Comparative transcriptomics of seven Impatiens species

AbstractImpatiens is a genus containing more than 1000 species. Thanks to its size, it is a unique system for studying species diversification in natural populations. This study focused on the characterization of novel transcriptomes from seven Impatiens species originating from Nepal. Leave transcriptome of Impatines balsamina L., I. racemosa DC., I. bicornuta Wall, I. falcifer Hook, I. devendrae Pusalkar, I. scullyi Hook and I. scabrida DC were sequenced and compared. Reads were de novo assembled and aligned to 92 035-226 081 contigs. We identified 14 728 orthology groups shared among all the species and 3 020 which were unique to a single species. In single species, 2536-3009 orthology groups were under selection from which 767 were common for all species. Six of the seven investigated species shared 77% of gene families with I. bicornuta being the most distinct species. Specific gene families involved in response to different environmental stimuli were closely described. Impatiens bicornuta selection profile shared selection on zing finger protein structures and flowering regulation and stress response proteins with the other investigated species. Overall, the study showed substantial similarity in patterns of selections on transcribed genes across the species suggesting similar evolutionary pressures. This suggests that the species group may have evolved via adaptive radiation.

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The chromosome-scale reference genome of black pepper provides insight into piperine biosynthesis

Nature Communications ◽

10.1038/s41467-019-12607-6 ◽

2019 ◽

Vol 10 (1) ◽

Cited By ~ 10

Author(s):

Lisong Hu ◽

Zhongping Xu ◽

Maojun Wang ◽

Rui Fan ◽

Daojun Yuan ◽

...

Keyword(s):

Reference Genome ◽

Gene Families ◽

Black Pepper ◽

Piper Nigrum ◽

Comparative Genomic ◽

Specific Gene ◽

Phylogenomic Analysis ◽

Genomic Analyses ◽

Species Specific ◽

Insight Into

Abstract Black pepper (Piper nigrum), dubbed the ‘King of Spices’ and ‘Black Gold’, is one of the most widely used spices. Here, we present its reference genome assembly by integrating PacBio, 10x Chromium, BioNano DLS optical mapping, and Hi-C mapping technologies. The 761.2 Mb sequences (45 scaffolds with an N50 of 29.8 Mb) are assembled into 26 pseudochromosomes. A phylogenomic analysis of representative plant genomes places magnoliids as sister to the monocots-eudicots clade and indicates that black pepper has diverged from the shared Laurales-Magnoliales lineage approximately 180 million years ago. Comparative genomic analyses reveal specific gene expansions in the glycosyltransferase, cytochrome P450, shikimate hydroxycinnamoyl transferase, lysine decarboxylase, and acyltransferase gene families. Comparative transcriptomic analyses disclose berry-specific upregulated expression in representative genes in each of these gene families. These data provide an evolutionary perspective and shed light on the metabolic processes relevant to the molecular basis of species-specific piperine biosynthesis.

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Identification of tissue-specific gene clusters and orthologues of nodulation-related genes in Vigna angularis

Plant Genetic Resources ◽

10.1017/s1479262114000185 ◽

2014 ◽

Vol 12 (S1) ◽

pp. S21-S26 ◽

Cited By ~ 1

Author(s):

Yang Jae Kang ◽

Jayern Lee ◽

Yong Hwan Kim ◽

Suk-Ha Lee

Keyword(s):

De Novo ◽

Transcriptome Assembly ◽

Lotus Japonicus ◽

Gene Clusters ◽

Specific Gene ◽

Vigna Angularis ◽

Model Legume ◽

Tissue Specific ◽

Autoregulation Of Nodulation ◽

Species Specific

Nitrogen fixation in legumes is an important agricultural trait that results from symbiosis between the root and rhizobia. To understand the molecular basis of nodulation, recent research has been focused on the identification of nodulation-related genes by functional analysis using two major model legumes, Medicago truncatula and Lotus japonicus. Thus far, three important processes have been discovered, namely Nod factor (NF) perception, NF signalling and autoregulation of nodulation. Nevertheless, application of the results of these studies is limited for non-model legume crops because a reference genome is unavailable. However, because the cost of whole-transcriptome analysis has dropped dramatically due to the Next generation sequencer (NGS) technology, minor crops for which reference sequences are yet to be constructed can still be studied at the genome level. In this study, we sequenced the leaf and root transcriptomes of Vigna angularis (accession IT213134) and de novo assembled. Our results demonstrate the feasibility of using the transcriptome assembly to effectively identify tissue-specific peptide clusters related to tissue-specific functions and species-specific nodulation-related genes.

