for future studies on the population genetics and phylogeography of this disjunct genus.
-
chloroplast genome analyses and genomic resource development for epilithic sister genera oresitrophe and mukdenia Saxifragaceae using genome skimming data
BMC Genomics, 2018Co-Authors: Luxian Liu, Yuewen Wang, Joongku Lee, Douglas E. SoltisAbstract:Epilithic sister genera Oresitrophe and Mukdenia (Saxifragaceae) have an epilithic habitat (rocky slopes) and a parapatric distribution in East Asia, which makes them an ideal model for a more comprehensive understanding of the demographic and divergence history and the influence of climate changes in East Asia. However, the genetic background and resources for these two genera are scarce. The complete chloroplast (cp) genomes of two Oresitrophe rupifraga and one Mukdenia rossii individuals were reconstructed and comparative analyses were conducted to examine the evolutionary pattern of chloroplast genomes in Saxifragaceae. The cp genomes ranged from 156,738 bp to 156,960 bp in length and had a typical quadripartite structure with a conserved genome arrangement. Comparative analysis revealed the intron of rpl2 has been lost in Heuchera parviflora, Tiarella polyphylla, M. rossii and O. rupifraga but presents in the reference genome of Penthorum chinense. Seven cp hotspot regions (trnH-psbA, trnR-atpA, atpI-rps2, rps2-rpoC2, petN-psbM, rps4-trnT and rpl33-rps18) were identified between Oresitrophe and Mukdenia, while four hotspots (trnQ-psbK, trnR-atpA, trnS-psbZ and rpl33-rps18) were identified within Oresitrophe. In addition, 24 polymorphic cpSSR loci were found between Oresitrophe and Mukdenia. Most importantly, we successfully developed 126 intergeneric polymorphic gSSR markers between Oresitrophe and Mukdenia, as well as 452 intrageneric ones within Oresitrophe. Twelve randomly selected intergeneric gSSRs have shown that these two genera exhibit a significant genetic structure. In this study, we conducted genome skimming for Oresitrophe rupifraga and Mukdenia rossii. Using these data, we were able to not only assemble their complete chloroplast genomes, but also develop abundant genetic resources (cp hotspots, cpSSRs, polymorphic gSSRs). The genomic patterns and genetic resources presented here will contribute to further studies on population genetics, phylogeny and conservation biology in Saxifragaceae.
-
Chloroplast genome analyses and genomic resource development for epilithic sister genera Oresitrophe and Mukdenia (Saxifragaceae), using genome skimming data
'Springer Science and Business Media LLC', 2018Co-Authors: Luxian Liu, Yuewen Wang, Joongku Lee, Douglas E. SoltisAbstract:Abstract Background Epilithic sister genera Oresitrophe and Mukdenia (Saxifragaceae) have an epilithic habitat (rocky slopes) and a parapatric distribution in East Asia, which makes them an ideal model for a more comprehensive understanding of the demographic and divergence history and the influence of climate changes in East Asia. However, the genetic background and resources for these two genera are scarce. Results The complete chloroplast (cp) genomes of two Oresitrophe rupifraga and one Mukdenia rossii individuals were reconstructed and comparative analyses were conducted to examine the evolutionary pattern of chloroplast genomes in Saxifragaceae. The cp genomes ranged from 156,738 bp to 156,960 bp in length and had a typical quadripartite structure with a conserved genome arrangement. Comparative analysis revealed the intron of rpl2 has been lost in Heuchera parviflora, Tiarella polyphylla, M. rossii and O. rupifraga but presents in the reference genome of Penthorum chinense. Seven cp hotspot regions (trnH-psbA, trnR-atpA, atpI-rps2, rps2-rpoC2, petN-psbM, rps4-trnT and rpl33-rps18) were identified between Oresitrophe and Mukdenia, while four hotspots (trnQ-psbK, trnR-atpA, trnS-psbZ and rpl33-rps18) were identified within Oresitrophe. In addition, 24 polymorphic cpSSR loci were found between Oresitrophe and Mukdenia. Most importantly, we successfully developed 126 intergeneric polymorphic gSSR markers between Oresitrophe and Mukdenia, as well as 452 intrageneric ones within Oresitrophe. Twelve randomly selected intergeneric gSSRs have shown that these two genera exhibit a significant genetic structure. Conclusions In this study, we conducted genome skimming for Oresitrophe rupifraga and Mukdenia rossii. Using these data, we were able to not only assemble their complete chloroplast genomes, but also develop abundant genetic resources (cp hotspots, cpSSRs, polymorphic gSSRs). The genomic patterns and genetic resources presented here will contribute to further studies on population genetics, phylogeny and conservation biology in Saxifragaceae
Hong Liu - One of the best experts on this subject based on the ideXlab platform.
