Tree Genome Research Articles

Identification and characterization of MAGO and Y14 genes in Hevea brasiliensis.

Mago nashi (MAGO) and Y14 proteins are highly conserved among eukaryotes. In this study, we identified two MAGO (designated as HbMAGO1 andHbMAGO2) and two Y14 (designated as HbY14aand HbY14b) genes in the rubber tree (Hevea brasiliensis) genome annotation. Multiple amino acid sequence alignments predicted that HbMAGO and HbY14 proteins are structurally similar to homologous proteins from other species. Tissue-specific expression profiles showed that HbMAGO and HbY14 genes were expressed in at least one of the tissues (bark, flower, latex, leaf and root) examined. HbMAGOs and HbY14s were predominately located in the nucleus and were found to interact in yeast two-hybrid analysis (YTH) and bimolecular fluorescence complementation (BiFC) assays. HbMAGOs and HbY14s showed the highest transcription in latex and were regulated by ethylene and jasmonate. Interaction between HbMAGO2 and gp91phox (a large subunit of nicotinamide adenine dinucleotide phosphate) was identified using YTH and BiFC assays. These findings suggested that HbMAGO may be involved in the aggregation of rubber particles in H. brasiliensis.

Forest tree genomics: 10 achievements from the past 10 years and future prospects

Key message This review highlights some of the discoveries and applications made possible by “omics” technologies over the last 10 years and provides perspectives for pioneering research to increase our understanding of tree biology.

Ghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses.

BackgroundFungi play critical roles in many ecosystems, cause serious diseases in plants and animals, and pose significant threats to human health and structural integrity problems in built environments. While most fungal diversity remains unknown, the development of PCR primers for the internal transcribed spacer (ITS) combined with next-generation sequencing has substantially improved our ability to profile fungal microbial diversity. Although the high sequence variability in the ITS region facilitates more accurate species identification, it also makes multiple sequence alignment and phylogenetic analysis unreliable across evolutionarily distant fungi because the sequences are hard to align accurately. To address this issue, we created ghost-tree, a bioinformatics tool that integrates sequence data from two genetic markers into a single phylogenetic tree that can be used for diversity analyses. Our approach starts with a “foundation” phylogeny based on one genetic marker whose sequences can be aligned across organisms spanning divergent taxonomic groups (e.g., fungal families). Then, “extension” phylogenies are built for more closely related organisms (e.g., fungal species or strains) using a second more rapidly evolving genetic marker. These smaller phylogenies are then grafted onto the foundation tree by mapping taxonomic names such that each corresponding foundation-tree tip would branch into its new “extension tree” child.ResultsWe applied ghost-tree to graft fungal extension phylogenies derived from ITS sequences onto a foundation phylogeny derived from fungal 18S sequences. Our analysis of simulated and real fungal ITS data sets found that phylogenetic distances between fungal communities computed using ghost-tree phylogenies explained significantly more variance than non-phylogenetic distances. The phylogenetic metrics also improved our ability to distinguish small differences (effect sizes) between microbial communities, though results were similar to non-phylogenetic methods for larger effect sizes.ConclusionsThe Silva/UNITE-based ghost tree presented here can be easily integrated into existing fungal analysis pipelines to enhance the resolution of fungal community differences and improve understanding of these communities in built environments. The ghost-tree software package can also be used to develop phylogenetic trees for other marker gene sets that afford different taxonomic resolution, or for bridging genome trees with amplicon trees.Availabilityghost-tree is pip-installable. All source code, documentation, and test code are available under the BSD license at https://github.com/JTFouquier/ghost-tree.Electronic supplementary materialThe online version of this article (doi:10.1186/s40168-016-0153-6) contains supplementary material, which is available to authorized users.

Breeding, genetics, and genomics of fruit trees.

Breeding, genetics, and genomics of fruit trees.

Genomics of pear and other Rosaceae fruit trees.

