Inheritance Of Chloroplast DNA Research Articles

Distribution of genetic variability in mature and progeny populations of Abies alba Mill. from the Polish Western and Eastern Carpathians

This study aimed to compare patterns in the genetic structure of 27 mature stands and the natural regeneration of A. alba in the Eastern and Western Carpathians within the introgression zone of two refugial lineages from the Apennine and Balkan peninsulas. The distribution of the genetic diversity of fir stands was analysed using paternally inherited chloroplast DNA and five nuclear dominant inter simple sequence repeat markers (ISSRs). The study showed that the Balkan haplotype prevailed in both parental and progeny populations, and this haplotype was found in many mature Eastern Carpathian stands. Relatively high levels of genetic diversity were found in the mature stands (effective number of alleles Ne = 1.517, Shannon index I = 0.436, expected heterozygosity He = 0.295) and progeny (Ne = 1.515, I = 0.436 and He = 0.294) of silver fir. The analysis of molecular variance (AMOVA) revealed slight differences among the mature fir stands from the Western and Eastern Carpathians, with a value of 1.1%. According to principal coordinates analysis (PCoA) and STRUCTURE analyses, the populations, including stands of mature and progeny trees, were genetically separated into two groups. Slight genetic differences between the mature and progeny populations in the Polish Carpathians indicate sound gene pool transmission, which is essential for creating new selection and breeding programmes.

Sex-linked deubiquitinase establishes uniparental transmission of chloroplast DNA

Most sexual organisms inherit organelles from one parent, commonly by excluding organelles from the smaller gametes. However, post-mating elimination of organelles derived from one gamete ensures uniparental inheritance, where the underlying mechanisms to distinguish organelles by their origin remain obscure. Mating in Chlamydomonas reinhardtii combines isomorphic plus and minus gametes, but chloroplast DNA from minus gametes is selectively degraded in zygotes. Here, we identify OTU2p (otubain protein 2), encoded in the plus mating-type locus MT+, as the protector of plus chloroplast. Otu2p is an otubain-like deubiquitinase, which prevents proteasome-mediated degradation of the preprotein translocase of the outer chloroplast membrane (TOC) during gametogenesis. Using OTU2p-knockouts and proteasome inhibitor treatment, we successfully redirect selective DNA degradation in chloroplasts with reduced TOC levels regardless of mating type, demonstrating that plus-specific Otu2p establishes uniparental chloroplast DNA inheritance. Our work documents that a sex-linked organelle quality control mechanism drives the uniparental organelle inheritance without dimorphic gametes.

Population Demographic History of a Rare and Endangered Tree Magnolia sprengeri Pamp. in East Asia Revealed by Molecular Data and Ecological Niche Analysis

Quaternary climate and environment oscillations have profoundly shaped the population dynamic history and geographic distributions of current plants. However, how the endangered and rare tree species respond to the climatic and environmental fluctuations in the subtropical regions of China in East Asia still needs elucidation. In this study, we collected 36 natural populations of an endangered and rare tree species Magnolia sprengeri Pamp. in subtropical China to determine the demographic history, and modeled the changes of geographic distributions of this species in East Asia based on the MaxEnt ecological niche analyses. In addition, we sequenced three maternally inherited chloroplast DNA fragments (matK, trnH-psbA, and rbcL) for all the natural populations which covered the whole geographic distributions of M. sprengeri. Population genetic analysis showed that the endangered tree species have a low level of chloroplast DNA diversity. However, the genetic variation contribution within populations was greater than that among populations (FST = 0.276), which demonstrated a high level of genetic differentiation. Interestingly, some unique chloroplast DNA haplotypes and higher genetic variations were identified in the Qinling-Daba Mountains, Central China, and Tianmu Mountains of Zhejiang province, East of China in East Asia. Combining with the species distribution modeling, we speculated that these areas might be the potential glacial refugia for the endangered plant M. sprengeri. Phylogeographic analysis demonstrated that the geographic factors (e.g., mountains, rivers, and other isolation barriers) had little effect on the genetic divergence among populations. Ecological niche modeling further revealed that the natural populations of M. sprengeri did not experience significant geographic distribution changes from the last glacial maximum to the present time. These findings are in line with the analysis results of the multimodal mismatch patterns of the chloroplast DNA variations. To protect the endangered species M. sprengeri, in situ and ex situ conservation strategies should be formulated for the natural populations with higher genetic variations.

