Exceptional reduction of the plastid genome of saguaro cactus (<i>Carnegiea gigantea</i>): Loss of the <i>ndh</i> gene suite and inverted repeat

Sanderson, Michael J.,Copetti, Dario,Bú,rquez, Alberto,Bustamante, Enriquena,Charboneau, Joseph L. M.,Eguiarte, Luis E.,Kumar, Sudhir,Lee, Hyun Oh,Lee, Junki,McMahon, Michelle,Steele, Kelly,Wing Botanical Society of America, Inc. (Columbus) * Bu 2015 American journal of botany Vol. No.

<P>• <I>Premise of the study:</I> Land-plant plastid genomes have only rarely undergone significant changes in gene content and order. Thus, discovery of additional examples adds power to tests for causes of such genome-scale structural changes.</P><P>• <I>Methods:</I> Using next-generation sequence data, we assembled the plastid genome of saguaro cactus and probed the nuclear genome for transferred plastid genes and functionally related nuclear genes. We combined these results with available data across Cactaceae and seed plants more broadly to infer the history of gene loss and to assess the strength of phylogenetic association between gene loss and loss of the inverted repeat (IR).</P><P>• <I>Key results:</I> The saguaro plastid genome is the smallest known for an obligately photosynthetic angiosperm (∼113 kb), having lost the IR and plastid <I>ndh</I> genes. This loss supports a statistically strong association across seed plants between the loss of <I>ndh</I> genes and the loss of the IR. Many nonplastid copies of plastid <I>ndh</I> genes were found in the nuclear genome, but none had intact reading frames; nor did three related nuclear-encoded subunits. However, nuclear <I>pgr5</I>, which functions in a partially redundant pathway, was intact.</P><P>• <I>Conclusions:</I> The existence of an alternative pathway redundant with the function of the plastid NADH dehydrogenase-like complex (NDH) complex may permit loss of the plastid <I>ndh</I> gene suite in photoautotrophs like saguaro. Loss of these genes may be a recurring mechanism for overall plastid genome size reduction, especially in combination with loss of the IR.</P>

Assessing the evolutionary history of the class Synurophyceae (Heterokonta) using molecular, morphometric, and paleobiological approaches

Siver, Peter A.,Jo, Bok Yeon,Kim, Jong Im,Shin, Woongghi,Lott, Anne Marie,Wolfe, Alexander P. Botanical Society of America, Inc. (Columbus) * Bu 2015 American journal of botany Vol. No.

<P>• <I>Premise of the study:</I> Heterokont algae of the class Synurophyceae, characterized by distinctive siliceous scales that cover the surface of the cell, are ecologically important in inland waters, yet their evolutionary history remains enigmatic. We explore phylogenetic relationships within this group of algae relative to geologic time, with a focus on evolution of siliceous components.</P><P>• <I>Methods:</I> We combined an expansive five-gene and time-calibrated molecular phylogeny of synurophyte algae with an extensive array of fossil specimens from the middle Eocene to infer evolutionary trends within the group.</P><P>• <I>Key results:</I> The group originated in the Jurassic approximately 157 million years ago (Ma), with the keystone genera <I>Mallomonas</I> and <I>Synura</I> diverging during the Early Cretaceous at 130 Ma. <I>Mallomonas</I> further splits into two major subclades, signaling the evolution of the V-rib believed to aid in the spacing and organization of scales on the cell covering. <I>Synura</I> also diverges into two primary subclades, separating taxa with forward-projecting spines on the scale from those with a keel positioned on the scale proper. Approximately one third of the fossil species are extinct, whereas the remaining taxa are linked to modern congeners.</P><P>• <I>Conclusions:</I> The taxonomy of synurophytes, which relies extensively on the morphology of the siliceous components, is largely congruent with molecular analyses. Scales of extinct synurophytes were significantly larger than those of modern taxa and may have played a role in their demise. In contrast, many fossil species linked to modern lineages were smaller in the middle Eocene, possibly reflecting growth in the greenhouse climatic state that characterized this geologic interval.</P>

Impact of global warming on a group of related species and their hybrids: cherry tree (Rosaceae) flowering at Mt. Takao, Japan

Miller-Rushing, Abraham J.,Katsuki, Toshio,Primack, Richard B.,Ishii, Yukio,Lee, Sang Don,Higuchi, Hiroyoshi Botanical Society of America, Inc. (Columbus) * Bu 2007 American journal of botany Vol.94 No.9

