The complete chloroplast genome of Gracilariopsis lemaneiformis (Rhodophyta) gives new insight into the evolution of family Gracilariaceae

The complete chloroplast genome of Gracilariopsis lemaneiformis was recovered from a Next Generation Sequencing data set. Without quadripartite structure, this chloroplast genome (183,013 bp, 27.40% GC content) contains 202 protein‐coding genes, 34 tRNA genes, 3 rRNA genes, and 1 tmRNA gene. Synteny analysis showed plasmid incorporation regions in chloroplast genomes of three species of family Gracilariaceae and in Grateloupia taiwanensis of family Halymeniaceae. Combined with reported red algal plasmid sequences in nuclear and mitochondrial genomes, we postulated that red algal plasmids may have played an important role in ancient horizontal gene transfer among nuclear, chloroplast, and mitochondrial genomes. Substitution rate analysis showed that purifying selective forces maintaining stability of protein‐coding genes of nine red algal chloroplast genomes over long periods must be strong and that the forces acting on gene groups and single genes of nine red algal chloroplast genomes were similar and consistent. The divergence of Gp. lemaneiformis occurred ~447.98 million years ago (Mya), close to the divergence time of genus Pyropia and Porphyra (443.62 Mya).     

Anaerobic Metabolism in Germinating Seeds of Echinochloa crus-galli (Barnyard Grass) : METABOLITE AND ENZYME STUDIES

Echinochloa crus-galli, a problem weed in rice fields, has the rare ability to germinate and to grow in a totally oxygen-free environment. After 7 days growth in the light or dark under N₂, E. crus-galli var. oryzicola produces a 2- to 3-centimeter nonpigmented shoot.     

Crop mimicry in weeds

The selective forces imposed by agricultural practices have resulted in the evolution of agricultural races of weeds or agroecotypes. Some agroecotypes are intimately associated with a specific crop. Such associations can involve a system of mimicry, whereby the weed resembles the crop at specific stages during its life history and, as a result of mistaken identity, evades eradication. Mimetic forms of weeds are most likely to be selected by handweeding of seedlings or by harvesting and seed cleaning procedures. A striking example of morphological and phenological resemblance is found in the cultivated rice mimic,Echinochloa crus-galli var.oryzicola, a native of Asian rice fields but now widely distributed in rice-growing areas of the world. Comparative studies of the growth, devel-opment and patterns of phenotypic variation of cultivated rice,E. crus-galli var.oryzicola andE. crus-galli var.crus-galli demonstrate that the crop mimic is more similar to rice in many attributes than it is to its close relative. It is proposed that intense handweeding practices in Asia constitute the main selective force favoring the evolution of rice mimicry inE. crus-galli var.oryzicola.     

Chloroplast genomic diversity in Bulbophyllum section Macrocaulia (Orchidaceae,Epidendroideae, Malaxideae): Insights into species divergence and adaptive evolution

Bulbophyllum is the largest genus in Orchidaceae with a pantropical distribution. Due to highly significant diversifications, it is considered to be one of the most taxonomically and phylogenetically complex taxa. The diversification pattern and evolutionary adaptation of chloroplast genomes are poorly understood in this species-rich genus, and suitable molecular markers are necessary for species determination and phylogenetic analysis. A natural Asian section Macrocaulia was selected to estimate the interspecific divergence of chloroplast genomes in this study. Here, we sequenced the complete chloroplast genome of four Bulbophyllum species, including three species from section Macrocaulia. The four chloroplast genomes had a typical quadripartite structure with a genome size ranged from 156,182 to 158,524 bp. The chloroplast genomes included 113 unique genes encoding 79 proteins, 30 tRNAs and 4 rRNAs. Comparison of the four chloroplast genomes showed that the three species from section Macrocaulia had similar structure and gene contents, and shared a number of indels, which mainly contribute to its monophyly. In addition, interspecific divergence level was also great. Several exclusive indels and polymorphism SSR loci might be used for taxonomical identification and determining interspecific polymorphisms. A total of 20 intergenic regions and three coding genes of the most variable hotspot regions were proposed as candidate effective molecular markers for future phylogenetic relationships at different taxonomical levels and species divergence in Bulbophyllum. All of chloroplast genes in four Bulbophyllum species were under purifying selection, while 13 sites within six genes exhibited site-specific selection. A whole chloroplast genome phylogenetic analysis based on Maximum Likelihood, Bayesian and Parsimony methods all supported the monophyly of section Macrocaulia and the genus of Bulbophyllum. Our findings provide valuable molecular markers to use in accurately identifying species, clarifying taxonomy, and resolving the phylogeny and evolution of the genus Bulbophyllum. The molecular markers developed in this study will also contribute to further research of conservation of Bulbophyllum species.     