The family Rosaceae includes many economically important fruit trees, such as pear, apple, peach, cherry, quince, apricot, plum, raspberry, and loquat. Over the past few years, whole-genome sequences have been released for Chinese pear, European pear, apple, peach, Japanese apricot, and strawberry. These sequences help us to conduct functional and comparative genomics studies and to develop new cultivars with desirable traits by marker-assisted selection in breeding programs. These genomics resources also allow identification of evolutionary relationships in Rosaceae, development of genome-wide SNP and SSR markers, and construction of reference genetic linkage maps, which are available through the Genome Database for the Rosaceae website. Here, we review the recent advances in genomics studies and their practical applications for Rosaceae fruit trees, particularly pear, apple, peach, and cherry.

The complete mitochondrial genome sequence of Ptyas mucosus

The complete mitochondrial genome sequence of the Ptyas mucosus was sequenced and reported for the first time using muscle tissue. The total length is 17 151 bp and sequence analysis showed its structure is in accordance with other snakes. The complete mitochondrial genome contains 2 rRNA genes, 21 tRNA genes, 13 protein-coding genes (PCGs), 2 control regions and 1 putative origin of L-strand replication. The gene order and nucleotide composition of P. mucosus are very similar with E. bimaculata, E. anomala and E. schrenckii. A phylogenetic tree of mitochondrial genomes indicated P. mucosus had the most closely relationship with E. bimaculata, and formed a monophyletic group with E. bimaculata, E. anomala and E. schrenckii.

Researches of pear tree (Pyrus spp.) genomics

배나무는 원산지와 분화방향에 따라 유럽, 미국, 호주 등에서 주로 재배되는 서양배와 중국, 일본, 한국 등 동남 아시아 지역을 중심으로 분포 및 재배되고 있는 동양배로 구분된다. 17개의 기본염색체를 가진 배나무는 대부분 이배성(2n=2x=34)이며, 단일 S 유전자좌에 의해 조절되는 자가불화합성과 과수 작물의 주요 특징인 유년성으로 인해 유전 연구 및 정밀한 품종 육성에 큰 제한을 받고 있다. 배나무속 식물의 유전연구는 분자생물학 관련 기술의 발달로 다양한 형태의 분자 표지의 개발이 이루어짐과 동시에 유연관계분석, 유전자지도작성, QTL 분석과 같은 다양한 유전연구에 활발히 이용되었다. 또한 배나무의 유전자지도는 병 저항성이나 다양한 유용형질과 연관된 QTL 확인을 위한 연구로 이어지고 있다. 대량 병렬 반응 및 다중처리를 토대로 획기적인 염기서열 분석 비용의 감소를 이뤄낸 NGS 기술은 대용량, 고효율, 저비용으로 식물 유전체 해독을 가능하게 하여, 중국배 'Danshansuli'와 유럽배 'Bartlett'에서 유전체 분석이 완료되었다. 최근 국내에서는 황금배, 청실리 및 미니배의 resequencing 및 GBS를 통한 SNP 탐색 등의 연구를 통해 화기, 숙기 당도 등 농업적으로 유용형질에 대한 게놈전체 연관분석을 수행하고 있다. 【Based on the place of its origin, pear tree (Pyrus spp.) is largely divided into European pears (P. communis, cultivated mainly in Europe and the U.S.) and Asian pears (P. pyrifolia, P. bretschneideri, and P. ussuriensis, distributed and grown in East Asian countries including China, Japan, and Korea). Most pear trees have 17 chromosomes (diploidy, 2n=2x=34). Their genetic studies and precise cultivar breeding are highly restricted by conditions such as self-incompatibility controlled by S-locus and juvenility as one major character of fruit crops. Genetic studies on Pyrus have been promoted by the development of various molecular markers. These markers are being utilized actively in various genetic studies, including genetic relationship analysis, genetic mapping, and QTL analysis. In addition, research on pear genetic linkage maps has been extended to studies for the identification of QTL for target traits such as disease resistance and genetic loci of useful traits. NGS technology has radically reduced sequencing expenses based on massive parallel reactions to enable high-capacity and high-efficiency. NGS based genome analyses have been completed for Chinese pear 'Danshansuli' and European pear 'Bartlett'. In Korea, GWAS for agricultural valuable traits such as floral structure, ripening, and total soluble contents have been conducted through resequencing. GBS has been performed for 'Whangkeumbae', 'Cheongsilri', and 'Minibae'.】

