Intron Length Research Articles

Hybrid between Lemna minor and L. turionifera (L. × japonica, Lemnaceae) in East Europe is more frequent than parental species and poorly distinguishable from them

Biodiversity studies and practical use of duckweeds are impossible without reliable species identification. Despite of clear genetic differentiation of L. minor, L. turionifera and their hybrid L. × japonica, their morphological discrimination is challenging even for professional botanists; consequently, the distribution of the two latter taxa is not precisely known. Although numerous determination keys exist, none of them is based on quantitative analysis of the morphological variation observed in nature. Thus, we aimed to study variation of morphological characteristics most frequently proposed for discrimination between L. minor, L. turionifera and L. × japonica (frond shape and pigmentation, papule presence along the median nerve) on specimens collected in the wild, which were taxonomically identified using molecular tools (intron length polymorphism in the β-tubulin gene). We focused on samples from the poorly studied East Europe, including some from the Russian Far East for comparison. Lemna × japonica appeared to be quite abundant in different regions of East Europe. The Far Eastern occurrences of L. minor and L. × japonica should be carefully verified. Even our limited sampling demonstrated that morphological characters conventionally used for delimitation of L. minor, L. turionifera and L. × japonica do not work in wild populations. Additional studies should be performed for verification of diagnostic value of generative characters. Large-scale genetic screening of Lemna populations in nature is also indispensable to clarify distribution of taxa from the L. minor complex.

The Chloroplast Genome of the Lichen Photobiont Trebouxiophyceae sp. DW1 and Its Phylogenetic Implications.

Lichens are symbiotic associations of algae and fungi. The genetic mechanism of the symbiosis of lichens and the influence of symbiosis on the size and composition of the genomes of symbiotic algae have always been intriguing scientific questions explored by lichenologists. However, there were limited data on lichen genomes. Therefore, we isolated and purified a lichen symbiotic alga to obtain a single strain (Trebouxiophyceae sp. DW1), and then obtained its chloroplast genome information by next-generation sequencing (NGS). The chloroplast genome is 129,447 bp in length, and the GC content is 35.2%. Repetitive sequences with the length of 30–35 bp account for 1.27% of the total chloroplast genome. The simple sequence repeats are all mononucleotide repeats. Codon usage analysis showed that the genome tended to use codon ending in A/U. By comparing the length of different regions of Trebouxiophyceae genomes, we found that the changes in the length of exons, introns, and intergenic sequences affect the size of genomes. Trebouxiophyceae had an unstable chloroplast genome structure, with IRs repeatedly losing during evolution. Phylogenetic analysis showed that Trebouxiophyceae is paraphyletic, and Trebouxiophyceae sp. DW1 is sister to the clade of Koliella longiseta and Pabia signiensis.

Analysis of Long Non-Coding RNA-Mediated Regulatory Networks of Plutella xylostella in Response to Metarhizium anisopliae Infection.

