The complete plastid genome of Cotinus coggygria and phylogenetic analysis of the Anacardiaceae

Cotinus coggygria Scop. (Anacardiaceae) is an important ornamental tree with beautiful characteristics that is grown in China. In this study, the complete plastid genome of C. coggygria was sequenced and assembled. This genome was 158,843 bp in size and presented a typical tetrad structure, consisting of a large single-copy region (87,121 bp), a pair of inverted repeat regions (26,829 bp), and a small single-copy region (18,064 bp). A total of 134 genes were annotated, including 88 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. We observed a deletion that caused the loss of the rpl32 gene, and a small expansion of IR regions resulted in the trnH gene accessing IR regions; two copies were obtained. Phylogenetic analysis showed that C. coggygria was most closely related to Pistacia, with 100% bootstrap support within Anacardiaceae. In this study, we report the plastid genome of Cotinus species for the first time, which provides insight into the evolution of the plastid genome in Anacardiaceae and promotes the understanding of Cotinus plants.     

Novel clades of chromodomain-containing Gypsy LTR retrotransposons from mosses (Bryophyta)

Retrotransposons are the major component of plant genomes. Chromodomain-containing Gypsy long terminal repeat (LTR) retrotransposons are widely distributed in eukaryotes. Four distinct clades of chromodomain-containing Gypsy retroelements are known from the vascular plants: Reina, CRM, Galadriel and Tekay. At the same time, almost nothing is known about the repertoire of LTR retrotransposons in bryophyte genomes. We have combined a search of chromodomain-containing Gypsy retroelements in Physcomitrella genomic sequences and an experimental investigation of diverse moss species. The computer-based mining of the chromodomain-containing LTR retrotransposons allowed us to describe four different elements from Physcomitrella. Four novel clades were identified that are evolutionarily distinct from the chromodomain-containing Gypsy LTR retrotransposons of other plants.     

Monoplastidic mitosis in the mossTimmiella barbuloides (Bryophyta)

Summary Mitotic cell division of monoplastidic sporogones was investigated in the mossTimmiella barbuloides (Brid.) Moenk. (Pottiales, Bryophyta) by TEM. Division polarity of sporogones is established by the interphase position of the single oblong cup-shaped plastid, which is orientated with its long axis parallel to one of the cell walls. In preprophase the plastid elongates and its extremities bend at right angles. Plastid growth is directed by microtubules and accompanied by plastid tubules. The plastid begins the process of duplication by constricting centrally in the plane of the future cytokinetic septum. There is no preprophase band of microtubules at the division site. The large central nucleus becomes fusiform and aligned parallel to the main plastid axis. By the end of prophase the daughter plastids are positioned at the opposite poles of the nucleus where they probably function as nucleating or organizing centres for the spindle microtubules. Metaphase and anaphase spindles contain long sheets of ER. Cytokinesis involves the formation of a well developed phragmoplast.Abbreviations TEM transmission electron microscopy - PPB preprophase band of microtubules - ER endoplasmic reticulum     

Ancestry of plant MADS-box genes revealed by bryophyte (Physcomitrella patens) homologues

Three MADS-box cDNA clones and two corresponding genomic sequences (gDNAs) have been isolated from the bryophyte Physcomitrella patens and sequenced. Our findings indicate that the genes may be expressed in a tissue- or age-specific manner, and that expression of one of them is regulated by an alternative splicing mechanism. Conceptual translation of the clones reveals that the encoded MADS-domain proteins have the typical plant-domain pattern (MIKC). Additionally, there is a high degree of conservation of intron number and positions between angiosperm MADS-box genes and the moss loci. These observations confirm the homology of moss and higher plant MADS-box genes. We conclude that the MIKC pattern evolved in MADS-box genes after the separation of the plant lineage from that of fungi and animals, and that it must have been present in the common ancestor of mosses, ferns and seed plants. Therefore it evolved at least 400 million yr ago. Phylogenetic analysis of a large subset of the sequenced plant MADS-box genes, incorporating those from P. patens , indicates that the bryophyte genes are not orthologues of spermatophyte genes belonging to any of the well recognized higher plant gene subfamilies. This conclusion accords well with reports that the known fern MADS-box genes also comprise subfamilies distinct from those of higher plants. Therefore we tentatively propose that the gene duplication and diversification events that created the MADS-box gene subfamilies, discernible in extant angiosperm and other spermatophyte groups, occurred after separation of the moss and fern lineages from the lineage which produced the higher plants.     