<P>Climate change is affecting plant phenology worldwide. Phenological responses vary among species, but it is not clear how responses differ among closely related species. We examined a 25-yr record (1981-2005) of flowering times for 97 trees, representing 17 species and hybrids of cherry (Cerasus sp. or Prunus sp.) grown at Mt. Takao, in Tokyo, Japan. The cherry trees flowered earlier over time, by an average of 5.5 d over the 25-yr study. Earlier flowering was explained largely by a 1.8C increase in February-March mean monthly temperatures. Most species and hybrids flowered 3-5 d earlier for each 1C increase in temperature, but early-flowering taxa flowered as much as 9 d earlier for each 1C increase in temperature. Flowering durations and differences in flowering times among species were greater in warm years than in cold years. Species and individual trees also flowered longer in warm years. These results show that the flowering times of closely related species may change similarly in response to climate change, but that early-flowering species may diverge from the overall trend in a predictable way. Such changes in flowering may affect gene flow and pollination as the length of the flowering season increases.</P>

Speciation pathway of Isoetes (Isoetaceae) in East Asia inferred from molecular phylogenetic relationships.

Kim, Changkyun,Shin, Hyunchur,Chang, Yung-Ta,Choi, Hong-Keun Botanical Society of America] 2010 American journal of botany Vol.97 No.6

<P>Polyploidy plays an important role in the speciation of Iso?tes. Increasing our knowledge about the specific origin of each polyploid or phylogenetic relationship among species has been hampered because of conserved morphological variation and scarce habitats. We present several hypotheses concerning the speciation pathways of Iso?tes species distributed in East Asia. Our hypotheses are inferred from phylogenetic relationships that were elucidated using sequences of the internal transcribed spacer regions of nuclear ribosomal DNA, a second intron of LEAFY, and chloroplast DNA trnS-psbC spacer regions. These inferred phylogenetic relationships indicated that (1) the Chinese tetraploid, I. sinensis, is closely related to I. yunguiensis; (2) the Korean endemic species, I. hallasanensis, is an autotetraploid derived from I. taiwanensis or closely related taxa; (3) the hexaploid I. coreana forms a clade and has its closest evolutionary relationships with I. taiwanensis or I. hallasanensis; and (4) the Japanese hexaploid I. japonica is closely related to I. taiwanensis-I. coreana and I. sinensis-I. yunguiensis. These results suggest that interspecific hybridization and polyploidization have played central roles in speciation of East Asian Iso?tes. Furthermore, I. taiwanensis, an endemic species in Taiwan, has been involved in at least three cases of autopolyploid or allopolyploid speciation in East Asia.</P>

Comparative genetic structure between <i>Sedum ussuriense</i> and <i>S. kamtschaticum</i> (Crassulaceae), two stonecrops co-occurring on rocky cliffs

Chung, Mi Yoon,Ló,pez-Pujol, Jordi,Chung, Myong Gi Botanical Society of America 2014 American journal of botany Vol.101 No.6

<P>• <I>Premise of the study:</I> Geographic isolation due to discontinuities of suitable habitat may have significant effects on the genetic structure of plant populations. Even within a few kilometers, physical barriers to gene flow may lead to considerable genetic differentiation among populations.</P><P>• <I>Methods: Sedum ussuriense</I> is a boreal species that in Korea occurs only in four valleys separated by mountain ranges in Juwangsan National Park and its vicinity (a range of ∼15 km). Its congener <I>S. kamtschaticum</I>, by contrast, co-occurs in the four valleys but also on the intervening mountains. Using 12 allozyme loci, we comparatively assessed genetic variability and structure in 12 population pairs of the two stonecrops.</P><P>• <I>Key results:</I> While we found high and comparable levels of within-population genetic variation for the two species, among-population divergence was significantly higher in <I>S. ussuriense</I> (<I>F</I><SUB>ST</SUB> = 0.261 vs. <I>F</I><SUB>ST</SUB> = 0.165). <I>Sedum ussuriense</I> also showed a much higher percentage of among-valley variation (19%) than <I>S. kamtschaticum</I> (4%).</P><P>• <I>Conclusions:</I> High levels of genetic diversity in the two <I>Sedum</I> species are consistent with the previous hypothesis that mountains of the Korean Peninsula served as glacial refugia for many boreal species. Given that the two congeners have similar life-history traits, the lower among-population differentiation in <I>S. kamtschaticum</I> is attributable to its higher abundance and more continuous distribution in the study area. This study confirms the central role of geographic isolation in the genetic structure of plant species even at very small scales.</P>