Lipid biochemistry of echinochloa crus-galli during anaerobic germination

Seven day old seedlings of Echinochloa crus-galli var. oryzicola (Vasing) had a higher total lipid content when germinated under N₂ than in air, although ungerminated seeds contained more lipid than either seedling. The triacylglycerol pool was not depleted under anaerobiosis as it was in air and only air-grown seedlings showed a net increase in free fatty acids and polar lipids. Concentrations of most of the individual acids of the total fatty acid profile declined during germination in air and in the free acid and polar lipid fractions of these seedlings the relative proportion of polyunsaturated fatty acids increased. Compared to air-grown seedlings, ungerminated seeds and N₂-grown seedlings had a similar qualitative and quantitative lipid composition. Our results show that mobilization of storage lipids was apparently severely inhibited under anoxia. The importance of lipid metabolism to the germination and growth of Echinochloa during anoxia is discussed in terms of maintaining membrane integrity and serving (indirectly) to reoxidize pyridine nucleotides.     

Analysis of complete nucleotide sequences of 12 gossypium chloroplast genomes: origin and evolution of allotetraploids

Background

Cotton (Gossypium spp.) is a model system for the analysis of polyploidization. Although ascertaining the donor species of allotetraploid cotton has been intensively studied, sequence comparison of Gossypium chloroplast genomes is still of interest to understand the mechanisms underlining the evolution of Gossypium allotetraploids, while it is generally accepted that the parents were A- and D-genome containing species. Here we performed a comparative analysis of 13 Gossypium chloroplast genomes, twelve of which are presented here for the first time.

Methodology/Principal Findings

The size of 12 chloroplast genomes under study varied from 159,959 bp to 160,433 bp. The chromosomes were highly similar having >98% sequence identity. They encoded the same set of 112 unique genes which occurred in a uniform order with only slightly different boundary junctions. Divergence due to indels as well as substitutions was examined separately for genome, coding and noncoding sequences. The genome divergence was estimated as 0.374% to 0.583% between allotetraploid species and A-genome, and 0.159% to 0.454% within allotetraploids. Forty protein-coding genes were completely identical at the protein level, and 20 intergenic sequences were completely conserved. The 9 allotetraploids shared 5 insertions and 9 deletions in whole genome, and 7-bp substitutions in protein-coding genes. The phylogenetic tree confirmed a close relationship between allotetraploids and the ancestor of A-genome, and the allotetraploids were divided into four separate groups. Progenitor allotetraploid cotton originated 0.43–0.68 million years ago (MYA).

Conclusion

Despite high degree of conservation between the Gossypium chloroplast genomes, sequence variations among species could still be detected. Gossypium chloroplast genomes preferred for 5-bp indels and 1–3-bp indels are mainly attributed to the SSR polymorphisms. This study supports that the common ancestor of diploid A-genome species in Gossypium is the maternal source of extant allotetraploid species and allotetraploids have a monophyletic origin. G. hirsutum AD1 lineages have experienced more sequence variations than other allotetraploids in intergenic regions. The available complete nucleotide sequences of 12 Gossypium chloroplast genomes should facilitate studies to uncover the molecular mechanisms of compartmental co-evolution and speciation of Gossypium allotetraploids.     