Simple SummaryPlutella xylostella is one of the most destructive insect pests of cruciferous crops worldwide. Notorious for its ability to resist a myriad of chemical insecticides, this pest has become a nuisance, leading scientists to probe for alternative eco-friendly control measures, such as Metarhizium anisopliae, an insect pathogenic fungus. In response to fungal infection, insects mount a wide array of immune responses mediated by several regulatory molecules, including long non-coding RNAs (lncRNAs). Evidence suggests that lncRNAs are significantly induced in response to pathogenic infection in plants and animals. However, their role during insect host–pathogen interactions is still in its infancy. In the current study, we employed a strand-specific RNA sequencing technique to decipher the role of lncRNAs in the P. xylostella fat body during M. anisopliae infection. Our findings will provide a genetic resource for future functional studies of lncRNAs and shed light on understanding insect–pathogen interactions. These findings would be helpful in designing pest management strategies via gene silencing technologies.Long non-coding RNAs (lncRNAs) represent a diverse class of RNAs that are structurally similar to messenger RNAs (mRNAs) but do not encode proteins. Growing evidence suggests that in response to biotic and abiotic stresses, the lncRNAs play crucial regulatory roles in plants and animals. However, the potential role of lncRNAs during fungal infection has yet to be characterized in Plutella xylostella, a devastating pest of cruciferous crops. In the current study, we performed a strand-specific RNA sequencing of Metarhizium anisopliae-infected (Px36hT, Px72hT) and uninfected (Px36hCK, Px72hCK) P. xylostella fat body tissues. Comprehensive bioinformatic analysis revealed a total of 5665 and 4941 lncRNAs at 36 and 72-h post-infection (hpi), including 563 (Px36hT), 532 (Px72hT) known and 5102 (Px36hT), 4409 (Px72hT) novel lncRNA transcripts. These lncRNAs shared structural similarities with their counterparts in other species, including shorter exon and intron length, fewer exon numbers, and a lower expression profile than mRNAs. LncRNAs regulate the expression of neighboring protein-coding genes by acting in a cis and trans manner. Functional annotation and pathway analysis of cis-acting lncRNAs revealed their role in several immune-related genes, including Toll, serpin, transferrin, βGRP etc. Furthermore, we identified multiple lncRNAs acting as microRNA (miRNA) precursors. These miRNAs can potentially regulate the expression of mRNAs involved in immunity and development, suggesting a crucial lncRNA–miRNA-mRNA complex. Our findings will provide a genetic resource for future functional studies of lncRNAs involved in P. xylostella immune responses to M. anisopliae infection and shed light on understanding insect host–pathogen interactions.

Evolutionary Transformations of Albumin Using the Example of Model Species of Jawless Agnatha and Bony Jawed Fish (Review)

Issues of the organization of albumin (a protein belonging to the superfamily of albuminoids) are considered using the example of model representatives of lower aquatic vertebrates: jawless Agnatha (Cyclostomata) and jawed bony lobe-finned (Sarcopterygii) and ray-finned (Actinopterygii: Chondrostei, Holostei, Teleostei) fish. A comparative analysis is carried out of the total length and the length of coding and noncoding sequences of the albumin gene; the number of exons, the length of introns, and the presence of repeated DNA elements in them; and the presence/absence of paralogous genes, their chromosomal affiliation, and the composition of syntenic groups. A comparative analysis of the length of the amino acid sequence, the number of domains, and S–S bonds in the albumin structure is also carried out. The issues of the emergence of the ancestral gene for albuminoids, the “expansion” and “narrowing” of the albuminoid repertoire in different groups of vertebrates, the appearance of a cluster of paralogous genes within a single chromosome in the Sarcopterygii branch and paralogous genes on different chromosomes in the Actinopterygii branch in the representatives of cartilaginous ganoids and teleost fish, the elongation of the gene and protein chain of albumin in the lamprey line, and losses of the albumin gene in the largest groups of teleost fish (Ostariophysi and Acanthopterygii) are discussed. The listed scenarios are considered in light of their consistency with the events of whole genome, local, and segment duplications. The problem of compensating for the functions of the “lost” albumin gene due to multiple osmotically active plasma proteins is discussed using the example of the group of teleost fish.

Cell-specific regulation of gene expression using splicing-dependent frameshifting

Precise and reliable cell-specific gene delivery remains technically challenging. Here we report a splicing-based approach for controlling gene expression whereby separate translational reading frames are coupled to the inclusion or exclusion of mutated, frameshifting cell-specific alternative exons. Candidate exons are identified by analyzing thousands of publicly available RNA sequencing datasets and filtering by cell specificity, conservation, and local intron length. This method, which we denote splicing-linked expression design (SLED), can be combined in a Boolean manner with existing techniques such as minipromoters and viral capsids. SLED can use strong constitutive promoters, without sacrificing precision, by decoupling the tradeoff between promoter strength and selectivity. AAV-packaged SLED vectors can selectively deliver fluorescent reporters and calcium indicators to various neuronal subtypes in vivo. We also demonstrate gene therapy utility by creating SLED vectors that can target PRPH2 and SF3B1 mutations. The flexibility of SLED technology enables creative avenues for basic and translational research.