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Discovery of a Natural Microsporidian Pathogen with a Broad Tissue Tropism in Caenorhabditis elegans

10.1101/047720 ◽

2016 ◽

Cited By ~ 2

Author(s):

Robert J. Luallen ◽

Aaron W. Reinke ◽

Linda Tong ◽

Michael R. Botts ◽

Marie-Anne Félix ◽

...

Keyword(s):

Caenorhabditis Elegans ◽

Single Species ◽

Microbial Pathogens ◽

Specific Gene ◽

Tissue Tropism ◽

Microsporidian Parasite ◽

C Elegans ◽

Host Microbe Interactions ◽

Species Specific ◽

Host Tissues

AbstractMicrobial pathogens often establish infection within particular niches of their host for replication. Determining how infection occurs preferentially in specific host tissues is a key aspect of understanding host-microbe interactions. Here, we describe the discovery of a natural microsporidian parasite of the nematode Caenorhabditis elegans that has a unique tissue tropism compared to other parasites of C. elegans. We characterize the life cycle of this new species, Nematocida displodere, including pathogen entry, intracellular replication, and exit. N. displodere can invade multiple host tissues, including the epidermis, muscle, neurons, and intestine of C. elegans. Despite robust invasion of the intestine very little replication occurs there, with the majority of replication occurring in the muscle and epidermis. This feature distinguishes N. displodere from two closely related microsporidian pathogens, N. parisii and N. sp. 1, which exclusively invade and replicate in the intestine. Comparison of the N. displodere genome with N. parisii and N. sp. 1 reveals that N. displodere is the earliest diverging species of the Nematocida genus and devotes over 10% of its genome to a single species-specific gene family that may be mediating host interactions upon infection. Altogether, this system provides a convenient whole-animal model to investigate factors responsible for pathogen growth in different tissue niches.

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Comparison of 15 dinoflagellate genomes reveals extensive sequence and structural divergence in family Symbiodiniaceae and genus Symbiodinium

BMC Biology ◽

10.1186/s12915-021-00994-6 ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Raúl A. González-Pech ◽

Timothy G. Stephens ◽

Yibi Chen ◽

Amin R. Mohamed ◽

Yuanyuan Cheng ◽

...

Keyword(s):

De Novo ◽

Gene Families ◽

Specific Gene ◽

Free Living ◽

Microbial Eukaryotes ◽

The Family ◽

Structural Divergence ◽

Genome Features ◽

Genome Divergence ◽

Genome Assemblies

Abstract Background Dinoflagellates in the family Symbiodiniaceae are important photosynthetic symbionts in cnidarians (such as corals) and other coral reef organisms. Breakdown of the coral-dinoflagellate symbiosis due to environmental stress (i.e. coral bleaching) can lead to coral death and the potential collapse of reef ecosystems. However, evolution of Symbiodiniaceae genomes, and its implications for the coral, is little understood. Genome sequences of Symbiodiniaceae remain scarce due in part to their large genome sizes (1–5 Gbp) and idiosyncratic genome features. Results Here, we present de novo genome assemblies of seven members of the genus Symbiodinium, of which two are free-living, one is an opportunistic symbiont, and the remainder are mutualistic symbionts. Integrating other available data, we compare 15 dinoflagellate genomes revealing high sequence and structural divergence. Divergence among some Symbiodinium isolates is comparable to that among distinct genera of Symbiodiniaceae. We also recovered hundreds of gene families specific to each lineage, many of which encode unknown functions. An in-depth comparison between the genomes of the symbiotic Symbiodinium tridacnidorum (isolated from a coral) and the free-living Symbiodinium natans reveals a greater prevalence of transposable elements, genetic duplication, structural rearrangements, and pseudogenisation in the symbiotic species. Conclusions Our results underscore the potential impact of lifestyle on lineage-specific gene-function innovation, genome divergence, and the diversification of Symbiodinium and Symbiodiniaceae. The divergent features we report, and their putative causes, may also apply to other microbial eukaryotes that have undergone symbiotic phases in their evolutionary history.