Parent–offspring variation transmission in full-sib families revealed predominantly paternal inheritance of chloroplast DNA in Pinus massoniana (Pinaceae)

Parent–offspring variation transmission in full-sib families revealed predominantly paternal inheritance of chloroplast DNA in Pinus massoniana (Pinaceae)

Geographical Structuring of Quercus robur (L.) Chloroplast DNA Haplotypes in Lithuania: Recolonization, Adaptation, or Overexploitation Effects?

We studied the maternally inherited chloroplast DNA polymorphism at three microsatellite loci of 157 Quercus robur trees from 38 native populations in Lithuania. We found high diversity of eight haplotypes from the Balkan lineage A (frequency 0.75) and the “German” subbranch of the Balkan lineage A (freq. 0.12), western and eastern Italian lineages C (freq. 0.05 and 0.06, respectively), and Iberian lineage B (freq. 0.03). The haplotypes were geographically well structured (among population differentiation index PhiPT = 0.30, the p-value < 0.001) that is unexpected for such a small territory as Lithuania. We raised a hypothesis on historical overexploitation of oaks by eliminating certain haplotypes in Lithuania, following a drastic felling of oak forests over the last few centuries.

Evolutionary history of a desert perennial Arnebia szechenyi (Boraginaceae): Intraspecific divergence, regional expansion and asymmetric gene flow

The complex interactions of historical, geological and climatic events on plant evolution have been an important research focus for many years. However, the role of desert formation and expansion in shaping the genetic structures and demographic histories of plants occurring in arid areas has not been well explored. In the present study, we investigated the phylogeography of Arnebia szechenyi, a desert herb showing a near-circular distribution surrounding the Tengger Desert in Northwest China. We measured genetic diversity of populations using three maternally inherited chloroplast DNA (cpDNA) fragments and seven bi-paternally inherited nuclear DNA (nDNA) loci that were sequenced from individuals collected from 16 natural populations across its range and modelled current and historical potential habitats of the species. Our data indicated a considerably high level of genetic variation within A. szechenyi and noteworthy asymmetry in historical migration from the east to the west. Moreover, two nuclear genetic groups of populations were revealed, corresponding to the two geographic regions separated by the Tengger Desert. However, analysis of cpDNA data did not show significant geographic structure. The most plausible explanation for the discrepancy between our findings based on cpDNA and nDNA data is that A. szechenyi populations experienced long periods of geographic isolation followed by range expansion, which would have promoted generalized recombination of the nuclear genome. Our findings further highlight the important role that the Tengger Desert, together with the Helan Mountains, has played in the evolution of desert plants and the preservation of biodiversity in arid Northwest China.

From allozymes to NGS: population genetics of forest trees in Slovakia in the past 40 years.

This review summarizes the development of population genetics and population genomics studies of forest trees in Slovakia during the past 40 years. Various protein and DNA markers have been applied during this period to address several topics in evolutionary genetics and biogeography of trees: allozymes, uniparentally inherited chloroplast and mitochondrial markers, simple sequence repeats and single nucleotide polymorphisms. The main object of studies of phylogeny and postglacial migration were Fagus sylvatica s.l. and eastern-Mediterranean firs (Abies Mill. section Abies), where the divergence of genetic lineages (species and subspecific taxa) in time, as well as colonization of the current ranges during the Holocene were reconstructed. The studies on intraspecific gene flow and homoploid hybridization focused on hybrid swarms Pinus sylvestris/P. mugo and firs. Unusual maternal inheritance of chloroplast DNA was revealed in P. mugo × P. sylvestris crosses. Contrasting geographical structures of hybrid zones were revealed in wind-dispersed vs. animal-dispersed trees. Within the studies of adaptation, signals of selection were identified both in field observations and common-garden experiments on Picea abies, F. sylvatica and A. alba. Perspectives of ongoing research employing next-generation sequencing were shortly outlined.