-
complete chloroplast genome sequence of chrysosplenium nudicaule Saxifragaceae
Mitochondrial DNA Part B, 2021Co-Authors: Wenjie Yan, Niyan Xiang, Tiange Yang, Rui Qin, Hong Liu, Xing LiuAbstract:Chrysosplenium nudicaule Bunge, Tibetan name ‘Yajima,’ growing in the highlands of China is a perennial herb belonging to the genus Chrysosplenium Saxifragaceae. As a traditional Chinese medicine, ...
-
chrysosplenium sangzhiense Saxifragaceae a new species from hunan china
PhytoKeys, 2021Co-Authors: Tiange Yang, Deqing Lan, Fang Wen, Hong LiuAbstract:Chrysosplenium sangzhiense Hong Liu, a new species from Hunan, China, is described and illustrated. The phylogenetic analysis revealed that the new species belongs to subgen. Chrysosplenium and is closely related to C. grayanum, C. nepalense and C. sinicum. The chromosome number of the new species is 2n = 46, indicating a novel basic number x = 23 in Chrysosplenium that is different from other species. This also suggests that C. sangzhiense is probably an allopolyploid derivative of a species with x = 11 and one with x = 12. Morphologically, C. sangzhiense can be easily distinguished from C. grayanum, C. nepalense, C. sinicum and C. cavaleriei, a species not included in our phylogenetic analysis by a suite of characters relating to the sterile shoots, basal leaves, cauline leaves, flowering stem, sepals, disc, capsule and seed. A global conservation assessment is performed, and classifies C. sangzhiense as Least Concern (LC).
-
analysis of six chloroplast genomes provides insight into the evolution of chrysosplenium Saxifragaceae
BMC Genomics, 2020Co-Authors: Rui Liao, Tiange Yang, Rui Qin, Xiang Dong, Deqing Lan, Hong LiuAbstract:Chrysosplenium L. (Saxifragaceae) is a genus of plants widely distributed in Northern Hemisphere and usually found in moist, shaded valleys and mountain slopes. This genus is ideal for studying plant adaptation to low light conditions. Although some progress has been made in the systematics and biogeography of Chrysosplenium, its chloroplast genome evolution remains to be investigated. To fill this gap, we sequenced the chloroplast genomes of six Chrysosplenium species and analyzed their genome structure, GC content, and nucleotide diversity. Moreover, we performed a phylogenetic analysis and calculated non-synonymous (Ka) /synonymous (Ks) substitution ratios using the combined protein-coding genes of 29 species within Saxifragales and two additional species as outgroups, as well as a pair-wise estimation for each gene within Chrysosplenium. Compared with the outgroups in Saxifragaceae, the six Chrysosplenium chloroplast genomes had lower GC contents; they also had conserved boundary regions and gene contents, as only the rpl32 gene was lost in four of the Chrysosplenium chloroplast genomes. Phylogenetic analyses suggested that the Chrysosplenium separated to two major clades (the opposite group and the alternate group). The selection pressure estimation (Ka/Ks ratios) of genes in the Chrysosplenium species showed that matK and ycf2 were subjected to positive selection. This study provides genetic resources for exploring the phylogeny of Chrysosplenium and sheds light on plant adaptation to low light conditions. The lower average GC content and the lacking gene of rpl32 indicated selective pressure in their unique habitats. Different from results previously reported, our selective pressure estimation suggested that the genes related to photosynthesis (such as ycf2) were under positive selection at sites in the coding region.
-
a new species of chrysosplenium Saxifragaceae from shaanxi north western china
PhytoKeys, 2020Co-Authors: Hong Liu, Rui Liao, Deqing Lan, Fang WenAbstract:Chrysosplenium zhouzhiense Hong Liu, a new species from Shaanxi, north-western China, is described and photographed. The new species belongs to Subgen. Gamosplenium Sect. Nephrophylloides Ser. Macrophylla and is most similar to C. macrophyllum and C. zhangjiajieense from which it differs by having a shorter stem, rhizome absent, basal leaf absent, sterile branch arising from the flowering stem and a light yellow flower with longer stamen. A global conservation assessment is performed and classifies C. zhouzhiense as Endangered (EN).
-
complete chloroplast genome sequence of chrysosplenium sinicum and chrysosplenium lanuginosum Saxifragaceae
Mitochondrial DNA Part B, 2019Co-Authors: Rui Liao, Rui Qin, Xiang Dong, Hong LiuAbstract:The complete chloroplast genome of Chrysosplenium sinicum Maxim and Chrysosplenium lanuginosum Hook. f. et Thoms. were reported in this study. The chloroplast genomes were 152,524 bp and 151,512 bp...
