Regulation of micro- and small-exon retention and other splicing processes by GRP20 for flower development.

Pre-mRNA splicing is crucial for gene expression and depends on the spliceosome and splicing factors. Plant exons have an average size of ~180 nucleotides and typically contain motifs for interactions with spliceosome and splicing factors. Micro exons (<51 nucleotides) are found widely in eukaryotes and in genes for plant development and environmental responses. However, little is known about transcript-specific regulation of splicing in plants and about the regulators for micro exon splicing. Here we report that glycine-rich protein 20 (GRP20) is an RNA-binding protein and required for splicing of ~2,100 genes including those functioning in flower development and/or environmental responses. Specifically, GRP20 is required for micro-exon retention in transcripts of floral homeotic genes; these micro exons are conserved across angiosperms. GRP20 is also important for small-exon (51-100 nucleotides) splicing. In addition, GRP20 is required for flower development. Furthermore, GRP20 binds to poly-purine motifs in micro and small exons and a spliceosome component; both RNA binding and spliceosome interaction are important for flower development and micro-exon retention. Our results provide new insights into the mechanisms of micro-exon retention in flower development.

Karyotype and genome size variation in Delphinium subg. Anthriscifolium (Ranunculaceae).

Five taxa of Delphiniumsubg.Anthriscifolium have been karyologically studied through chromosome counting, chromosomal measurement, and karyotype symmetry. Each taxon that we investigated has a basic chromosome number of x = 8, D.anthriscifoliumvar.savatieri, D.anthriscifoliumvar.majus, D.ecalcaratum, and D.callichromum were diploid with 2n = 16, while D.anthriscifoliumvar.anthriscifolium was tetraploid with 2n = 32. Monoploid chromosome sets of the investigated diploid taxa contained 1 metacentric chromosome, 3 submetacentric chromosomes, and 4 subtelocentric chromosomes. Higher interchromosomal asymmetry (CVCL) was present in D.ecalcaratum and D.callichromum than in other taxa. The highest levels of intrachromosomal asymmetry (MCA) and heterogeneity in centromere position (CVCI) were found in D.anthriscifoliumvar.majus. Diploid and tetraploid genome sizes varied by 3.02-3.92 pg and 6.04-6.60 pg, respectively. Karyotype and genome size of D.anthriscifoliumvar.savatieri, D.anthriscifoliumvar.majus, D.callichromum, and D.ecalcaratum were reported for the first time. Finally, based on cytological and morphological data, the classification of Delphiniumanthriscifolium was revised.

Gelidocalamuszixingensis (Poaceae, Bambusoideae, Arundinarieae), a new species from southern China revealed by morphological and molecular evidence.

The genus Gelidocalamus T. H. Wen, endemic to southern China, is a small but taxonomically problematic genus of Arundinarieae (Poaceae, Bambusoideae). During field work, a population of Gelidocalamus from Zixing, Hunan, was discovered, appearing to be distinct from our previously identified collection. Comparisons of the population of Zixing were performed by using scanning electron microscopy (SEM) and a plastid genome-based phylogeny. Morphologically, it was mostly similar to G.multifolius, but differed by culm leaf erect with densely white pubescence, apical branch sheath much longer than the internodes and foliage leaf larger. Phylogenetically, the new species was well-supported as a sister to the clade of G.multifolius + G.tessellatus, and the above three taxa were clustered in the Shibataea clade (IV) of Arundinarieae. Thus, the new species, formally named as Gelidocalamuszixingensis W.G.Zhang, G.Y.Yang & C.K.Wang, was described and illustrated herein.

The nearly complete assembly of the Cercis chinensis genome and Fabaceae phylogenomic studies provide insights into new gene evolution.