Molecular Phylogeography and Evolutionary History of the Endemic Species Corydalis hendersonii (Papaveraceae) on the Tibetan Plateau Inferred From Chloroplast DNA and ITS Sequence Variation

In response to past climatic changes, the species with different habits or adaptive traits likely have experienced very different evolutionary histories, especially for species that restricted to high mountain areas. In order to trace how Quaternary climatic oscillations affected range distributions and intraspecific divergence of such alpine plants on the Tibetan Plateau, here, we investigated maternally inherited chloroplast DNA (cpDNA) markers and biparentally inherited nuclear ribosomal internal transcribed spacer (ITS) DNA variations and aimed to explore the phylogeographic history of the endemic alpine species Corydalis hendersonii Hemsl. (Papaveraceae). We sequenced four cpDNA fragments (trnS-trnG, trnT-trnL, atpH-atpI, and psbE-petL) and also the nuclear (ITS) region in 368 individuals from 30 populations across the species' range. The network and phylogenetic analysis based on cpDNA variations identified 15 chlorotypes that cluster into three distinct clades. However, our nuclear DNA results demonstrated that there were four genetic/geographical groups within C. hendersonii. Some common and highly divergent cpDNA and ITS haplotypes were distributed in the populations of central and northeastern Tibetan Plateau, and the highest nucleotide diversity and genetic differentiation were detected in the central region. Demographic tests further indicated that the populations of southwestern and western Tibet may have experienced recent range expansion, which most likely occurred during the last glacial maximum (LGM) and continued its expansion after the beginning of the Holocene. These two different groups of this species may have derived from potential refugia that existed in the central and/or northeastern regions of Tibet during recent interglacial periods. In addition, our AMOVA analyses detected high genetic differentiation along with the whole sampling range. Also, distinct phylogeographic structures were detected among populations of C. hendersonii based on both of cpDNA and ITS variation. These findings shed new light on the importance of climatic oscillations during Quaternary and complex local topography as causes of intraspecific diversification and demographic changes within cold-tolerant herbs in the Tibetan Plateau biodiversity hotspot.

Character expression, reproductive barriers, and origin of the rare fern hybrid Asplenium ×aran-tohanum (Aspleniaceae)

Hybridization is a ubiquitous force in plant evolution. In ferns, hybrids are often easily recognized by their intermediate morphology and abortive spores and thus provide a good model for studying reproductive isolating barriers between species. Asplenium ×aran-tohanum is a rare fern hybrid, despite wide coexistence of its parental species (A. billotii and A. trichomanes subsp. quadrivalens) in Western Europe. We made a complete characterization of its three known individuals, including macro- and micromorphology, sporogenesis, gametophyte reproduction, and chloroplast DNA inheritance and evolution. The hybrid expressed morphological characters that were mostly intermediate between those of the parents, but some characters were more similar to one parent or the other. Sizes of both guard cells and spores indicate that the hybrid is tetraploid, as are both parents, and one parent (A. billotii) consistently acted as the female. A very small fraction of spores (~ 7%) were viable and the resulting gametophytes could not form sporophytes, either sexually or apogamously, suggesting that effective postzygotic barriers exist between the parents. The lineages of these taxa diverged about 35 million years ago, which may explain the strong reproductive isolation and rarity of the hybrid. Asplenium ×aran-tohanum appears to be an evolutionary dead end, probably formed recurrently at the places where it grows, but incapable of completing its life cycle or producing viable offspring.

What nature separated, and human joined together: About a spontaneous hybridization between two allopatric dogwood species (Cornus controversa and C. alternifolia).