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Eukaryote-Conserved Methylarginine Is Absent in Diplomonads and Functionally Compensated in Giardia

Molecular Biology and Evolution ◽

10.1093/molbev/msaa186 ◽

2020 ◽

Vol 37 (12) ◽

pp. 3525-3549 ◽

Cited By ~ 3

Author(s):

Samantha J Emery-Corbin ◽

Joshua J Hamey ◽

Brendan R E Ansell ◽

Balu Balan ◽

Swapnil Tichkule ◽

...

Keyword(s):

Coiled Coil ◽

Giardia Duodenalis ◽

Elongation Factor ◽

Gene Families ◽

Cyst Formation ◽

Arginine Methylation ◽

Specific Gene ◽

Parasitic Protist ◽

Higher Eukaryotes ◽

Species Specific

Abstract Methylation is a common posttranslational modification of arginine and lysine in eukaryotic proteins. Methylproteomes are best characterized for higher eukaryotes, where they are functionally expanded and evolved complex regulation. However, this is not the case for protist species evolved from the earliest eukaryotic lineages. Here, we integrated bioinformatic, proteomic, and drug-screening data sets to comprehensively explore the methylproteome of Giardia duodenalis—a deeply branching parasitic protist. We demonstrate that Giardia and related diplomonads lack arginine-methyltransferases and have remodeled conserved RGG/RG motifs targeted by these enzymes. We also provide experimental evidence for methylarginine absence in proteomes of Giardia but readily detect methyllysine. We bioinformatically infer 11 lysine-methyltransferases in Giardia, including highly diverged Su(var)3-9, Enhancer-of-zeste and Trithorax proteins with reduced domain architectures, and novel annotations demonstrating conserved methyllysine regulation of eukaryotic elongation factor 1 alpha. Using mass spectrometry, we identify more than 200 methyllysine sites in Giardia, including in species-specific gene families involved in cytoskeletal regulation, enriched in coiled-coil features. Finally, we use known methylation inhibitors to show that methylation plays key roles in replication and cyst formation in this parasite. This study highlights reduced methylation enzymes, sites, and functions early in eukaryote evolution, including absent methylarginine networks in the Diplomonadida. These results challenge the view that arginine methylation is eukaryote conserved and demonstrate that functional compensation of methylarginine was possible preceding expansion and diversification of these key networks in higher eukaryotes.

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Additional description and genome analyses of Caenorhabditis auriculariae representing the basal lineage of genus Caenorhabditis

Scientific Reports ◽

10.1038/s41598-021-85967-z ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Mehmet Dayi ◽

Natsumi Kanzaki ◽

Simo Sun ◽

Tatsuya Ide ◽

Ryusei Tanaka ◽

...

Keyword(s):