Current Status of Knowledge and Research Perspectives in Korean Pear Genomics

The pear (Pyrus spp.) is most important fruit crop in the world. The genus Pyrus belongs to the subfamily Maloideae in the Rosaceae family and contains at least 22 primary species; however, only a few species, including P. pyrifolia, P. ussuriensis, P. bretschneideri, and P. communis have been utilized for fruit production. In Korea, awareness of the importance of the fruit industry and fruit tree breeding is low, and there is little support for genetic and genomic studies of fruit trees. In foreign countries, studies have focused on obtaining genomic information of fruit crops and the development of important agronomic trait-related molecular markers, providing a genomic framework for fruit tree breeding. Although Korea does not actively participate in research on the genomics of fruit trees, it is not far behind other countries in terms of technology and is therefore still competitive in research and development. The resequencing of 'Whangkeumbae' and 'Minibae' pears has been performed using the Illumina Hiseq 2000 platform as a part of the Biogreen 21 project, offering novel, rapid methods for identification of molecular marker, such as single nucleotide polymorphisms, insertion-deletions, and simple sequence repeats, through next-generation sequencing (NGS) technology. These NGS-based molecular markers are useful for genetic studies of Asian pears, e.g., for construction of genetic linkage maps, mapping of quantitative trait loci, and marker-assisted selection.

Complete Genome Sequence of a Chinese Isolate of Melon Necrotic Spot Virus and its Phylogenetic Relationship

The full-length nucleotide sequence and genomic organization of a melon necrotic spot virus isolate from Haimen, China (MNSV-HM), were determined. The MNSV-HM genome consists of a positive sense single-stranded RNA, 4267 nt in length, with at least five open reading frames (ORFs) encoding p29, p89, p42, and two small 7-kDa proteins (p7A and p7B). p89 shares a common start codon with p29 and continues through the amber stop codon of p29 to produce an 89-kDa protein. The p7A ORF terminates in an amber codon whose read-through could generate a 14-kDa protein. Phylogenetic analyses based on the p42 amino acid sequence and complete genomic sequence placed MNSV-HM and Spanish isolates of the virus in a major cluster, indicating a close genetic relationship. In conclusion, we report the full-length sequence of MNSV-HM and its translation strategy. The obtained genomic organization and phylogenetic trees indicate that MNSV-HM belongs to the MNSV genus Carmovirus. To the best of our knowledge, this is the first demonstration of the complete nucleotide sequence of an MNSV isolate from China.

Genome-wide identification of rubber tree (Hevea brasiliensis Muell. Arg.) aquaporin genes and their response to ethephon stimulation in the laticifer, a rubber-producing tissue.

BackgroundNatural rubber, an important industrial raw material, is specifically synthesized in laticifers located inside the rubber tree (Hevea brasiliensis Muell. Arg.) trunk. Due to the absence of plasmodesmata, the laticifer water balance is mediated by aquaporins (AQPs). However, to date, the characterization of H. brasiliensis AQPs (HbAQPs) is still in its infancy.ResultsIn this study, 51 full-length AQP genes were identified from the rubber tree genome. The phylogenetic analysis assigned these AQPs to five subfamilies, including 15 plasma membrane intrinsic proteins (PIPs), 17 tonoplast intrinsic proteins (TIPs), 9 NOD26-like intrinsic proteins (NIPs), 4 small basic intrinsic proteins (SIPs) and 6 X intrinsic proteins (XIPs). Functional prediction based on the analysis of the aromatic/arginine (ar/R) selectivity filter, Froger’s positions and specificity-determining positions (SDPs) showed a remarkable difference in substrate specificity among subfamilies. Homology analysis supported the expression of 44 HbAQP genes in at least one of the examined tissues. Furthermore, deep sequencing of the laticifer transcriptome in the form of latex revealed a key role of several PIP subfamily members in the laticifer water balance, and qRT-PCR analysis showed diverse expression patterns of laticifer-expressed HbAQP genes upon ethephon treatment, a widely-used practice for the stimulation of latex yield.ConclusionsThis study provides an important genetic resource of HbAQP genes, which will be useful to improve the water use efficiency and latex yield of Hevea.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2152-6) contains supplementary material, which is available to authorized users.