Activities of isolated mitochondria and mitochondrial enzymes from aerobically and anaerobically germinated barnyard grass (echinochloa) seedlings

Activity of mitochondria isolated from whole seedlings of Echinochloa crus-galli (L.) Beauv. var oryzicola germinated under aerobic and anaerobic conditions for 5 to 7 days was investigated. Mitochondria from both treatments exhibited good respiratory control and ADP/O ratios. Although O₂ uptake was low in anaerobic mitochondria, activity rapidly increased when the seedlings were transferred to air. Mitochondria from both aerobically and anaerobically grown seedlings of E. crus-galli var oryzicola maintained up to 66% of their initial respiration rate in the presence of both cyanide and salicylhydroxamic acid, and the inhibitory effects of cyanide and azide were additive. In addition, antimycin A was not an effective inhibitor of respiration. Reduced-minus-oxidized absorption spectra revealed that cytochromes a, a₃, and b were reduced to a greater extent and cytochrome c was reduced to a lesser extent in anaerobically germinated seedlings relative to that in aerobically germinated seedlings. An absorption maximum in the cytochrome d region of the spectrum was reduced to the same extent under both germination conditions and an absorption maximum at 577 nm was present only in anaerobically germinated seedlings. Anaerobically germinated seedlings contained 70% of the cytochrome c oxidase activity found in air grown seedlings. Upon exposure to air, the developmental pattern of this enzyme in anaerobically germinated seedlings was similar to air controls. Succinate dehydrogenase activity in anaerobic seedlings was only 45% of the activity found in aerobically germinated seeds, but within 1 hour of exposure to air, the activity had increased to control levels. The results suggest that mitochondria isolated from E. crus-galli var oryzicola differ from other plants studied and that the potential for mitochondrial function during anaerobiosis exists.     

Germination and seedling growth under anaerobic conditions in Echinochloa crus-galli (barnyard grass)*

Abstract Although rice has long been recognized to be uniquely adapted for growth in low oxygen environments of flooded rice fields, rice weeds of the Echinochloa crus-galli complex appear to be at least as well specialized for germination and growth under such unusual biological conditions. Seeds of two varieties of E. crus-galli germinate and grow for prolonged periods in a totally oxygen-free environment. E. crus-galli germinates as well as rice (Oryza sativa) under a total nitrogen atmosphere and produces as large a seedling in spite of its much smaller seed size. Like rice, the seedlings of E. crus-galli are unpigmented, the primary leaves do not emerge from the coleoptile and no root growth occurs without oxygen. Of particular interest is the ultrastructure of mitochondria from anaerobically-grown seedlings. Mitochondrial profiles from the primary leaf of seedlings grown continuously in nitrogen are very similar to those grown aerobically. The size and shape of the mitochondria are similar and the cristae are numerous and normal in appearance. This is in sharp contrast to previous studies of other species which have reported that mitochondria were vesiculate and tended to lose their normal fine-structure after similar periods without oxygen. Finally, based on ultrastructure and ¹⁴C labeling studies, anaerobically-grown seedlings are highly active metabolically, which may explain, at least for E. crus-galli var. oryzicola, its ability to germinate and emerge from flooded rice fields.     

Anaerobiosis in Echinochloa crus-galli (Barnyard Grass) Seedlings : Intermediary Metabolism and Ethanol Tolerance

Tolerance to ethanol and the ability to metabolize key intermediary substrates under anaerobiosis were studied in Echinochloa crus-galli (L.) Beauv. var oryzicola seeds to further characterize the mechanisms which enable it to germinate and grow without O₂.

Our results indicate that E. crus-galli var oryzicola possesses an inherently high tolerance to ethanol and is able to metabolize low levels of ethanol in the absence of O₂. Concentrations of ethanol 45-fold greater than endogenous levels did not prove toxic to germinating seeds.

Five-day anaerobically grown seedlings of E. crus-galli var oryzicola metabolized added [¹⁴C]sucrose primarily to CO₂ and ethanol. Of the soluble compounds labeled, the phosphorylated intermediates of glycolysis and the oxidative pentose phosphate pathway predominated more under anaerobiosis than in air. In addition, organic acids and lipids were labeled from [¹⁴C]sucrose, the latter indicating that metabolism of carbohydrate via acetyl-CoA occurred in the absence of O₂. Lipids were also labeled when seeds were supplied with [¹⁴C]ethanol or [¹⁴C]acetate. Labeling experiments using the above compounds plus [¹⁴C]NaHCO₃, showed further labeling of organic acids; succinate and citrate being labeled under nitrogen, while fumarate was formed in air.