In this study, possible hybridization between two allopatric species, Cornus controversa and Cornus alternifolia, was explored using molecular and morphological approaches. Scanning electron microscope analyses of the adaxial and the abaxial leaf surfaces yielded a few new not yet described characters typical for the particular species and intermediate for hybrids. With the use of 14 Random Amplified Polymorphic DNA and 5 Amplified Fragment Length Polymorphism primer combinations, 44 fragments species specific to C. controversa and 51 species specific to C. alternifolia were obtained. Most of these bands were also found in putative hybrids. All clustering analyses based on binary data combined from both methods confirmed a separate and intermediate status of the hybrids. Hybrid index estimates for hybrids C1-C5 indicated that all were the first generation of offspring (F1). Chloroplast intergenic spacers (trnF-trnL and psbC-trnS) were used to infer the hybridization direction. Based on the assumption of maternal inheritance of chloroplast DNA, C. controversa seems to be the maternal parent of the hybrid. Internal transcribed spacer sequences of the five hybrids analyzed here indicated higher similarity with the sequences of C. controversa (all shared the majority of its single nucleotide polymorphisms). Sequence analysis of PI-like genes fully confirmed the hybrid origin of C1-C5 hybrids. Our results also showed that two specimens in the C. alternifolia group, A1 and A3, are not free of introgression. They are probably repeated backcrosses toward C. alternifolia. Furthermore, molecular data seem to point not only to unidirectional introgression toward C. controversa (the presence of hybrids) but to bidirectional introgression as well, since the presence of markers specific for C. controversa in the profiles of C. alternifolia specimen A3 was observed.

Evolution, Initiation, and Diversity in Early Plant Embryogenesis.

During embryogenesis in plants, cell identities are specified de novo, starting from a single cell. By combining imaging, genomic profiling, and genetics, principles of early plant development have been unraveled in the dicotyledonous plant Arabidopsis. A central emerging question, however, is how well zygotic embryogenesis in Arabidopsis reflects homologous processes in other plant species, including early diverging, non-flowering, and non-seed plants. Here, we consider plant embryogenesis with an emphasis on its evolutionary history, the diverse modes of its initiation, and the concepts in pattern formation among morphologically distinct plant groups. Furthermore, we explore challenges and future directions in plant embryogenesis research.

Species Boundaries Between Three Sympatric Oak Species: Quercus aliena, Q. dentata, and Q. variabilis at the Northern Edge of Their Distribution in China.

Oaks are important timber trees with wide distributions in China, but few genetic studies have been conducted on a fine scale. In this study, we seek to investigate the genetic diversity and differentiation of three sympatric oak species (Quercus aliena Blume, Quercus dentata Thunb. ex Murray, and Quercus variabilis Blume) in their northern distribution in China using 17 bi-parentally inherited nSSRs markers and five maternally inherited chloroplast DNA (cpDNA) fragments. Both the cpDNA and the nSSRs show a high level of genetic differentiation between different oak sections. The chloroplast haplotypes are clustered into two lineages. Clear species boundaries are detected between Q. variabilis and either Q. aliena or Q. dentata. The sharing of chloroplast haplotype H1 between Q. aliena and Q. dentata suggests very recent speciation and incomplete lineage sorting or introgression of H1 from one species to another. The nSSRs data indicate a complete fixation of variation within sites for all three oak species, and that extensive gene flow occurs within species whereas only limited gene flow is detected between Q. aliena and Q. dentata and nearly no gene flow can be detected between Q. aliena and Q. variabilis and between Q. dentata and Q. variabilis. Prezygotic isolation may have contributed to the species boundaries of these three sympatric oak species.

Field-based artificial crossings indicate partial compatibility of reciprocal crosses between Pinus sylvestris and Pinus mugo and unexpected chloroplast DNA inheritance

Crossability relationships between Scots pine (Pinus sylvestris L.) and mountain dwarf pine (Pinus mugo Turra) was studied, using artificial pollination approach. Partial compatibility of the reciprocal crossings of these species was proved experimentally, validating the idea of a spontaneous formation of their hybrid swarms under natural conditions. The hybrids were validated using organellar DNA markers and nuclear DNA microsatellites. Based on the percentage of filled seeds, the interspecific crossings were less efficient than the intraspecific cross-pollinations of P. sylvestris and P. mugo individuals. Both species were found to intercross readily with individuals of their putative hybrid swarm, P. mugo exhibiting a higher hybridological affinity towards putatively hybrid individuals than P. sylvestris. Validation of the hybrids confirmed the paternal inheritance of chloroplast DNA (cpDNA) in the combination P. sylvestris × P. mugo only. Surprisingly, in the reciprocal crossing P. mugo × P. sylvestris, maternal inheritance of cpDNA was revealed. Obtained results offer a new insight into the direction and intensity of gene flow within the hybrid swarms of Scots pine and mountain dwarf pine.