Evolutionary history of Apocheima cinerarius (Lepidoptera: Geometridae), a female flightless moth in northern China

The alterations in the phylogeographical structures of insects in response to the uplift of the Qinghai–Tibet Plateau and the Quaternary glaciations in eastern Asia, particularly in northern China, remain largely unknown. In this study, we selected Apocheima cinerarius, a moth with flightless females, using molecular data (complete mitochondrial genomes and nuclear data) and ecological niche modelling (ENM) to investigate the effects of paleoclimatic changes on the evolutionary history of insects in the area of northern China. The phylogenetic tree of complete mitochondrial genomes indicated that there were two lineages, the western and eastern lineages. The nuclear gene analyses also detected unique haplotypes in each lineage. Time of the most recent common ancestor (TMRCA) of the two lineages was approximately in Early–Middle Pleistocene. Bayesian skyline plots revealed that the western lineage underwent a population expansion event after the Last Glacial Maximum, whereas the eastern lineage underwent expansion between the Last Interglacial and the Last Glacial Maximum. Our results suggest that A. cinerarius expanded eastward from western sites until the moth was distributed across the entire region of northern China. Then, A. cinerarius underwent contraction into isolated glacial refugia followed by subsequent expansion driven by Pleistocene climate changes, which established a narrow sympatric area. Our results indicate that the Quaternary environmental fluctuations had profound influences on the diversification and demography of an insect in northern China, and the same species in north‐western China and north‐eastern China have different demographic histories.

An assembly and alignment-free method of phylogeny reconstruction from next-generation sequencing data.

BackgroundNext-generation sequencing technologies are rapidly generating whole-genome datasets for an increasing number of organisms. However, phylogenetic reconstruction of genomic data remains difficult because de novo assembly for non-model genomes and multi-genome alignment are challenging.ResultsTo greatly simplify the analysis, we present an Assembly and Alignment-Free (AAF) method (https://sourceforge.net/projects/aaf-phylogeny) that constructs phylogenies directly from unassembled genome sequence data, bypassing both genome assembly and alignment. Using mathematical calculations, models of sequence evolution, and simulated sequencing of published genomes, we address both evolutionary and sampling issues caused by direct reconstruction, including homoplasy, sequencing errors, and incomplete sequencing coverage. From these results, we calculate the statistical properties of the pairwise distances between genomes, allowing us to optimize parameter selection and perform bootstrapping. As a test case with real data, we successfully reconstructed the phylogeny of 12 mammals using raw sequencing reads. We also applied AAF to 21 tropical tree genome datasets with low coverage to demonstrate its effectiveness on non-model organisms.ConclusionOur AAF method opens up phylogenomics for species without an appropriate reference genome or high sequence coverage, and rapidly creates a phylogenetic framework for further analysis of genome structure and diversity among non-model organisms.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1647-5) contains supplementary material, which is available to authorized users.

A unifying experimental design for dissecting tree genomes.

Linkage mapping and association mapping are adopted as an approach of choice for dissecting complex traits, but each shows a limitation when used alone. We propose an open-pollinated (OP) family design to integrate these two approaches into an organizing framework. The design unifies the strengths of population and quantitative genetic studies for evolutionary inference and high-resolution gene mapping. It particularly suits genome dissection of forest trees given their extant populations that are mostly undomesticated.

Across language families: Genome diversity mirrors linguistic variation within Europe.

ABSTRACT Objectives: The notion that patterns of linguistic and biological variation may cast light on each other and on population histories dates back to Darwin's times; yet, turning this intuition into a proper research program has met with serious methodological difficulties, especially affecting language comparisons. This article takes advantage of two new tools of comparative linguistics: a refined list of Indo‐European cognate words, and a novel method of language comparison estimating linguistic diversity from a universal inventory of grammatical polymorphisms, and hence enabling comparison even across different families. We corroborated the method and used it to compare patterns of linguistic and genomic variation in Europe. Materials and Methods: Two sets of linguistic distances, lexical and syntactic, were inferred from these data and compared with measures of geographic and genomic distance through a series of matrix correlation tests. Linguistic and genomic trees were also estimated and compared. A method (Treemix) was used to infer migration episodes after the main population splits. Results: We observed significant correlations between genomic and linguistic diversity, the latter inferred from data on both Indo‐European and non‐Indo‐European languages. Contrary to previous observations, on the European scale, language proved a better predictor of genomic differences than geography. Inferred episodes of genetic admixture following the main population splits found convincing correlates also in the linguistic realm. Discussion: These results pave the ground for previously unfeasible cross‐disciplinary analyses at the worldwide scale, encompassing populations of distant language families. Am J Phys Anthropol 157:630–640, 2015. © 2015 Wiley Periodicals, Inc.