The above metabolic characteristics would allow for the maintenance of an active alcoholic fermentation system which, along with high alcohol dehydrogenase activity, would continue to recycle NAD and result in continued energy production without O₂. In addition, Echinochloa's ability to metabolize carbohydrate intermediates and to synthesize lipids indicates that mechanisms exist for providing the carbon intermediates for biosynthesis, particularly membrane synthesis for growth, even in the absence of O₂.

     

Analysis of the hypervariable region of the Salmonella enterica genome associated with tRNA(leuX)

The divergence of Salmonella enterica and Escherichia coli is estimated to have occurred approximately 140 million years ago. Despite this evolutionary distance, the genomes of these two species still share extensive synteny and homology. However, there are significant differences between the two species in terms of genes putatively acquired via various horizontal transfer events. Here we report on the composition and distribution across the Salmonella genus of a chromosomal region designated SPI-10 in Salmonella enterica serovar Typhi and located adjacent to tRNA(leuX). We find that across the Salmonella genus the tRNA(leuX) region is a hypervariable hot spot for horizontal gene transfer; different isolates from the same S. enterica serovar can exhibit significant variation in this region. Many P4 phage, plasmid, and transposable element-associated genes are found adjacent to tRNA(leuX) in both Salmonella and E. coli, suggesting that these mobile genetic elements have played a major role in driving the variability of this region.     

GERMINATION AND SEEDLING GROWTH IN ECHINOCHLOA CRUS-GALLI VAR. ORYZICOLA UNDER ANOXIC CONDITIONS: STRUCTURAL ASPECTS

The morphological and cellular basis of anoxic germination in Echinochloa crus-galli var. oryzicola is reported. The embryo of E. crus-galli var. oryzicola is typically panicoid in its overall morphology, and is relatively large with a prominent coleoptile and mesocotyl. The response to anoxia is essentially the same in light and dark. Shoot growth occurs in both mesocotyl and coleoptile by cell elongation with no cell division. There is no emergence of the radicle without oxygen. Under anoxia the growth response is not the same as etiolation; there is no plumule elongation within the coleoptile, no protochlorophyll(ide) is found, and limited mesocotyl elongation occurs without oxygen. Air-dark treatment after anoxic germination results in a typical etiolated morphological response, including a resumption of mesocotyl growth, elongation of the plumule within the coleoptile, and initiation of pigment synthesis. These results indicate the effects of anoxia are not permanent but rather limiting and reversible.     

High Level of Interspecific Divergence in the <Emphasis Type="Italic">Salamandrella</Emphasis> Genus Based on Variability of the <Emphasis Type="Italic">RAG2</Emphasis> Gene

Previously, a very low level of divergence between the species of the genus Salamandrella—S. keyserlingii and S. schrenckii—was detected on the basis of variability of the nucleotide sequences of three genes of the nuclear genome (BDNF, POMC, and RAG1). Fixed interspecific differences were detected only in one nucleotide position of the RAG1 gene, and the level of interspecific divergence for this gene was only 0.07%. In this paper, we present the results of a study of the variability of the ENC1, MGAT4C, and RAG2 nuclear genes. The level of interspecific divergence for the MGAT4C gene was 0.14%, and for the RAG2 gene, it was 0.8%. The results of a phylogenetic analysis of the nucleotide sequences of the RAG2 gene in representatives of the family Hynobiidae indicate that the separation of the Salamandrella branch, which is basal for the genera Batrachuperus, Liua, Hynobius, and Pseudohynobius, occurred approximately 55 million years ago. The time of divergence between species of the Salamandrella genus was approximately 21 million years ago.     

Recent structural variations in the Medicago chloroplast genomes and their horizontal transfer into nuclear chromosomes