Evaluation of 10 plant barcodes in Bryophyta (Mosses)

DNA barcoding is a molecular tool that uses a standardized DNA region to identify species. Our preliminary study reported here is the first attempt to specifically focus on universality and attributes of candidate barcodes across a wide systematic range of mosses. We tested eight previously proposed plant barcoding regions (atpF-atpH, ITS2, marK, psbK-psbI, rbcL, rpoB, rpoC1, and trnH-psbA) and two popular phylogenetic markers (rps4 and trnL-trnF of cpDNA) in 49 moss species and 9 liverwort species, representing half of the orders in moss lineages. The ITS2, rbcL, rpoC1, rps4, trnH-psbA and trnL-trnF regions showed good universality, and therefore the efficacy of these loci as DNA barcodes was further evaluated in 36 mosses and 2 liverworts, each of which included two to three individuals per taxa. The five loci, viz. rbcL, rpoC1, rps4, trnH-psbA and trnL-trnF, were easy to amplify and sequence and showed significant inter-specific genetic variability, making them potentially useful DNA barcodes for mosses. The best performing single loci were the rbcL and rpoC1 coding regions. Several loci showed equivalent performance and combinations of them did not greatly increase their discrimination capacity. In addition, phylogenies generated from each of the separate regions and multi-locus combinations by using best-fit and Kimura 2-parameter models were compared, but no significant difference was found.     

Evaluation of ten plant barcodes in Bryophyta (Mosses)

DNA barcoding is a molecular tool that uses a standardized DNA region to identify species. Our preliminary study reported here is the first attempt to specifically focus on universality and attributes of candidate barcodes across a wide systematic range of mosses. We tested eight previously proposed plant barcoding regions (atpF-atpH, ITS2, matK, psbK-psbI, rbcL, rpoB, rpoC1, trnH-psbA) and two popular phylogenetic markers (rps4 and trnL-trnF of cpDNA) in 49 moss species and 9 liverwort species, representing half of the orders in moss lineages. The ITS2, rbcL, rpoC1, rps4, trnH-psbA and trnL-trnF regions showed good universality, and therefore the efficacy of these loci as DNA barcodes was further evaluated in 36 mosses and 2 liverworts, each of which included two to three individuals per taxa. The five loci, viz. rbcL, rpoC1, rps4, trnH-psbA and trnL-trnF, were easy to amplify and sequence and showed significant interspecific genetic variability, making them potentially useful DNA barcodes for mosses. The best performing single loci were the rbcL and rpoC1 coding regions. Several loci showed equivalent performance and combinations of them did not greatly increase their discrimination capacity. In addition, phylogenies generated from each of the separate regions and multi-locus combinations by using best-fit and Kimura 2-parameter models were compared, but no significant difference was found.     

Observations of spore morphology of some Pottiaceae Schimp. species (Bryophyta) in Turkey

The spores of Syntrichia ruralis (Hedw.) F. Weber and D. Mohr., S. princeps (De Not.) Mitt., S. subulata (Hedw.) F.Weber and D.Mohr var. subulata, S. subulata (Hedw.) F.Weber and D.Mohr var. angustata (Schimp.) J.J. Amann and S. subulata (Hedw.) F.Weber and D.Mohr var. graeffii Warnst. were studied by light and scanning electron microscopy for the first time. The apertural region consists of a leptoma in all spores. All taxa of the family are uniform in their spore morphology. The spores of the five taxa are of granuloid type. The spore wall of the Pottiaceae family includes sclerine (the distinction between exine and perine may be difficult to define) and intine. The taxonomy of the genus Syntrichia is discussed on the basis of its spore morphology.     

Corrected sequence of the wheat plastid genome

Wheat is the most important cereal in the world in terms of acreage and productivity. We sequenced and assembled the plastid genome of one Egyptian wheat cultivar using next-generation sequence data. The size of the plastid genome is 133,873 bp, which is 672 bp smaller than the published plastid genome of “Chinese Spring” cultivar, due mainly to the presence of three sequences from the rice plastid genome. The difference in size between the previously published wheat plastid genome and the sequence reported here is due to contamination of the published genome with rice plastid DNA, most of which is present in three sequences of 332, 131 and 131 bp. The corrected plastid genome of wheat has been submitted to GenBank (accession number KJ592713) and can be used in future comparisons.     