Construction of a high-density integrated genetic linkage map of rubber tree (Hevea brasiliensis) using genotyping-by-sequencing (GBS).

Construction of linkage maps is crucial for genetic studies and marker-assisted breeding programs. Recent advances in next generation sequencing technologies allow for the generation of high-density linkage maps, especially in non-model species lacking extensive genomic resources. Here, we constructed a high-density integrated genetic linkage map of rubber tree (Hevea brasiliensis), the sole commercial producer of high-quality natural rubber. We applied a genotyping-by-sequencing (GBS) technique to simultaneously discover and genotype single nucleotide polymorphism (SNP) markers in two rubber tree populations. A total of 21,353 single nucleotide substitutions were identified, 55% of which represented transition events. GBS-based genetic maps of populations P and C comprised 1704 and 1719 markers and encompassed 2041 cM and 1874 cM, respectively. The average marker densities of these two maps were one SNP in 1.23–1.25 cM. A total of 1114 shared SNP markers were used to merge the two component maps. An integrated linkage map consisted of 2321 markers and spanned the cumulative length of 2052 cM. The composite map showed a substantial improvement in marker density, with one SNP marker in every 0.89 cM. To our knowledge, this is the most saturated genetic map in rubber tree to date. This integrated map allowed us to anchor 28,965 contigs, covering 135 Mb or 12% of the published rubber tree genome. We demonstrated that GBS is a robust and cost-effective approach for generating a common set of genome-wide SNP data suitable for constructing integrated linkage maps from multiple populations in a highly heterozygous agricultural species.

Function-selective domain architecture plasticity potentials in eukaryotic genome evolution.

To help evaluate how protein function impacts on genome evolution, we introduce a new concept of ‘architecture plasticity potential’ – the capacity to form distinct domain architectures – both for an individual domain, or more generally for a set of domains grouped by shared function. We devise a scoring metric to measure the plasticity potential for these domain sets, and evaluate how function has changed over time for different species. Applying this metric to a phylogenetic tree of eukaryotic genomes, we find that the involvement of each function is not random but highly selective. For certain lineages there is strong bias for evolution to involve domains related to certain functions. In general eukaryotic genomes, particularly animals, expand complex functional activities such as signalling and regulation, but at the cost of reducing metabolic processes. We also observe differential evolution of transcriptional regulation and a unique evolutionary role of channel regulators; crucially this is only observable in terms of the architecture plasticity potential. Our findings provide a new layer of information to understand the significance of function in eukaryotic genome evolution. A web search tool, available at http://supfam.org/Pevo, offers a wide spectrum of options for exploring functional importance in eukaryotic genome evolution.

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes.

Large-scale recovery of genomes from isolates, single cells, and metagenomic data has been made possible by advances in computational methods and substantial reductions in sequencing costs. Although this increasing breadth of draft genomes is providing key information regarding the evolutionary and functional diversity of microbial life, it has become impractical to finish all available reference genomes. Making robust biological inferences from draft genomes requires accurate estimates of their completeness and contamination. Current methods for assessing genome quality are ad hoc and generally make use of a limited number of “marker” genes conserved across all bacterial or archaeal genomes. Here we introduce CheckM, an automated method for assessing the quality of a genome using a broader set of marker genes specific to the position of a genome within a reference genome tree and information about the collocation of these genes. We demonstrate the effectiveness of CheckM using synthetic data and a wide range of isolate-, single-cell-, and metagenome-derived genomes. CheckM is shown to provide accurate estimates of genome completeness and contamination and to outperform existing approaches. Using CheckM, we identify a diverse range of errors currently impacting publicly available isolate genomes and demonstrate that genomes obtained from single cells and metagenomic data vary substantially in quality. In order to facilitate the use of draft genomes, we propose an objective measure of genome quality that can be used to select genomes suitable for specific gene- and genome-centric analyses of microbial communities.