Spatial distribution of genetic diversity in populations of Hagenia abyssinica (Bruce) J.F. Gmel from Ethiopia

Genetic variation among 596 individuals from 22 natural and 3 planted populations of Hagenia abyssinica (Rosaceae) sampled from the montane forests of Ethiopia was investigated at amplified fragment length polymorphism (AFLP) loci. We observed 106 unequivocally scorable AFLP markers out of which 91.5 percent were polymorphic. Populations harbored varying genetic diversities (He = 0.139-0.362), and showed low but significant genetic differentiation among them (FST = 0.077). Significant differentiation was observed even though previous paleoecological studies indicated that Hagenia abyssinica recolonized Ethiopia only after the Last Glacial Maximum, and our earlier analyses of maternally inherited chloroplast DNA revealed low mixing of recolonizing lineages through seeds and rare long distance seed dispersal. Genetic diversity did not decrease along recolonization routes, confirming effective gene flow, most likely through pollen, among populations. The observed variation at putatively neutral AFLPs does not reflect clinal variation patterns. As expected, population differentiation is lower at anonymous, mostly biparentally inherited, AFLPs than at maternally inherited chloroplast haplotypes. Despite presumably efficient seed and pollen dispersal of H. abyssinica by wind, a significant non-random fine-scale spatial genetic structure was observed up to 80 m in some populations. Due to significant pair-wise differentiation observed between populations, as many populations as possible should be considered for conservation, tree improvement and forestation programs.