Genome-wide identification and development of miniature inverted-repeat transposable elements and intron length polymorphic markers in tea plant (Camellia sinensis)

Marker-assisted breeding and tagging of important quantitative trait loci for beneficial traits are two important strategies for the genetic improvement of plants. However, the scarcity of diverse and informative genetic markers covering the entire tea genome limits our ability to achieve such goals. In the present study, we used a comparative genomic approach to mine the tea genomes of Camellia sinensis var. assamica (CSA) and C. sinensis var. sinensis (CSS) to identify the markers to differentiate tea genotypes. In our study, 43 and 60 Camellia sinensis miniature inverted-repeat transposable element (CsMITE) families were identified in these two sequenced tea genomes, with 23,170 and 37,958 putative CsMITE sequences, respectively. In addition, we identified 4912 non-redundant, Camellia sinensis intron length polymorphic (CsILP) markers, 85.8% of which were shared by both the CSS and CSA genomes. To validate, a subset of randomly chosen 10 CsMITE markers and 15 CsILP markers were tested and found to be polymorphic among the 36 highly diverse tea genotypes. These genome-wide markers, which were identified for the first time in tea plants, will be a valuable resource for genetic diversity analysis as well as marker-assisted breeding of tea genotypes for quality improvement.

Allelic variation in shrunken2 gene affecting kernel sweetness in exotic-and indigenous-maize inbreds.

Sweet corn has become a popular food worldwide. It possesses six-times more sugar than field corn due to the presence of recessive shrunken2 (sh2) gene. Despite availability of diverse sweet corn germplasm, comprehensive characterization of sh2 has not been undertaken so far. Here, entire Sh2 gene (7320 bp) among five field corn-(Sh2Sh2) and six sweet corn-(sh2sh2) inbreds was sequenced. A total of 686 SNPs and 372 InDels were identified, of which three SNPs differentiated the wild-(Sh2) and mutant-(sh2) allele. Ten InDel markers were developed to assess sh2 gene-based diversity among 23 sweet corn and 25 field corn lines. Twenty-five alleles and 47 haplotypes of sh2 were identified among 48 inbreds. Among markers, MGU-InDel-2, MGU-InDel-3, MGU-InDel-5 and MGU-InDel-8 had PIC>0.5. Major allele frequency varied from 0.458–0.958. The gene sequence of these maize inbreds was compared with 25 orthologues of monocots. Sh2 gene possessed 15–18 exons with 6-225bp among maize, while it was 6–21 exons with 30-441bp among orthologues. While intron length across maize genotypes varied between 67-2069bp, the same among orthologues was 57–2713 bp. Sh2-encoded AGPase domain was more conserved than NTP transferase domain. Nucleotide and protein sequences of sh2 in maize and orthologues revealed that rice orthologue was closer to maize than other monocots. The study also provided details of motifs and domains present in sh2 gene, physicochemical properties and secondary structure of SH2 protein in maize inbreds and orthologues. This study reports detailed characterization and diversity analysis in sh2 gene of maize and related orthologues in various monocots.

Identification and expression profile analysis of the SnRK2 gene family in cucumber.

The sucrose non-fermenting-1-related protein kinase 2 (SnRK2) is a plant-specific type of serine/threonine protein kinase that plays an important role in the physiological regulation of stress. The objective of this study was to identify and analyze the members of the SnRK2 gene family in cucumber and lay a foundation for further exploration of the mechanism of CsSnRK2 resistance to stress. Here, 12 SnRK2 genes were isolated from cucumber and distributed on five chromosomes, phylogenetic clustering divided these into three well-supported clades. In addition, collinearity analysis showed that the CsSnRK2 gene family underwent purifying selection pressure during evolution. CsSnRK2 genes of the same group have similar exons and conserved motifs, and intron length may be a specific imprint for the evolutionary amplification of the CsSnRK2 gene family. By predicting cis elements in the promoter, we found that the promoter region of CsSnRK2 gene members had various cis-regulatory elements in response to hormones and stress. Relative expression analysis showed that CsSnRK2.11 (group II) and CsSnRK2.12 (group III) were strongly induced by ABA, NaCl and PEG stress; whereas CsSnRK2.2 (group III) was not activated by any treatment. The response of group I CsSnRK2 to ABA, NaCl and PEG was weak. Furthermore, protein interaction prediction showed that multiple CsSnRK2 proteins interacted with four proteins including protein phosphatase 2C (PP2C), and it is speculated that the CsSnRK2 genes may also an independent role as a third messenger in the ABA signaling pathway. This study provides a reference for analyzing the potential function of CsSnRK2 genes in the future research.