Identification and characterization of the EIN3/EIL gene family in Hevea brasiliensis

Ethylene-insensitive3/ethylene-insensitive3-like (EIN3/EIL) transcription factor is a key transcription factor involved in the ethylene signal transduction pathway in plants. Although the genome-wide analysis of this family has been carried out in certain plant species, little is known about EIN3/EIL genes in rubber tree (Hevea brasiliensis). In this study, we identified four EIN3/EIL genes (designated as HbEIN3-1 to HbEIN3-4) in the rubber tree genome annotation. Tissue-specific expression profiles showed that four HbEIN3s were expressed in at least one of the tested tissues. The four HbEIN3s responded to ethylene (ET) and jasmonic acid (JA) treatment, which suggested that HbEIN3s were involved in response to JA and ET signaling. HbEIN3s showed transactivation activity in yeast. HbEIN3-1 bound to the promoter of the rubber transferase gene, suggesting that HbEIN3-1 may be involved in the regulation of natural rubber biosynthesis. The N-terminal basic domain II was required for the HbEIN3-1 binding with the promoter of the rubber transferase gene.

Genome-wide analysis of the AP2/ERF family in Eucalyptus grandis: an intriguing over-representation of stress-responsive DREB1/CBF genes.

BackgroundThe AP2/ERF family includes a large number of developmentally and physiologically important transcription factors sharing an AP2 DNA-binding domain. Among them DREB1/CBF and DREB2 factors are known as master regulators respectively of cold and heat/osmotic stress responses.Experimental ApproachesThe manual annotation of AP2/ERF family from Eucalyptus grandis, Malus, Populus and Vitis genomes allowed a complete phylogenetic study for comparing the structure of this family in woody species and the model Arabidopsis thaliana. Expression profiles of the whole groups of EgrDREB1 and EgrDREB2 were investigated through RNAseq database survey and RT-qPCR analyses.ResultsThe structure and the size of the AP2/ERF family show a global conservation for the plant species under comparison. In addition to an expansion of the ERF subfamily, the tree genomes mainly differ with respect to the group representation within the subfamilies. With regard to the E. grandis DREB subfamily, an obvious feature is the presence of 17 DREB1/CBF genes, the maximum reported to date for dicotyledons. In contrast, only six DREB2 have been identified, which is similar to the other plants species under study, except for Malus. All the DREB1/CBF and DREB2 genes from E. grandis are expressed in at least one condition and all are heat-responsive. Regulation by cold and drought depends on the genes but is not specific of one group; DREB1/CBF group is more cold-inducible than DREB2 which is mainly drought responsive.ConclusionThese features suggest that the dramatic expansion of the DREB1/CBF group might be related to the adaptation of this evergreen tree to climate changes when it expanded in Australia.

Natural hybridization in eastern-Mediterranean firs: The case of Abies borisii-regis

The genus Abies is represented in southern Balkans by A. alba, A. cephalonica, and A. borisii-regis. To infer the status of southern-Balkans firs, as well as the extent and patterns of introgression within this taxonomical complex, we analyzed genetic variation patterns of 29 indigenous fir populations in Bulgaria, Macedonia, Greece, and Calabria using a combination of maternally and biparentally inherited markers. Three mitochondrial lineages were observed, one comprising Calabrian populations and two distributed in the Balkans, coinciding with A. alba and A. cephalonica. The boundary between lineages is sharp; only two populations containing a mixture of haplotypes were found. Bayesian analysis of population structure based on seven nuclear microsatellite (nSSR) loci revealed the existence of two clusters whose proportions exhibited a latitudinal cline with a width of 2.3° ( ≈ 255 km). Populations in the center of the latitudinal cline exhibit the most symmetrical, the flattest, and the broadest distributions of cluster proportions within individual tree genomes. A neighbor-net network reflects the cline resulting from the Bayesian analysis. The observed variation patterns are not consistent with the hypothesis of A. borisii-regis as a monophyletic taxon or a stabilized hybridogenous species resulted from ancient hybridization; the taxon rather is a product of recent introgression.