수염녹두말속(Chlamydomonas) 단세포 녹조의 유성생식

이 논문은 다세포 녹색식물의 조상으로 생각되는 단세포인 수염녹두말속(Chlamydomonas) 녹조의 복잡한 유성생식 과정을 종합적으로 이해하기 위해서 기술되었다. 모델생물로 알려진 클래미도모나스 레인하르티(Chlamydomonas reinhardtii)의 유성생식 생활사는 배우자발생, 배우자 활성화, 세포융합, 접합자 성숙, 감수분열과 발아 등의 다섯 시기로 구별된다. 배우자발생은 서식지에서 질소가 결핍되어 시작된다. 그 결과, 교배형 유전자자리(<TEX>$MT^+$</TEX> 또는 <TEX>$MT^-$</TEX>)에 의해 조절된 두 가지 교배형(<TEX>$mt^+$</TEX> 및 <TEX>$mt^-$</TEX>)의 배우자들이 발생된다. 유성생식을 위한 두 번째 자극원인 청색광이 교배능력을 갖고 있지 않는 예비배우자 세포에 조사되면 교배능력을 가진 배우자로 분화된다. 배우자발생의 초기에, 두 배우자 세포들은 응집소(agglutin) 분자들을 합성한다. 즉, <TEX>$mt^+$</TEX> 응집소 및 <TEX>$mt^-$</TEX> 응집소는 상염색체에 있는 성응집(SAG1) 및 성접착(SAD1) 유전자들이 발현되어 각각 합성된다. 응집소들에 의해서 두 배우자 세포들의 편모가 접착되면 cAMP가 신호전달 경로를 작동시켜서 편모의 끝 부부을 활성화시킨다. cAMP의 신호에 반응하여 두 배우자들의 세포벽이 벗겨지고 2개의 편모 사이에서 각각의 교배구조(mating structure)가 발달한다. 교배구조의 원형질막에는 <TEX>$mt^+$</TEX> 및 <TEX>$mt^-$</TEX> 배우자-특이 융합 단백질인 Fus1 및 Hap2/Gcs1이 있다. 이 단백질들의 상호작용으로 두 교배구조가 접촉되면, 두 배우자 사이에 세포질이 연결되어 수정세관(fertilization tubule)이 발달한다. <TEX>$mt^+$</TEX> 및 <TEX>$mt^-$</TEX> 배우자들의 핵과 엽록체가 융합되면 2배체의 접합자가 형성된다. 그 후 배우자들의 특성은 사라지며 융합단백질들(Fus1 및 Hap2)이 분해되고 접합자-특이(zygote-specific) 유전자들이 활성화 된다. 접합자는 24시간에 걸쳐 두꺼운 세포벽을 가진 접합포자(zygospore)로 발달한다. 어린 접합자에서 교배 후 60분 이내에 <TEX>$mt^-$</TEX> 엽록체 DNA와 <TEX>$mt^+$</TEX> 미토콘드리아 DNA가 선택적으로 제거된다. 따라서 이 두 소기관들은 각각 <TEX>$mt^-$</TEX> 미토콘드리아 DNA와 <TEX>$mt^+$</TEX> 엽록체 DNA만 남아서 단친유전(uniparental inheritance)이 이루어진다. 적당한 조건이 되면 접합포자가 감수분열과 발아 과정을 거쳐 반수체 영양세포가 방출되어 새로운 세대가 다시 시작된다. The sexual reproduction of the unicellular green alga Chlamydomonas is reviewed for a comprehensive understanding of the complex processes. The sexual life cycle of C. reinhardtii is distinguished into five main stages: gametogenesis, gamete activation, cell fusion, zygote maturation, and meiosis and germination. Gametogenesis is induced by nitrogen starvation in the environment. C. reinhardtii has two mating types: mating type plus (<TEX>$mt^+$</TEX>) and mating type minus (<TEX>$mt^-$</TEX>), controlled by a single complex mating type locus (<TEX>$MT^+$</TEX> or <TEX>$MT^-$</TEX>) on linkage group VI. In the early gametogenesis agglutinins are synthesized. The <TEX>$mt^+$</TEX> and <TEX>$mt^-$</TEX> agglutinins are encoded by the autosomal genes SAG1 (Sexual AGglutination1) and SAD1 (Sexual ADhesion1), respectively. The agglutinins are responsible for the flagellar adhesion of the two mating type of gametes. The flagellar adhesion initiates a cAMP mediated signal transduction pathways and activates the flagellar tips. In response to the cAMP signal, mating structures between two flagella are activated. The <TEX>$mt^+$</TEX> and <TEX>$mt^-$</TEX> gamete-specific fusion proteins, Fus1 and Hap2/Gcs1, are present on the plasma membrane of the two mating structures. Contact of the two mating structures leads to develop a fertilization tubule forming a cytoplasmic bridge between the two gametes. Upon fusion of nuclei and chloroplasts of <TEX>$mt^+$</TEX> and <TEX>$mt^-$</TEX> cells, the zygotes become zygospores. It is notable that the young zygote shows uniparental inheritance of chloroplast DNA from the <TEX>$mt^+$</TEX> parent and mitochondrial DNA from the <TEX>$mt^-$</TEX> parent. Under the favorable conditions, the zygospores divide meiotically and germinate and then new haploid progenies, vegetative cells, are released.

Spatial Pattern of the Mitochondrial and Chloroplast Genetic Variation in Poland as a Result of the Migration of Abies alba Mill. from Different Glacial Refugia

Currently, the information on the gene pool of silver fir (Abies alba Mill.) at the northeastern edge of its distribution in Poland is scarce and insufficient. Using the advantage provided by markers with different modes of inheritance, a hypothesis that gene flow via both seeds and pollen contributed to the genetic structure across the entire analyzed region was investigated. The geographic distribution of maternally inherited mitochondrial DNA (mtDNA, nad5-4) and paternally inherited chloroplast DNA (cpDNA, psbC) variation was studied in 81 Polish populations and three reference populations from Ukraine and Romania. The spatial pattern of mtDNA haplotypes (dispersed via seeds) indicated that the Apennine Peninsula was the only maternal glacial refugium for the entire territory of Poland and also the Ukraine no 1 population, whereas the other two populations—Ukraine no 2 and Romania—had the haplotype representing the Balkan origin. By contrast, the cpDNA haplotypes (dispersed via pollen) from all studied Polish and reference populations showed that A. alba colonized the current natural range from two genetically distinct glacial refugia located on the Apennine and Balkan peninsulas. The occurrence of cpDNA haplotypes varied among the studied populations. Additionally, statistical analyses were used to infer the genetic structure of examined populations. Two distinct groups of A. alba populations were identified showing the postglacial geographic distribution of haplotypes of both mtDNA and cpDNA. A. alba is an important ecological and economic component of forest ecosystems in Europe. An understanding of the Holocene history of this species is relevant for planning sustainable forest management, and acquired data can contribute to strategies of conservation and restoration.