Fabaceae is a large family of angiosperms with high biodiversity that contains a variety of economically important crops and model plants for the study of biological nitrogen fixation. Polyploidization events have been extensively studied in some Fabaceae plants, but the occurrence of new genes is still concealed, owing to a lack of genomic information on certain species of the basal clade of Fabaceae. Cercis chinensis (Cercidoideae) is one such species; it diverged earliest from Fabaceae and is essential for phylogenomic studies and new gene predictions in Fabaceae. To facilitate genomic studies on Fabaceae, we performed genome sequencing of C. chinensis and obtained a 352.84 Mb genome, which was further assembled into seven pseudochromosomes with 30 612 predicted protein-coding genes. Compared with other legume genomes, that of C. chinensis exhibits no lineage-specific polyploidization event. Further phylogenomic analyses of 22 legumes and 11 other angiosperms revealed that many gene families are lineage specific before and after the diversification of Fabaceae. Among them, dozens of genes are candidates for new genes that have evolved from intergenic regions and are thus regarded as de novo-originated genes. They differ significantly from established genes in coding sequence length, exon number, guanine-cytosine content, and expression patterns among tissues. Functional analysis revealed that many new genes are related to asparagine metabolism. This study represents an important advance in understanding the evolutionary pattern of new genes in legumes and provides a valuable resource for plant phylogenomic studies.

Comparative phylogenomic analyses and co-expression gene network reveal insights in flowering time and aborted meiosis in woody bamboo, Bambusa oldhamii 'Xia Zao' ZSX.

Woody bamboos have peculiar flowering characteristics with intervals ranging from several years to more than 100 years. Elucidating flowering time and reproductive development in bamboo could be beneficial for both humans and wildlife. To identity the mechanisms responsible for flowering time and embryo abortion in Bambusa oldhamii 'Xia Zao' ZSX, a transcriptome sequencing project was initiated to characterize the genes involved in developing flowers in this bamboo species. Morphological studies showed that pollen abortion in this bamboo species was mainly caused by a delay in tapetum degradation and abnormal meiotic process. Differential expression (DE) and optimized hierarchical clustering analyses identified three of nine gene expression clusters with decreasing expression at the meiosis of flowering stages. Together with enriched Gene Ontology Biological Process terms for meiosis, this suggests that their expression pattern may be associated with aborted meiosis in B. oldhamii 'Xia Zao'. Moreover, our large-scale phylogenomic analyses comparing meiosis-related transcripts of B. oldhamii 'Xia Zao' with well annotated genes in 22 representative angiosperms and sequence evolution analyses reveal two core meiotic genes NO EXINE FORMATION 1 (NFE1) and PMS1 with nonsense mutations in their coding regions, likely providing another line of evidence supporting embryo abortion in B. oldhamii 'Xia Zao'. Similar analyses, however, reveal conserved sequence evolution in flowering pathways such as LEAFY (LFY) and FLOWERING LOCUS T (FT). Seventeen orthogroups associated with flowering were identified by DE analyses between nonflowering and flowering culm buds. Six regulators found primarily in several connected network nodes of the photoperiod pathway were confirmed by mapping to the flowering time network in rice, such as Heading date (Hd3a) and Rice FT-like 1 (RFT1) which integrate upstream signaling into the downstream effectors. This suggests the existence of an intact photoperiod pathway is likely the key regulators that switch on/off flowering in B. oldhamii 'Xia Zao'.

A spatiotemporal atlas of organogenesis in the development of orchid flowers.

Development of floral organs exhibits complex molecular mechanisms involving the co-regulation of many genes specialized and precisely functioning in various tissues and developing stages. Advance in spatial transcriptome technologies allows for quantitative measurement of spatially localized gene abundance making it possible to bridge complex scenario of flower organogenesis with genome-wide molecular phenotypes. Here, we apply the 10× Visium technology in the study of the formation of floral organs through development in an orchid plant, Phalaenopsis Big Chili. Cell-types of early floral development including inflorescence meristems, primordia of floral organs and identity determined tissues, are recognized based on spatial expression distribution of thousands of genes in high resolution. In addition, meristematic cells on the basal position of floral organs are found to continuously function in multiple developmental stages after organ initiation. Particularly, the development of anther, which primordium starts from a single spot to multiple differentiated cell-types in later stages including pollinium and other vegetative tissues, is revealed by well-known MADS-box genes and many other downstream regulators. The spatial transcriptome analyses provide comprehensive information of gene activity for understanding the molecular architecture of flower organogenesis and for future genomic and genetic studies of specific cell-types.