Phylogenetic Analyses ◽

Morphological Characteristics ◽

Gene Families ◽

Single Copy ◽

Specific Gene ◽

Protein Coding ◽

Molecular Phylogenetic ◽

Tight Association ◽

Genome Analyses ◽

Species Specific

AbstractCaenorhabditis auriculariae, which was morphologically described in 1999, was re-isolated from a Platydema mushroom-associated beetle. Based on the re-isolated materials, some morphological characteristics were re-examined and ascribed to the species. In addition, to clarify phylogenetic relationships with other Caenorhabditis species and biological features of the nematode, the whole genome was sequenced and assembled into 109.5 Mb with 16,279 predicted protein-coding genes. Molecular phylogenetic analyses based on ribosomal RNA and 269 single-copy genes revealed the species is closely related to C. sonorae and C. monodelphis placing them at the most basal clade of the genus. C. auriculariae has morphological characteristics clearly differed from those two species and harbours a number of species-specific gene families, indicating its usefulness as a new outgroup species for Caenorhabditis evolutionary studies. A comparison of carbohydrate-active enzyme (CAZy) repertoires in genomes, which we found useful to speculate about the lifestyle of Caenorhabditis nematodes, suggested that C. auriculariae likely has a life-cycle with tight-association with insects.

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Comprehensive genome analysis and comparisons of the swine pathogen, Chlamydia suis reveals unique ORFs and candidate host-specificity factors

Pathogens and Disease ◽

10.1093/femspd/ftaa035 ◽

2020 ◽

Author(s):

Zoe E Dimond ◽

P Scott Hefty

Keyword(s):

Comparative Genomics ◽

Membrane Proteins ◽

Host Specificity ◽

High Throughput Sequencing ◽

De Novo ◽

Gene Families ◽

Specific Gene ◽

Swine Pathogen ◽

Key Species ◽

Chlamydia Suis

Abstract Chlamydia suis, a ubiquitous swine pathogen, has the potential for zoonotic transmission to humans and often encodes for resistance to the primary treatment antibiotic, tetracycline. Because of this emerging threat, comparative genomics for swine isolate R19 with inter- and intra-species genomes was performed. A 1.094Mb genome was determined through de novo assembly of Illumina high throughput sequencing reads. Annotation and subsystem analyses were conducted, revealing 986 putative genes (Chls_###) that are predominantly orthologs to other known Chlamydia genes. Subsequent comparative genomics revealed a high level of genomic synteny and overall sequence identity with other Chlamydia while 92 unique C. suis open reading frames were annotated. Direct comparison of Chlamydia-specific gene families that included the plasticity zone, inclusion membrane proteins, polymorphic membrane proteins, and the major outer membrane protein, demonstrated high gene content identity with C. trachomatis and C. muridarum. These comparisons also identified diverse components that potentially could contribute to host-specificity. This study constitutes the first genome-wide comparative analysis for C. suis, generating a fully annotated reference genome. These studies will enable focused efforts on factors that provide key species specificity and adaptation to cognate hosts that are attributed to chlamydial infections, including humans.

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Differentiating Groups of Abies Species With a Simple Molecular Marker

Silvae Genetica ◽

10.1515/sg-2005-0019 ◽

2005 ◽

Vol 54 (1-6) ◽

pp. 123-126 ◽

Cited By ~ 22

Author(s):

B. Ziegenhagen ◽

B. Fady ◽

V. Kuhlenkamp ◽

S. Liepelt

Keyword(s):

Eastern Mediterranean ◽

Group Identification ◽

Single Species ◽

Forest Tree ◽

Species Group ◽

Near Eastern ◽

Forest Reproductive Material ◽

Diagnosis Method ◽

Reproductive Material ◽

Species Specific

AbstractThe unambiguous identification of closely related species is useful for many practical purposes in forest tree species. For example, international laws require timber identification and the control of the origin of forest reproductive material. In this paper, we present a mitochondrial DNA marker which can be used to differentiate among groups of fir species (Abies spp.). Eight Mediterranean and one North American fir species (used as reference) were analysed at the fourth intron of the NAD subunit 5 gene. A total of six different haplotypes was identified, one in the American Abies concolor, the other five in Mediterranean species. Two different haplotypes were found each in the widespread A. alba and in A. cephalonica, one haplotype being shared among the two species. A single species specific haplotype was found in the near-eastern A. cilicica. The two southwestern species A. pinsapo and A. numidica shared one haplotype. The fifth haplotype was shared by all remaining eastern Mediterranean firs, A. cephalonica, A. bornmuelleriana, A. equi-troiani, and A. nordmanniana. Differences in haplotype sequences were mainly due to large insertions/deletions. Agarose gel electrophoresis thus provides a fast, cheap and reliable diagnosis method for species or species group identification.