Higher substitution rates and lower dN/dS for the plastid genes in Gnetales than other gymnosperms

Previous studies have shown that Gnetales exhibit an increase in the rates of substitution in plastid genes. However, the relative roles of selection and drift in driving the observed increase in substitution rate remain unclear. Here we estimated the nonsynonymous (dN) and synonymous (dS) substitution rates and the dN/dS ratios for 59 plastid protein-coding genes conserved across Gnetales and other gymnosperms with maximum likelihood methods. Our results show that: (1) values of dN and dS for 48 and 50 genes, respectively, are significantly higher in Gnetales relative to the other sampled gymnosperms; (2) the acceleration of dN is of lower magnitude than that of dS; (3) dN/dS is significantly reduced for 22 of the 59 plastid genes in Gnetales; and (4) dN/dS is extremely heterogeneous among the Gnetalean genes, varying by up to a factor of 40. We propose that while biological characteristics such as generation time and plant height may contribute to the rate increase in Gnetales, the special habitats that they occupy are linked to the gene-specific reduction of dN/dS.     

Exploring the plastid genome disparity of liverworts

Sequencing the plastid genomes of land plants provides crucial improvements to our understanding of the plastome evolution of land plants. Although the number of available complete plastid genome sequences has rapidly increased in the recent years, only a few sequences have been yet released for the three bryophyte lineages, namely hornworts, liverworts, and mosses. Here, we explore the disparity of the plastome structure of liverworts by increasing the number of sequenced liverwort plastomes from five to 18. The expanded sampling included representatives of all major lineages of liverworts including the genus Haplomitrium. The disparity of the liverwort genomes was compared with other 2386 land plant plastomes with emphasis on genome size and GC‐content. We found evidence for structural conservatism of the plastid genomes in liverworts and a trend towards reduced plastome sequence length in liverworts and derived mosses compared to other land plants, including hornworts and basal lineages of mosses. Furthermore, Aneura and Haplomitrium were distinct from other liverworts by an increased GC content, with the one found in Haplomitrium only second to the lycophyte Selaginella. The results suggest the hypothesis that liverworts and other land plants inherited and conserved the plastome structure of their most recent algal ancestors.     

The (in)complete organelle genome: exploring the use and nonuse of available technologies for characterizing mitochondrial and plastid chromosomes

Not long ago, scientists paid dearly in time, money and skill for every nucleotide that they sequenced. Today, DNA sequencing technologies epitomize the slogan ‘faster, easier, cheaper and more’, and in many ways, sequencing an entire genome has become routine, even for the smallest laboratory groups. This is especially true for mitochondrial and plastid genomes. Given their relatively small sizes and high copy numbers per cell, organelle DNAs are currently among the most highly sequenced kind of chromosome. But accurately characterizing an organelle genome and the information it encodes can require much more than DNA sequencing and bioinformatics analyses. Organelle genomes can be surprisingly complex and can exhibit convoluted and unconventional modes of gene expression. Unravelling this complexity can demand a wide assortment of experiments, from pulsed‐field gel electrophoresis to Southern and Northern blots to RNA analyses. Here, we show that it is exactly these types of ‘complementary’ analyses that are often lacking from contemporary organelle genome papers, particularly short ‘genome announcement’ articles. Consequently, crucial and interesting features of organelle chromosomes are going undescribed, which could ultimately lead to a poor understanding and even a misrepresentation of these genomes and the genes they express. High‐throughput sequencing and bioinformatics have made it easy to sequence and assemble entire chromosomes, but they should not be used as a substitute for or at the expense of other types of genomic characterization methods.     

The polarity of gravitropism in the moss Physcomitrella patens is reversed during mitosis and after growth on a clinostat

Abstract. We report two situations in which the polarity of gravitropism of single protonemal cells of the moss Physcomitrella patens is reversed. Dark-grown protonemata of wild-type P. patens grow negatively gravitropically. Time-lapse video-microscopy reveals that a temporary reversal of growth polarity occurs during mitotic division which is independent of the cells' growth rate. A transitory reversal of growth direction is also observed when the unidirectional gravitropic stimulus is interrupted by a period of growth on a clinostat. A third situation, in which a mutant class responds by growing positively gravitropically, has been described previously (Jenkins, Courtice & Cove, 1986). These observations are discussed in terms of possible mechanisms for cell morphogenesis and tropic growth.     

A vertically transmitted amalgavirus is present in certain accessions of the bryophyte Physcomitrium patens

In the last few years, next-generation sequencing techniques have started to be used to identify new viruses infecting plants. This has allowed to rapidly increase our knowledge on viruses other than those causing symptoms in economically important crops. Here we used this approach to identify a virus infecting Physcomitrium patens that has the typical structure of the double-stranded RNA endogenous viruses of the Amalgaviridae family, which we named Physcomitrium patens amalgavirus 1, or PHPAV1. PHPAV1 is present only in certain accessions of P. patens, where its RNA can be detected throughout the cell cycle of the plant. Our analysis demonstrates that PHPAV1 can be vertically transmitted through both paternal and maternal germlines, in crosses between accessions that contain the virus with accessions that do not contain it. This work suggests that PHPAV1 can replicate in genomic backgrounds different from those that actually contain the virus and opens the door for future studies on virus–host coevolution.     