Characterization of the complete chloroplast genome of Pterocarya macroptera var. delavayi (Juglandaceae).

In this study, the complete chloroplast genome sequence of Pterocarya macroptera var. delavayi was reported and characterized. The chloroplast genome is 160,168 bp in length, and consists the typical quadripartite structure, a pair of inverted repeats (IRs, 26,007 bp) separated by a large single-copy region (89,701 bp) and a small single-copy region (18,453 bp). A total of 136 unique genes were predicted, including 88 protein-coding genes, 40 tRNA genes, and 8 rRNA genes. The GC content of the chloroplast genome is 36.2%. Phylogenetic analysis confirmed the close relationship between Pterocarya and Juglans.

The complete chloroplast genome of Phyllostachys glauca (Bambusoideae), a dominant bamboo species in limestone mountains endemic to China.

Phyllostachys glauca is a dominant species in limestone mountains endemic to China. Here, we characterized its complete chloroplast genome. It is a circular DNA molecule of 139,689 bp in length, including a pair of 21,798 bp inverted repeats (IRs), a 12,872 bp small single-copy (SSC) region and an 83221 bp large single-copy (LSC) region. The total GC content of P. glauca chloroplast genome was 38.9%, and it encodes a total of 137 functional genes, including 89 protein-coding genes, 40 tRNA genes, and 8 rRNA genes. The phylogenetic analysis shows that P. glauca is highly clustered in the Phyllostachys clade (V), sister to the lineage of P. nigra var. henonis + P. sulphurea.

Chloroplast genomic data provide new and robust insights into the phylogeny and evolution of the Ranunculaceae.

The family Ranunculaceae, a member of early-diverging eudicots that is increasingly being used as a model for the study of plant developmental evolution, has been the focus of systematic studies for centuries. Recent studies showed that the family can be divided into 14 tribes, with Glaucideae, Hydrastideae, and Coptideae being the successive basal-most lineages. The relationships among the remaining 11 tribes, however, remain controversial, so that a clear picture of character evolution within the family is still lacking. In this study, by sequencing, assembling and analyzing the chloroplast (cp) genomes of 35 species representing 31 genera of the 14 tribes, we resolved the relationships among the tribes and genera of the Ranunculaceae and clarified several long-standing controversies. We found that many of the characters that were once widely used for taxonomic and systematic considerations were actually results of parallel, convergent or even reversal evolution, suggestive of unreliability. We also found that the family has likely experienced two waves of radiative evolution, through which most of the extant tribes and genera were generated. Notably, both waves of radiation were correlated with the increase in the temperature of the earth, suggesting that global warming may have been the driving force of the radiation events. Based on these observations, we hypothesize that global warming and the associated decrease in the type and number of animal pollinators may have been the main reason why taxa with highly elaborate petals as well as those without petal were generated during each of the two waves of radiation.

Complete chloroplast genome of a rare deciduous tree species, Sinomanglietia glauca (Magnoliaceae).

The complete chloroplast genome of a rare deciduous tree species with ornamental value, Sinomanglietia glauca, was first determined. It was 160,170 bp in length, including a pair of inverted repeat (IR, 26,567 bp) regions separated by a small single copy (SSC, 18,842 bp) sequence and a large single copy (LSC, 88,194 bp) sequence. The chloroplast genome contained 132 genes, consisting of 87 CDS, 8 rRNA genes, and 37 tRNA genes. Thirty-four SSR sites were detected in the chloroplast genome. The phylogenetic analysis revealed that all sampled Manglietia species were clustered together, and S. glauca was placed as sister to the clade Manglietia, indicated that the genus Sinomanglietia may be legitimate and should be recovered.