Intron size minimisation in teleosts

BackgroundSpliceosomal introns are parts of primary transcripts that are removed by RNA splicing. Although introns apparently do not contribute to the function of the mature transcript, in vertebrates they comprise the majority of the transcribed region increasing the metabolic cost of transcription. The persistence of long introns across evolutionary time suggests functional roles that can offset this metabolic cost. The teleosts comprise one of the largest vertebrate clades. They have unusually compact and variable genome sizes and provide a suitable system for analysing intron evolution.ResultsWe have analysed intron lengths in 172 vertebrate genomes and show that teleost intron lengths are relatively short, highly variable and bimodally distributed. Introns that were long in teleosts were also found to be long in mammals and were more likely to be found in regulatory genes and to contain conserved sequences. Our results argue that intron length has decreased in parallel in a non-random manner throughout teleost evolution and represent a deviation from the ancestral state.ConclusionOur observations indicate an accelerated rate of intron size evolution in the teleosts and that teleost introns can be divided into two classes by their length. Teleost intron sizes have evolved primarily as a side-effect of genome size evolution and small genomes are dominated by short introns (<256 base pairs). However, a non-random subset of introns has resisted this process across the teleosts and these are more likely have functional roles in all vertebrate clades.

Development of ILP-markers for Aegilops tauschii and their application in molecular genetic analysis

To develop marker systems based on the study of intron length polymorphism of various genes (ILP) in Ae. tauschii, to test the possibility of their use for genetic differentiation of Ae. tauschii and Ae. biuncialis. Methods. The NCBI database was used to obtain EST sequences, online tools CD-HIT, BLAST and Primer3Plus (for the development of primers). The polymerase chain reaction (PCR) method with the developed primers was done. Amplified fragments were separated by non-denaturing polyacrylamide gel electrophoresis and stained with silver. Results. Molecular markers Aet_ILP1, Aet_ILP6 were developed and tested for different genotypes of Ae. tauschii and Ae. biuncialis. No intraspecific differentiation was observed in all studied samples, but amplicons of introns of different species differed significantly. It was also found that the studied species had one copy of the HO222074.1 gene and 1 to 3 copies of the CX244643.1 gene. Conclusions. The obtained results indicate a low level of intraspecific variability of the developed ILP markers and the possibility of their use for interspecific differentiation of Ae. tauschii and Ae. biuncialis.

Comparison of methods of DNA extraction from herbarium specimens of little-pod false flax (Camelina microcarpa Andrz. Ex Dc.)

Aim. The aim of this research was to compare the efficiency of DNA isolation methods from herbarium specimens of Camelina microcarpa Andrz. Ex DC., further modification of these methods to increase DNA yield, and determine the method that would provide the best yield of isolated DNA. Methods. Modifications of the DNA isolation methods using the DNeasy Plant Mini Kit (QIAgen) and the CTAB method were used. PCR was performed using degenerate primers for method of β-tubulin intron length polymorphism (TBP). Amplicons were fractionated in polyacrylamide gel followed by visualization by silver nitrate staining. Results. DNA was successfully extracted from C. microcarpa herbarium specimens sampled with leaf parts and seeds, using the modified by CTAB method, and four modified methods using DNeasy Plant Mini Kit (QIAgen). Conclusions. The study revealed that the most effective method tested was the DNeasy Plant Mini Kit (QIAgen) No. 2. Prolongation of the cell lysis stage had the best effect on the increase of DNA yield. We found that the success of DNA isolation was influenced not so much by the age of the herbarium specimen as by the methods of drying and storing the plants in the collection.