Sequencing and phylogenetic analysis of the Pyrgilauda ruficollis(Aves,Passeridae) complete mitochondrial genome

In this study,both long PCR and conserved primers walking sequencing methods were used to determine the complete sequence of the of Pyrgilauda ruficollis mitochondrial genome(KC836121).The results showed that the complete mitochondrial genome of P.ruficollis is 16909 bp in length with 55.0%A+T content,harboring the typical 37 genes.The mitogenome had the same gene order with that of Podoces hendersoni.All protein coding genes started with ATG codon,except ND3 with GTG.For the stop codon usage,most genes terminate with codons TAA or TAG,but ND5 terminated with AGA,while ND1 and COI genes with AGG,and both the genes COIII and ND4 have an incomplete termination codon(T).The secondary structures of 22 tRNA genes were also predicted,showing that all tRNAs can form typical clover-leaf secondary structures,except for the tRNASer(AGN)which loses the DHU arm,while tRNAPhe harbor an extra nucleotide inserted in the TψC arm.The predicted secondary structures of 12S rRNA and16S rRNA exhibit 47 helices in 4 domains and 60 helices in 6 domains respectively.The control region of P.ruficollis with the length of 1 305 bp was located between tRNAGlu and tRNAPhe,and typical domains of which could be found as other bird groups.Using the data from 13 mitochondrial protein-coding genes,results of a final phylogenetic analysis strongly supports the traditional view that P.ruficollis is closely related with Passeridae and Fringillidae.     

石松类和蕨类植物质体基因组结构演化研究进展

近年来, 随着测序技术的发展, 石松类和蕨类植物的核基因组、质体基因组以及线粒体基因组研究发展迅速, 质体基因组研究工作更是呈爆发式增长。截至2019年3月1日, GenBank公布的石松类和蕨类植物的175个质体基因组中, 约3/4为最近两年新增。研究内容从早期对个别质体基因组结构和序列特征的简单报道, 逐渐发展到综合性的比较基因组学和系统发育基因组学研究。目前已发表的质体基因组覆盖了石松类和蕨类植物的所有目和大部分科, 这两大类群的质体基因组结构变异和系统发育的基本框架已逐渐清晰。这些研究为我们理解维管植物的早期演化提供了重要参考。本文对石松类和蕨类植物的质体基因组结构特征进行了系统梳理, 发现其结构变异主要包括大片段倒位、IR区边界变动、基因或内含子丢失等, 其中一些结构变异可作为较高分类阶元的共衍征。RNA编辑和长片段非编码序列插入普遍存在于石松类和蕨类植物的质体基因组中, 但其起源、演化机制和功能等仍不清楚。我们对质体基因组的应用、系统发育研究中质体和核基因组的优劣性, 以及系统发育基因组学的前景进行了评述。     

The complete mitochondrial genome of Diaphorina citri (Hemiptera: Psyllidae) and phylogenetic analysis

The Asian citrus psyllid, Diaphorina citri Kuwayama (Hemiptera: Psyllidae) is the most serious pest of citrus as the vector of Huanglongbing (HLB), the citrus greening disease. In this study, the complete mitochondrial genome (mitogenome) of D. citri has been sequenced and annotated, and a comparative analysis is provided with known Psylloidea species. The mitogenome of D. citri is a typical circular molecular of 15,038 bp in length with an A + T content of 74.56%, contains the typical 37 genes and the gene order is identical to the other Psylloidea mitogenomes. The nucleotide composition and codon usage of D. citri are similar to the four Psylloidea species. All protein-coding genes (PCGs) use standard initiation codons (TAN), stop with TAA and TAG except ND2 and ND5 which stop with incomplete termination codon T. All tRNAs have the typical clover-leaf structure, with the exception of trnS1 lacking the dihydrouridine (DHU) arm. The control region is located between rrnL and the trnI gene with the highest A + T content among the five Psylloidea species. Phylogenetic analysis is conducted based on the 13 PCGs or/and 2 rRNAs of 23 Sternorrhycha mitogenomes. Both maximum likelihood (ML) and Bayesian inference (BI) analysis suggest a clear relationship of Psylloidea, Aleyrodoidea and Aphidoidea within Sternorrhycha, which support the traditional morphological classification.