The complete chloroplast genome sequence of Gelidocalamus xunwuensis (Bambusoideae: Arundinarieae): a shrubby bamboo endemic to China.

The complete chloroplast genome sequence of Gelidocalamus xunwuensis, firstly determined here, is 139,705 bp in length, inclusive of a pair of inverted repeat (IR, 21,817 bp) regions separated by a small single copy (SSC, 12,803 bp) and a large single copy (LSC, 83,268 bp). It contains 132 genes, such as 85 CDS, 8 rRNA genes, and 39 tRNA genes, respectively. The phylogenetic analysis shows that G. xunwuensis is highly clustered in the shibataea clade (III) of Arundinarieae, sister to the clade of G. tessellatus + Ferrocalamus rimosivaginus.

A well-resolved fern nuclear phylogeny reveals the evolution history of numerous transcription factor families.

Ferns account for 80% of nonflowering vascular plant species and are the sister lineage of seed plants. Recent molecular phylogenetics have greatly advanced understanding of fern tree of life, but relationships among some major lineages remain unclear. To better resolve the phylogenetic relationships of ferns, we generated transcriptomes from 125 ferns and two lycophytes, with three additional public datasets, to represent all 11 orders and 85% of families of ferns. Our nuclear phylogeny provides strong supports for the monophyly of all four subclasses and nearly all orders and families, and for relationships among these lineages. The only exception is Gleicheniales, which was highly supported as being paraphyletic with Dipteridaceae sister to a clade with Gleicheniaceae + Hymenophyllales. In addition, new and strongly supported phylogenetic relationships are found for suborders and families in Polypodiales. We provide the first dated fern phylogenomic tree using many nuclear genes from a large majority of families, with an estimate for separation of the ancestors of ferns and seed plants in early Devonian at ∼400 Mya and subsequent gradual divergences of fern orders from ∼380 to 200 Mya. Moreover, the newly obtained fern phylogeny provides a framework for gene family analyses, which indicate that the vast majority of transcription factor families found in seed plants were already present in the common ancestor of extant vascular plants. In addition, fern transcription factor genes show similar duplication patterns to those in seed plants, with some showing stable copy number and others displaying independent expansions in both ferns and seed plants. This study provides a robust phylogenetic and gene family evolution framework, as well as rich molecular resources for understanding the morphological and functional evolution in ferns.

Degradation of unmethylated miRNA/miRNA*s by a DEDDy-type 3' to 5' exoribonuclease Atrimmer 2 in Arabidopsis.

The 3' end methylation catalyzed by HUA Enhancer 1 (HEN1) is a crucial step of small RNA stabilization in plants, yet how unmethylated small RNAs undergo degradation remains largely unknown. Using a reverse genetic approach, we here show that Atrimmer 2 (ATRM2), a DEDDy-type 3' to 5' exoribonuclease, acts in the degradation of unmethylated miRNAs and miRNA*s in Arabidopsis Loss-of-function mutations in ATRM2 partially suppress the morphological defects caused by HEN1 malfunction, with restored levels of a subset of miRNAs and receded expression of corresponding miRNA targets. Dysfunction of ATRM2 has negligible effect on miRNA trimming, and further increase the fertility of hen1 heso1 urt1, a mutant with an almost complete abolishment of miRNA uridylation, indicating that ATRM2 may neither be involved in 3' to 5' trimming nor be the enzyme that specifically degrades uridylated miRNAs. Notably, the fold changes of miRNAs and their corresponding miRNA*s were significantly correlated in hen1 atrm2 versus hen1 Unexpectedly, we observed a marked increase of 3' to 5' trimming of several miRNA*s but not miRNAs in ATRM2 compromised backgrounds. These data suggest an action of ATRM2 on miRNA/miRNA* duplexes, and the existence of an unknown exoribonuclease for specific trimming of miRNA*. This asymmetric effect on miRNA/miRNA* is likely related to Argonaute (AGO) proteins, which can distinguish miRNAs from miRNA*s. Finally, we show that ATRM2 colocalizes and physically interacts with Argonaute 1 (AGO1). Taken together, our results suggest that ATRM2 may be involved in the surveillance of unmethylated miRNA/miRNA* duplexes during the initiation step of RNA-induced silencing complex assembly.