Chromosome-specific potential intron polymorphism markers for large-scale genotyping applications in pomegranate.

Despite the availability of whole genome assemblies, the identification and utilization of gene-based marker systems has been limited in pomegranate. In the present study, we performed a genome-wide survey of intron length (IL) markers in the 36,524 annotated genes of the Tunisia genome. We identified and designed a total of 8,812 potential intron polymorphism (PIP) markers specific to 3,445 (13.40%) gene models that span 8 Tunisia chromosomes. The ePCR validation of all these PIP markers on the Tunisia genome revealed single-locus amplification for 1,233 (14%) markers corresponding to 958 (27.80%) genes. The markers yielding single amplicons were then mapped onto Tunisia chromosomes to develop a saturated linkage map. The functional categorization of 958 genes revealed them to be a part of the nucleus and the cytoplasm having protein binding and catalytic activity, and these genes are mainly involved in the metabolic process, including photosynthesis. Further, through ePCR, 1,233 PIP markers were assayed on multiple genomes, which resulted in the identification of 886 polymorphic markers with an average PIC value of 0.62. In silico comparative mapping based on physically mapped PIP markers indicates a higher synteny of Tunisia with the Dabenzi and Taishanhong genomes (>98%) in comparison with the AG2017 genome (95%). We then performed experimental validation of a subset of 100 PIP primers on eight pomegranate genotypes and identified 76 polymorphic markers, with 15 having PIC values ≥0.50. We demonstrated the potential utility of the developed markers by analyzing the genetic diversity of 31 pomegranate genotypes using 24 PIP markers. This study reports for the first time large-scale development of gene-based and chromosome-specific PIP markers, which would serve as a rich marker resource for genetic variation studies, functional gene discovery, and genomics-assisted breeding of pomegranate.

Genome-Wide Analysis of Odorant and Gustatory Receptors in Six Papilio Butterflies (Lepidoptera: Papilionidae).

Simple SummaryThe butterflies of the Lepidoptera are representatives of herbivorous insects. Host plant diversities may shape the evolution of chemosensory receptors in butterflies. However, little is known about whether the host plant range is correlated with the size differences of chemoreceptors as key molecular targets for butterfly–plant chemical interactions. Here, we characterized 381 odorant (ORs) and 328 gustatory (GRs) receptors in one Papilio generalist and five other Papilio specialists regarding their comprehensive annotation, gene structure, phylogenetics and expression profiles. Among six Papilio species, orthologous ORs or GRs shared conserved gene structure, but the differences in intron size frequencies were observed between the generalist and the specialists. Furthermore, expression profiles identified candidate OR and GR genes in antennae, foretarsi or reproductive tissues of P. xuthus. This study addresses, for the first time, the issue that the breath of host plants does not appear to result in the obvious expansions of ORs and GRs in Papilio butterflies and identifies candidate molecular targets associated with olfaction, oviposition or reproduction in P. xuthus.The chemical interactions of insects and host plants are shaping the evolution of chemosensory receptor gene families. However, the correlation between host range and chemoreceptor gene repertoire sizes is still elusive in Papilionidae. Here, we addressed the issue of whether host plant diversities are correlated with the expansions of odorant (ORs) or gustatory (GRs) receptors in six Papilio butterflies. By combining genomics, transcriptomics and bioinformatics approaches, 381 ORs and 328 GRs were annotated in the genomes of a generalist P. glaucus and five specialists, P. xuthus, P. polytes, P. memnon, P. machaon and P. dardanus. Orthologous ORs or GRs in Papilio had highly conserved gene structure. Five Papilio specialists exhibited a similar frequency of intron lengths for ORs or GRs, but which was different from those in the generalist. Phylogenetic analysis revealed 60 orthologous OR groups, 45 of which shared one-to-one relationships. Such a single gene in each butterfly also occurred in 26 GR groups. Intriguingly, bitter GRs had fewer introns than other GRs and clustered into a large clade. Focusing on the two chemoreceptor gene families in P. xuthus, most PxutORs (52/58) were expressed in antennae and 31 genes in reproductive tissues. Eleven out of 28 foretarsus-expressed PxutGRs were female-biased genes, as strong candidates for sensing oviposition stimulants. These results indicate that the host range may not shape the large-scale expansions of ORs and GRs in Papilio butterflies and identify important molecular targets involved in olfaction, oviposition or reproduction in P. xuthus.