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Prediction and characterization of transcription factors involved in drought stress response

10.1101/2020.04.29.068379 ◽

2020 ◽

Author(s):

Chirag Gupta ◽

Venkategowda Ramegowda ◽

Supratim Basu ◽

Andy Pereira

Keyword(s):

Machine Learning ◽

Transcription Factors ◽

Drought Stress ◽

Stress Response ◽

Drought Tolerance ◽

Web Application ◽

Protein Structures ◽

Gene Families ◽

Supervised Machine Learning ◽

Specific Gene

AbstractTranscription factors (TFs) play a central role in regulating molecular level responses of plants to external stresses such as water limiting conditions, but identification of such TFs in the genome remains a challenge. Here, we describe a network-based supervised machine learning framework that accurately predicts and ranks all TFs in the genome according to their potential association with drought tolerance. We show that top ranked regulators fall mainly into two ‘age’ groups; genes that appeared first in land plants and genes that emerged later in the Oryza clade. TFs predicted to be high in the ranking belong to specific gene families, have relatively simple intron/exon and protein structures, and functionally converge to regulate primary and secondary metabolism pathways. Repeated trials of nested cross-validation tests showed that models trained only on regulatory network patterns, inferred from large transcriptome datasets, outperform models trained on heterogenous genomic features in the prediction of known drought response regulators. A new R/Shiny based web application, called the DroughtApp, provides a primer for generation of new testable hypotheses related to regulation of drought stress response. Furthermore, to test the system we experimentally validated predictions on the functional role of the rice transcription factor OsbHLH148, using RNA sequencing of knockout mutants in response to drought stress and protein-DNA interaction assays. Our study exemplifies the integration of domain knowledge for prioritization of regulatory genes in biological pathways of well-studied agricultural traits.One Sentence SummaryNetwork-based supervised machine learning accurately predicts transcription factors involved in drought tolerance.

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Three new genome assemblies support a rapid radiation in Musa acuminata (wild banana)

10.1101/306605 ◽

2018 ◽

Cited By ~ 1

Author(s):

M Rouard ◽

G Droc ◽

G Martin ◽

J Sardos ◽

Y Hueber ◽

...

Keyword(s):

De Novo ◽

Gene Annotation ◽

Incomplete Lineage Sorting ◽

Gene Tree ◽

Gene Families ◽

Musa Acuminata ◽

Specific Gene ◽

Rapid Radiation ◽

High Sequence Identity ◽

Short Period

AbstractEdible bananas result from interspecific hybridization between Musa acuminata and Musa balbisiana, as well as among subspecies in M. acuminata. Four particular M. acuminata subspecies have been proposed as the main contributors of edible bananas, all of which radiated in a short period of time in southeastern Asia. Clarifying the evolution of these lineages at a whole-genome scale is therefore an important step toward understanding the domestication and diversification of this crop. This study reports the de novo genome assembly and gene annotation of a representative genotype from three different subspecies of M. acuminata. These data are combined with the previously published genome of the fourth subspecies to investigate phylogenetic relationships and genome evolution. Analyses of shared and unique gene families reveal that the four subspecies are quite homogenous, with a core genome representing at least 50% of all genes and very few M. acuminata species-specific gene families. Multiple alignments indicate high sequence identity between homologous single copy-genes, supporting the close relationships of these lineages. Interestingly, phylogenomic analyses demonstrate high levels of gene tree discordance, due to both incomplete lineage sorting and introgression. This pattern suggests rapid radiation within Musa acuminata subspecies that occurred after the divergence with M. balbisiana. Introgression between M. a. ssp. malaccensis and M. a. ssp. burmannica was detected across a substantial portion of the genome, though multiple approaches to resolve the subspecies tree converged on the same topology. To support future evolutionary and functional analyses, we introduce the PanMusa database, which enables researchers to exploration of individual gene families and trees.

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