Widespread Whole Genome Duplications Contribute to Genome Complexity and Species Diversity in Angiosperms.

Gene duplications provide evolutionary potentials for generating novel functions, while polyploidization or whole genome duplication (WGD) doubles the chromosomes initially and results in hundreds to thousands of retained duplicates. WGDs are strongly supported by evidence commonly found in many species-rich lineages of eukaryotes, and thus are considered as a major driving force in species diversification. We performed comparative genomic and phylogenomic analyses of 59 public genomes/transcriptomes and 46 newly sequenced transcriptomes covering major lineages of angiosperms to detect large-scale gene duplication events by surveying tens of thousands of gene family trees. These analyses confirmed most of the previously reported WGDs and provided strong evidence for novel ones in many lineages. The detected WGDs supported a model of exponential gene loss during evolution with an estimated half-life of approximately 21.6 million years, and were correlated with both the emergence of lineages with high degrees of diversification and periods of global climate changes. The new datasets and analyses detected many novel WGDs widely spread during angiosperm evolution, uncovered preferential retention of gene functions in essential cellular metabolisms, and provided clues for the roles of WGD in promoting angiosperm radiation and enhancing their adaptation to environmental changes.

MeioBase: a comprehensive database for meiosis.

Meiosis is a special type of cell division process necessary for the sexual reproduction of all eukaryotes. The ever expanding meiosis research calls for an effective and specialized database that is not readily available yet. To fill this gap, we have developed a knowledge database MeioBase (http://meiosis.ibcas.ac.cn), which is comprised of two core parts, Resources and Tools. In the Resources part, a wealth of meiosis data collected by curation and manual review from published literatures and biological databases are integrated and organized into various sections, such as Cytology, Pathway, Species, Interaction, and Expression. In the Tools part, some useful tools have been integrated into MeioBase, such as Search, Download, Blast, Comparison, My Favorites, Submission, and Advice. With a simplified and efficient web interface, users are able to search against the database with gene model IDs or keywords, and batch download the data for local investigation. We believe that MeioBase can greatly facilitate the researches related to meiosis.

Disruption of the petal identity gene APETALA3-3 is highly correlated with loss of petals within the buttercup family (Ranunculaceae).

Absence of petals, or being apetalous, is usually one of the most important features that characterizes a group of flowering plants at high taxonomic ranks (i.e., family and above). The apetalous condition, however, appears to be the result of parallel or convergent evolution with unknown genetic causes. Here we show that within the buttercup family (Ranunculaceae), apetalous genera in at least seven different lineages were all derived from petalous ancestors, indicative of parallel petal losses. We also show that independent petal losses within this family were strongly associated with decreased or eliminated expression of a single floral organ identity gene, APETALA3-3 (AP3-3), apparently owing to species-specific molecular lesions. In an apetalous mutant of Nigella, insertion of a transposable element into the second intron has led to silencing of the gene and transformation of petals into sepals. In several naturally occurring apetalous genera, such as Thalictrum, Beesia, and Enemion, the gene has either been lost altogether or disrupted by deletions in coding or regulatory regions. In Clematis, a large genus in which petalous species evolved secondarily from apetalous ones, the gene exhibits hallmarks of a pseudogene. These results suggest that, as a petal identity gene, AP3-3 has been silenced or down-regulated by different mechanisms in different evolutionary lineages. This also suggests that petal identity did not evolve many times independently across the Ranunculaceae but was lost in numerous instances. The genetic mechanisms underlying the independent petal losses, however, may be complex, with disruption of AP3-3 being either cause or effect.

Divergence of duplicate genes in exon-intron structure.