Splice site proximity influences alternative exon definition

ABSTRACT Alternative splicing enables higher eukaryotes to expand mRNA diversity from a finite number of genes through highly combinatorial splice site selection mechanisms that are influenced by the sequence of competing splice sites, cis-regulatory elements binding trans-acting factors, the length of exons and introns harbouring alternative splice sites and RNA secondary structures at putative splice junctions. To test the hypothesis that the intron definition or exon definition modes of splice site recognition direct the selection of alternative splice patterns, we created a database of alternative splice site usage (ALTssDB). When alternative splice sites are embedded within short introns (intron definition), the 5′ and 3′ splice sites closest to each other across the intron preferentially pair, consistent with previous observations. However, when alternative splice sites are embedded within large flanking introns (exon definition), the 5′ and 3′ splice sites closest to each other across the exon are preferentially selected. Thus, alternative splicing decisions are influenced by the intron and exon definition modes of splice site recognition. The results demonstrate that the spliceosome pairs splice sites that are closest in proximity within the unit of initial splice site selection.

Genomic insights into positive selection during barley domestication

BackgroundCultivated barley (Hordeum vulgare) is widely used in animal feed, beverages, and foods and has become a model crop for molecular evolutionary studies. Few studies have examined the evolutionary fates of different types of genes in barley during the domestication process.ResultsThe rates of nonsynonymous substitution (Ka) to synonymous substitution (Ks) were calculated by comparing orthologous genes in different barley groups (wild vs. landrace and landrace vs. improved cultivar). The rates of evolution, properties, expression patterns, and diversity of positively selected genes (PSGs) and negatively selected genes (NSGs) were compared. PSGs evolved more rapidly, possessed fewer exons, and had lower GC content than NSGs; they were also shorter and had shorter intron, exon, and first exon lengths. Expression levels were lower, the tissue specificity of expression was higher, and codon usage bias was weaker for PSGs than for NSGs. Nucleotide diversity analysis revealed that PSGs have undergone a more severe genetic bottleneck than NSGs. Several candidate PSGs were involved in plant growth and development, which might make them as excellent targets for the molecular breeding of barley.ConclusionsOur comprehensive analysis of the evolutionary, structural, and functional divergence between PSGs and NSGs in barley provides new insight into the evolutionary trajectory of barley during domestication. Our findings also aid future functional studies of PSGs in barley.

Molecular characterization of short-day onion genotypes by intron length polymorphic (ILP) markers

Molecular characterization of short-day onion genotypes by intron length polymorphic (ILP) markers

Comparative Study of Starch Phosphorylase Genes and Encoded Proteins in Various Monocots and Dicots with Emphasis on Maize.

Starch phosphorylase (PHO) is a multimeric enzyme with two distinct isoforms: plastidial starch phosphorylase (PHO1) and cytosolic starch phosphorylase (PHO2). PHO1 specifically resides in the plastid, while PHO2 is found in the cytosol. Both play a critical role in the synthesis and degradation of starch. This study aimed to report the detailed structure, function, and evolution of genes encoding PHO1 and PHO2 and their protein ligand-binding sites in eight monocots and four dicots. “True” orthologs of PHO1 and PHO2 of Oryza sativa were identified, and the structure of the enzyme at the protein level was studied. The genes controlling PHO2 were found to be more conserved than those controlling PHO1; the variations were mainly due to the variable sequence and length of introns. Cis-regulatory elements in the promoter region of both genes were identified, and the expression pattern was analyzed. The real-time quantitative polymerase chain reaction indicated that PHO2 was expressed in all tissues with a uniform pattern of transcripts, and the expression pattern of PHO1 indicates that it probably contributes to the starch biosynthesis during seed development in Zea mays. Under abscisic acid (ABA) treatment, PHO1 was found to be downregulated in Arabidopsis and Hordeum vulgare. However, we found that ABA could up-regulate the expression of both PHO1 and PHO2 within 12 h in Zea mays. In all monocots and dicots, the 3D structures were highly similar, and the ligand-binding sites were common yet fluctuating in the position of aa residues.