Complete Chloroplast Genome Sequence of Corroborates Structural Heterogeneity of Inverted Repeats in Wild Progenitors of Cultivated Bananas and Plantains.

Complete genome sequencing of cytoplasmically inherited chloroplast DNA provides novel insights into the origins of clonally propagated crops such as banana and plantain ( spp.). This study describes the structural organization of the chloroplast genome of Colla and its phylogenetic relationship with other wild progenitors of the domesticated banana cultivars. The chloroplast genome was sequenced using Illumina HiSeq 2000 platform, followed by a combination of de novo short-read assembly and reference-guided mapping of contigs to generate complete plastome sequence. The chloroplast genome is 169,503 bp in length, exhibits a typical quadripartite structural organization with a large single-copy (LSC; 87,828 bp) region and a small single-copy (SSC; 11,547 bp) region interspersed between inverted repeat (IRa/b; 35,064 bp) regions. Overall, its gene content, size, and gene order were identical to that of Colla with extensive expansion of the inverted repeat-small single-copy (IR-SSC) junctions. Comparative analyses revealed the conserved IRa-SSC expansion in three wild species and members of the order Zingiberales. In contrast, IRb-SSC expansion was conspicuously absent in the sister taxon Nee and related species of Zingiberales. Interestingly, phylogenomic assessment based on whole-plastome and protein-coding gene sets have provided robust support for the association of and as a sister group, despite the variation in IRb-SSC expansion. Although the current study substantiates the infrageneric IRb-SSC fluctuations in Musaceae, extensive taxon sampling is necessary to confirm whether the accessions of section have undergone independent IRb-SSC expansion relative to section .

Genetic origin and composition of a natural hybrid poplar Populus × jrtyschensis from two distantly related species.

BackgroundThe factors that contribute to and maintain hybrid zones between distinct species are highly variable, depending on hybrid origins, frequencies and fitness. In this study, we aimed to examine genetic origins, compositions and possible maintenance of Populus × jrtyschensis, an assumed natural hybrid between two distantly related species. This hybrid poplar occurs mainly on the floodplains along the river valleys between the overlapping distributions of the two putative parents.ResultsWe collected 566 individuals from 45 typical populations of P. × jrtyschensis, P. nigra and P. laurifolia. We genotyped them based on the sequence variations of one maternally inherited chloroplast DNA (cpDNA) fragment and genetic polymorphisms at 20 SSR loci. We further sequenced eight nuclear genes for 168 individuals from 31 populations. Two groups of cpDNA haplotypes characteristic of P. nigra and P. laurifolia respectively were both recovered for P. × jrtyschensis. Genetic structures and coalescent tests of two sets of nuclear population genetic data suggested that P. × jrtyschensis originated from hybridizations between the two assumed parental species. All examined populations of P. × jrtyschensis comprise mainly F1 hybrids from interspecific hybridizations between P. nigra and P. laurifolia. In the habitats of P. × jrtyschensis, there are lower concentrations of soil nitrogen than in the habitats occupied by the other two species.ConclusionsOur extensive examination of the genetic composition of P. × jrtyschensis suggested that it is typical of F1-dominated hybrid zones. This finding plus the low concentration of soil nitrogen in the floodplain soils support the F1-dominated bounded hybrid superiority hypothesis of hybrid zone maintenance for this particular hybrid poplar.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-016-0776-6) contains supplementary material, which is available to authorized users.