Gene duplication plays key roles in organismal evolution. Duplicate genes, if they survive, tend to diverge in regulatory and coding regions. Divergences in coding regions, especially those that can change the function of the gene, can be caused by amino acid-altering substitutions and/or alterations in exon-intron structure. Much has been learned about the mode, tempo, and consequences of nucleotide substitutions, yet relatively little is known about structural divergences. In this study, by analyzing 612 pairs of sibling paralogs from seven representative gene families and 300 pairs of one-to-one orthologs from different species, we investigated the occurrence and relative importance of structural divergences during the evolution of duplicate and nonduplicate genes. We found that structural divergences have been very prevalent in duplicate genes and, in many cases, have led to the generation of functionally distinct paralogs. Comparisons of the genomic sequences of these genes further indicated that the differences in exon-intron structure were actually accomplished by three main types of mechanisms (exon/intron gain/loss, exonization/pseudoexonization, and insertion/deletion), each of which contributed differently to structural divergence. Like nucleotide substitutions, insertion/deletion and exonization/pseudoexonization occurred more or less randomly, with the number of observable mutational events per gene pair being largely proportional to evolutionary time. Notably, however, compared with paralogs with similar evolutionary times, orthologs have accumulated significantly fewer structural changes, whereas the amounts of amino acid replacements accumulated did not show clear differences. This finding suggests that structural divergences have played a more important role during the evolution of duplicate than nonduplicate genes.

Petal-specific subfunctionalization of an APETALA3 paralog in the Ranunculales and its implications for petal evolution.

• The petals of the lower eudicot family Ranunculaceae are thought to have been derived many times independently from stamens. However, investigation of the genetic basis of their identity has suggested an alternative hypothesis: that they share a commonly inherited petal identity program. This theory is based on the fact that an ancient paralogous lineage of APETALA3 (AP3) in the Ranunculaceae appears to have a conserved, petal-specific expression pattern. • Here, we have used a combination of approaches, including RNAi, comparative gene expression and molecular evolutionary studies, to understand the function of this petal-specific AP3 lineage. • Functional analysis of the Aquilegia locus AqAP3-3 has demonstrated that the paralog is required for petal identity with little contribution to the identity of the other floral organs. Expanded expression studies and analyses of molecular evolutionary patterns provide further evidence that orthologs of AqAP3-3 are primarily expressed in petals and are under higher purifying selection across the family than the other AP3 paralogs. • Taken together, these findings suggest that the AqAP3-3 lineage underwent progressive subfunctionalization within the order Ranunculales, ultimately yielding a specific role in petal identity that has probably been conserved, in stark contrast with the multiple independent origins predicted by botanical theories.

The SEPALLATA-like gene OsMADS34 is required for rice inflorescence and spikelet development.

Grass plants develop distinct inflorescences and spikelets that determine grain yields. However, the mechanisms underlying the specification of inflorescences and spikelets in grasses remain largely unknown. Here, we report the biological role of one SEPALLATA (SEP)-like gene, OsMADS34, in controlling the development of inflorescences and spikelets in rice (Oryza sativa). OsMADS34 encodes a MADS box protein containing a short carboxyl terminus without transcriptional activation activity in yeast cells. We demonstrate the ubiquitous expression of OsMADS34 in roots, leaves, and primordia of inflorescence and spikelet organs. Compared with the wild type, osmads34 mutants developed altered inflorescence morphology, with an increased number of primary branches and a decreased number of secondary branches. In addition, osmads34 mutants displayed a decreased spikelet number and altered spikelet morphology, with lemma/leaf-like elongated sterile lemmas. Moreover, analysis of the double mutant osmads34 osmads1 suggests that OsMADS34 specifies the identities of floral organs, including the lemma/palea, lodicules, stamens, and carpel, in combination with another rice SEP-like gene, OsMADS1. Collectively, our study suggests that the origin and diversification of OsMADS34 and OsMADS1 contribute to the origin of distinct grass inflorescences and spikelets.