Medicago is a genus of legumes (Fabaceae) that resemble common clovers with pinnately trifoliate leaves and spirally coiled seed pods, and Medicago sativa is a famous forage crop throughout the world. In this study, we systematically assembled the complete plastid genomes of 18 Medicago species, representing 35 Medicago accessions, whose genome size ranged from ~119 to 125 kb, and identified one novel inverted repeat (IR) in two accessions of Medicago soleirolii (PI537242 and PI537243), albeit of no IRs in the most accessions. We built a phylogenetic tree based on common protein-coding sequences of 55 Medicago accessions in 38 species, which were placed into five clades with a divergence since 9.37 million years ago. Global alignment revealed independent genome evolution events, including eight inversions in nine species and four intron losses (ILs) in 10 species, among which four inversions and two ILs have not been reported previously. Within 109–111 unique genes, ndhA, rpl2, and ycf3 were under positive selection in 54 Medicago accessions. Finally, by aligning chloroplast genes against the nuclear genome assembly of M. sativa cultivar “Zhongmu No.1”, we found that a large number of chloroplast gene fragments were horizontally transferred to nuclear chromosomes in alfalfa, especially on the chr3:47518422–48722257 coordinates of chromosome 3. Our comprehensive exploration of Medicago chloroplast genomes provided insights for the understanding of Medicago diversity and their genomic evolution events.     

Chloroplast genome evolution in the genus Avena

The genus Avena contains five different chloroplast genomes, I-V. A physical map of chloroplast (ct) DNA of Avena sativa (type I chloroplast genome) was constructed using three restriction endonucleases, PstI, SalI and SmaI. This genome is ca. 135.5 kbp in size, and contains two inverted repeats of ca. 22.5 kbp each, separated by a large (ca. 79.0 kbp) and small (ca. 12.5 kbp) single copy region. The rbcL gene which codes for the large subunit of ribulose 1,5-bisphosphate carboxylase, was located in the map. Restriction fragment patterns of all five chloroplast genomes were compared, and among them five fragment size and five restriction site mutations were disclosed. Four site mutations were found in two or more chloroplast genomes, the other site and five fragment size mutations were specific to one or another of the chloroplast genomes. A dendrogram showing phylogenetic relationships among the five chloroplast genomes, based on the distribution of the common and specific mutations among them, indicates that chloroplast genome divergence characterized by three restriction site mutations occurred first between two diploid groups, each carrying A and C genome (nuclear), respectively, followed by further speciation in each group.     

Molecular-based estimate of species number,phylogenetic relationships and divergence times for the genus Stenotaenia (Chilopoda,Geophilomorpha) in the Italian region

Stenotaenia is one of the largest and most widespread genera of geophilid centipedes in the Western Palearctic, with a very uniform morphology and about fifteen species provisionally recognized. For a better understanding of Stenotaenia species-level taxonomy, we have explored the possibility of using molecular data. As a preliminary assay, we sampled twelve populations, mainly from the Italian region, and analyzed partial sequences of the two genes COI and 28S. We employed a DNA-barcoding approach, complemented by a phylogenetic analysis coupled with divergence time estimation. Assuming a barcoding gap of 10–16% K2P pairwise distances, we found evidence for the presence of at least six Stenotaenia species in the Italian region, which started diverging about 50 million years ago, only partially matching with previously recognized species. We found that small-sized oligopodous species belong to a single clade that originated about 33 million years ago, and obtained some preliminary evidence of the related genus Tuoba being nested within Stenotaenia.     

Germination of Echinochloa crus-galli (Barnyard Grass) Seeds under Anaerobic Conditions : Respiration and Response to Metabolic Inhibitors

Echinochloa crus-galli L. Beauv., a rice-field weed, can germinate and grow for extended periods of time in an anaerobic environment. Compared to pea, which does not germinate under anaerobiosis, the evolution of CO₂ in Echinochloa and rice is lower and the peak rate of CO₂ evolution is delayed when germinated without oxygen. The plants studied also differ with respect to their respiration ratio ([CO₂] N₂/[CO₂] air) and metabolism used during the early stages of germination. Echinochloa does not increase its glycolytic rate under anaerobiosis, whereas pentose phosphate pathway activity appears to increase during the first 40 to 50 hours of germination.

Based on its response to metabolic inhibitors (NaF, dinitrophenol, and malonate), anaerobic metabolism in Echinochloa proceeds primarily through glycolysis, with partial operation of the tricarboxylic acid cycle and little or no oxidative phosphorylation. Also, Echinochloa is sensitive to CN during aerobic germination, whereas rice appears to be able to shift to CN-insensitive electron transport. Finally, the effectiveness of cyanide and azide on inhibiting germination of Echinochloa in N₂, but not CO, suggests that cytochrome oxidase is not used to reoxidize pyridine nucleotides in the absence of oxygen. The possible existence of an alternate electron acceptor is discussed.