Father hands it down: patrilineal inheritance of chloroplast DNA in conifers may help to uncover relations of reproduction, population biology and longevity of trees

Organelles such as the mitochondria and plastids contain their own DNA, and with their transfer across generations there is organelle-bound inheritance. Mitochondrial inheritance in recent times has increasingly been regarded as a focus of general interest. Such interest includes the public media, because it can be used in studies of molecular phylogenetics of mammals and especially our own lineage of the genus Homo. Various theories of phylogeny and of global human migrations, with their time scales given by the molecular clock, can be investigated thanks to the uniqueness of mitochondrial DNA (mtDNA) inheritance mechanisms. Mitochondrial inheritance in mammals is matrilinear, i.e., mtDNA is only derived from the mother. The female egg contains many mitochondria, while the male sperm has only a few, which are destroyed in fecundation when the sperm merges with an egg. For studying molecular phylogenetics and molecular systematics, mtDNA has a number of advantages over nuclear DNA (ncDNA) (Cann et al. 1987): (1) it is easier to extract; (2) there are many copies in each cell; (3) mutations accumulate several times faster in mtDNA than in ncDNA, so that dynamics can be better documented; (4) there is no recombination of mtDNA between generations, so that individuals can be related to one another, which is important in population biology; and (5) if uniparental as in mammals, it allows direct genetic tracing of lines. Mammals, of course, do not have plastids, but in plants there is organelle-related inheritance via both mitochondria and chloroplasts. There is uniparental inheritance, which may be not only matrilinear but also patrilinear, and both may be combined in biparental inheritance. As in animals, the patrilinear inheritance is rare case because organelles come mainly from the egg cells (Kadereit et al. 2014). Thus, patrilinear inheritance via plastid DNA (plDNA) among some plant lineages, particularly in the conifers, is a case of special interest. This is described in the review on ‘‘Archegonium and fertilization in Coniferopsida’’ by Zhang and Zheng (2016) in this issue of Trees: Structure and Function. The authors review the structure of the female gametophyte of conifers. They also summarize the molecular evidence available on the genetic regulation of development of the female apparatus for fertilization. However, knowledge is still very limited. This is particularly challenging in view of the implications of patrilinear plDNA inheritance. What happens to maternal plDNA in the conifers? In the egg cells of developing archegonia, plastids are degraded to produce proteid vacuoles, which are cellular bodies formed in the egg cells. Proteid vacuoles accumulate protein and are likely to serve as nutrition for fertilization and early proembryo development. When the egg cell has reached maturity, the remaining maternal plastids are degraded. Thus, the fertilized egg cells lack maternal plastids, so that plastids in the embryo are exclusively derived from the pollen giving the patrilinear plDNA inheritance. These observations offer new approaches for the study of conifers. In analogy to mtDNA, plDNA may have similar advantages for molecular phylogeny and molecular systematics. Beyond the analogies with matrilinear inheritance of mtDNA in mammals mentioned above, the peculiarities of the Coniferopsida may help to uncover interesting features of trees. In the patrilinear inheritance it is not the mother, but the father who hands down inheritance. We may learn more about the roles of dioecy and & Ulrich Luttge luettge@bio.tu-darmstadt.de

Sharing of chloroplast haplotypes among red oak species suggests interspecific gene flow between neighboring populations

The North American red oak species Quercus rubra L., Quercus ellipsoidalis E. J. Hill, Quercus velutina Lam., and Quercus coccinea Münchh. are morphologically similar and showed very low interspecific differentiation at most nuclear genetic markers in our earlier analyses (&lt;10%). However, a few genetic markers showed interspecific differentiation values (up to 84%) above neutral expectations, a pattern of genomic divergence consistent with models of ecological speciation in the face of gene flow and strong divergent selection. Accordingly, these interfertile species are predicted to maintain differential adaptations to drought, while neutral regions of the genome appear to be homogenized by interspecific gene flow. According to this model of maintenance of species integrity by divergent selection with gene flow, we expect a sharing of chloroplast haplotypes between interspecific population pairs. We analyzed maternally inherited chloroplast DNA markers for the first time in interspecific populations of the red oaks (section Lobatae) to provide additional evidence for contemporary gene flow between Q. rubra and Q. ellipsoidalis and between Q. velutina and Q. ellipsoidalis. Very low interspecific differentiation (GST= 0.023), but pronounced genetic differentiation among populations from different regions (GST= 0.277) across species, and sharing of regional chloroplast haplotypes between species in sympatric and neighboring populations provided strong evidence for contemporary interspecific gene flow. The pattern of divergence at chloroplast DNA markers in red oaks suggests interspecific gene flow that resulted in a sharing of chloroplast types while the ecological and morphological distinctness of species was maintained.