CHERP Regulates the Alternative Splicing of pre-mRNAs in the Nucleus.

Calcium homeostasis endoplasmic reticulum protein (CHERP) is colocalized with the inositol 1,4,5-trisphosphate receptor (IP3R) in the endoplasmic reticulum or perinuclear region, and has been involved in intracellular calcium signaling. Structurally, CHERP carries the nuclear localization signal and arginine/serine-dipeptide repeats, like domain, and interacts with the spliceosome. However, the exact function of CHERP in the nucleus remains unknown. Here, we showed that poly(A)+ RNAs accumulated in the nucleus of CHERP-depleted U2OS cells. Our global analysis revealed that CHERP regulated alternative mRNA splicing events by interaction with U2 small nuclear ribonucleoproteins (U2 snRNPs) and U2 snRNP-related proteins. Among the five alternative splicing patterns analyzed, intron retention was the most frequently observed event. This was in accordance with the accumulation of poly(A)+ RNAs in the nucleus. Furthermore, intron retention and cassette exon choices were influenced by the strength of the 5′ or 3′ splice site, the branch point site, GC content, and intron length. In addition, CHERP depletion induced anomalies in the cell cycle progression into the M phase, and abnormal cell division. These results suggested that CHERP is involved in the regulation of alternative splicing.

Chinese pine (Pinus tabuliformis Carr.)

Pinus tabuliformis, commonly called Chinese pine, is a drought- and cold-tolerant heliophilous, indigenous conifer species, widespread in China. It has a giant genome comprising 25.4 Gb, with 12 huge chromosomes. The recently released nearly complete genome of P. tabuliformis provides new perspectives on genome expansion and adaptative and reproductive evolution of conifers. With an expansion of the genome, a multitude of long introns were observed in the P. tabuliformis genome. Interestingly, large genes with ultra-long introns tend to be expressed at higher levels, which suggests that intron length may serve as an evolutionary force in gymnosperms, though the underlying molecular mechanism is still unknown.

Characterization and phylogenetic analysis of the complete mitochondrial genome of the pathogenic fungus Ilyonectria destructans

Ilyonectria destructans is a pathogenic fungus causing root rot and other symptoms on trees and many crops. This paper analyses the mitochondrial genome of I. destructans and compares it with other published Nectriaceae mitogenomes. The I. destructans mitogenome appears as a circular DNA molecule of 42,895 bp and an overall GC content of 28.23%. It contains 28 protein-coding genes (15 core protein genes and 13 free-standing ORFs), two rRNAs and 27 tRNAs. The gene content and order were found to be conserved in the mitogenome of I. destructans and other Nectriaceae, although the genome size varies because of the variation in the number and length of intergenic regions and introns. For most core protein-coding genes in Nectriaceae species, Ka/Ks < 1 indicates purifying selection. Among some Nectriaceae representatives, only the rps3 gene was found under positive selection. Phylogenetic analyses based on nucleotide sequences of 15 protein-coding genes divided 45 Hypocreales species into six major clades matching the families Bionectriaceae, Cordycipitaceae, Clavicipitaceae, Ophiocordycipitaceae, Hypocreaceae and Nectriaceae. I. destructans appeared as a sister species to unidentified Ilyonectia sp., closely related to C. ilicicola, N. cinnabarina and a clad of ten Fusarium species and G. moniliformis. The complete mitogenome of I. destructans reported in the current paper will facilitate the study of epidemiology, biology, genetic diversity of the species and the evolution of family Nectriace and the Hypocreales order.