     

藏波罗花叶绿体基因组分析

藏波罗花（Incarvillea younghusbandii Sprague）是一种传统的补益类中药。其根作草药使用,用于滋补强壮,治产后少乳、久病虚弱、头晕、贫血等症。但目前关于藏波罗花分子遗传信息的研究很少。本研究基于高通量测序技术对藏波罗花叶绿体基因组进行测序、组装和注释,并对其序列特征、密码子偏好性、重复序列、系统发育和分化时间进行分析。结果表明,藏波罗花叶绿体基因组全长为159 323 bp,包含1个大单拷贝区（80 197 bp）、1个小单拷贝区（9 030 bp）和2个反向重复区（35 048 bp）;共注释出120个基因,包括77个蛋白编码基因、8个rRNA基因和35个tRNA基因;密码子偏好性分析显示,AAA是藏波罗花叶绿体基因组中使用最频繁的密码子;从藏波罗花叶绿体基因组中共检测到42个简单重复序列（simple sequence repeats,SSR）;系统发育分析表明,藏波罗花与密生波罗花（Incarvillea compacta）的亲缘关系最近,且在大概466万年前产生分化。本研究对藏波罗花相关资源的科学保护和开发具有重要的现实意义,也可以为后续角蒿属（Incarvillea）的物种鉴定、紫葳科（Bignoniaceae）的种群遗传多样性研究提供基本的遗传资源。     

New dates and new rates for divergence across the Isthmus of Panama

Sister species separated by the Isthmus of Panama have been widely used to estimate rates of molecular evolution. These estimates are based on the assumption that geographic isolation occurred nearly simultaneously for most taxa, when connections between the Caribbean and eastern Pacific closed approximately three million years ago. Here we show that this assumption is invalid for the only genus for which many taxa and multiple genetic markers have been analysed. Patterns of divergence exhibited by allozymes and the mitochondrial COI gene are highly concordant for 15 pairs of snapping shrimp in the genus Alpheus, indicating that they provide a reasonable basis for estimating time since cessation of gene flow. The extent of genetic divergence between pairs of sister species varied over fourfold. Sister species from mangrove environments showed the least divergence, as would be expected if these were among the last habitats to be divided. Using this pair yields a rate of sequence divergence of 1.4% per one million years, with implied times of separation for the 15 pairs of 3 to 18 million years ago. Many past studies may have overestimated rates of molecular evolution because they sampled pairs that were separated well before final closure of the Isthmus.     

Complete Chloroplast Genome of Sedum sarmentosum and Chloroplast Genome Evolution in Saxifragales

Comparative chloroplast genome analyses are mostly carried out at lower taxonomic levels, such as the family and genus levels. At higher taxonomic levels, chloroplast genomes are generally used to reconstruct phylogenies. However, little attention has been paid to chloroplast genome evolution within orders. Here, we present the chloroplast genome of Sedum sarmentosum and take advantage of several available (or elucidated) chloroplast genomes to examine the evolution of chloroplast genomes in Saxifragales. The chloroplast genome of S. sarmentosum is 150,448 bp long and includes 82,212 bp of a large single-copy (LSC) region, 16.670 bp of a small single-copy (SSC) region, and a pair of 25,783 bp sequences of inverted repeats (IRs).The genome contains 131 unique genes, 18 of which are duplicated within the IRs. Based on a comparative analysis of chloroplast genomes from four representative Saxifragales families, we observed two gene losses and two pseudogenes in Paeonia obovata, and the loss of an intron was detected in the rps16 gene of Penthorum chinense. Comparisons among the 72 common protein-coding genes confirmed that the chloroplast genomes of S. sarmentosum and Paeonia obovata exhibit accelerated sequence evolution. Furthermore, a strong correlation was observed between the rates of genome evolution and genome size. The detected genome size variations are predominantly caused by the length of intergenic spacers, rather than losses of genes and introns, gene pseudogenization or IR expansion or contraction. The genome sizes of these species are negatively correlated with nucleotide substitution rates. Species with shorter duration of the life cycle tend to exhibit shorter chloroplast genomes than those with longer life cycles.