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

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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Genomic sequencing of Phyllosticta citriasiana provide insight into its conservation and diversification with closely related Phyllosticta species associated with citrus

10.1101/740852 ◽

2019 ◽

Author(s):

Mingshuang Wang ◽

Bei Liu ◽

Ruoxin Ruan ◽

Yibing Zeng ◽

Jinshui Luo ◽

...

Keyword(s):

Tan Spot ◽

Secreted Proteins ◽

Comparative Genomic ◽

Orphan Genes ◽

Core Set ◽

Genomic Analyses ◽

Genetic Mechanisms ◽

Or Gene ◽

Species Specific ◽

Insight Into

AbstractPhyllosticta citriasiana is the causal agent of the pomelo tan spot. Here, we presented the ~34Mb genome of P. citriasiana. The genome is organized in 92 contigs, encompassing 9202 predicted genes. Comparative genomic analyses with other two Phyllosticta species (P. citricarpa and P. capitalensis) associated with citrus was conducted to understand their evolutionary conservation and diversification. Pairwise genome alignments revealed that these species are highly syntenic. All species encode similar numbers of CAZymes and secreted proteins. However, the molecular functions of the secretome showed that each species contains some enzymes with distinct activities. Three Phyllosticta species shared a core set of 7261 protein families. P. capitalensis had the largest set of orphan genes (2040), in complete contrast to that of P. citriasiana (371) and P. citricarpa (262). Most of the orphan genes were functionally unknown, but they contain a certain number of species-specific secreted proteins. A total of 23 secondary metabolites (SM) biosynthesis clusters were identified in the three Phyllosticta species, 21 of them are highly conserved among these species while the remaining 2 showed whole cluster gain and loss polymorphisms or gene content polymorphisms. Taken together, our study reveals insights into the genetic mechanisms of host adaptation of Phyllosticta species associated with citrus and paves the way to identify effectors that function in infection of citrus plants.

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Comparative genomic analyses illuminate the distinct evolution of megabats within Chiroptera

DNA Research ◽

10.1093/dnares/dsaa021 ◽

2020 ◽

Vol 27 (4) ◽

Author(s):

Masato Nikaido ◽

Shinji Kondo ◽

Zicong Zhang ◽

Jiaqi Wu ◽

Hidenori Nishihara ◽

...

Keyword(s):

Gene Families ◽

Comparative Genomic ◽

Fruit Bat ◽

Chemosensory Gene ◽

Short Period ◽

Genomic Analyses ◽

Trace Amine ◽

Trace Amine Receptor ◽

Low Activity ◽

Insight Into

Abstract The revision of the sub-order Microchiroptera is one of the most intriguing outcomes in recent mammalian molecular phylogeny. The unexpected sister–taxon relationship between rhinolophoid microbats and megabats, with the exclusion of other microbats, suggests that megabats arose in a relatively short period of time from a microbat-like ancestor. In order to understand the genetic mechanism underlying adaptive evolution in megabats, we determined the whole-genome sequences of two rousette megabats, Leschenault’s rousette (Rousettus leschenaultia) and the Egyptian fruit bat (R. aegyptiacus). The sequences were compared with those of 22 other mammals, including nine bats, available in the database. We identified that megabat genomes are distinct in that they have extremely low activity of SINE retrotranspositions, expansion of two chemosensory gene families, including the trace amine receptor (TAAR) and olfactory receptor (OR), and elevation of the dN/dS ratio in genes for immunity and protein catabolism. The adaptive signatures discovered in the genomes of megabats may provide crucial insight into their distinct evolution, including key processes such as virus resistance, loss of echolocation, and frugivorous feeding.

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Comparative Genomics Highlight the Importance of Lineage-Specific Gene Families in Evolutionary Divergence of the Coral Genus, Montipora

10.21203/rs.3.rs-944849/v1 ◽

2021 ◽

Author(s):

Yuki Yoshioka ◽

Go Suzuki ◽

Yuna Zayasu ◽

Hiroshi Yamashita ◽

Chuya Shinzato

Keyword(s):

Positive Selection ◽

Early Life ◽

Gene Families ◽

Comparative Genomic ◽

Specific Gene ◽

Biological Traits ◽

Life Stages ◽

Early Life Stages ◽

Genomic Analyses ◽

Lineage Specific Gene

Abstract Background: Scleractinian corals of the genus Montipora (Anthozoa, Cnidaria) possess some unusual biological traits, such as vertical transmission of algal symbionts; however, the genetic bases for those traits remain unknown. We performed extensive comparative genomic analyses among members of the family Acroporidae (Montipora, Acropora and Astreopora) to explore genomic novelties to explain unique biological traits of Montipora using improved genome assemblies and gene predictions for M. cactus, M. efflorescens and Astreopora myriophthalma. Results: We obtained genomic data for the three species, of comparable high quality to other published coral genomes. Comparative genomic analyses revealed that the number of gene families restricted to Montipora are significantly higher than those of Acropora and Astreopora, but their functions are largely unknown. The number of gene families specifically expanded in Montipora was much lower than the number specifically expanded in Acropora. In addition, we found that evolutionary rates of the Montipora-specific gene families were significantly higher than other gene families shared with Acropora and/or Astreopora. Of 40 gene families under positive selection (Ka/Ks ratio > 1) in Montipora, 30 were specifically detected in Montipora-specific gene families. Comparative transcriptome analysis of early life stages of Montipora, which possesses maternally inherited symbionts, and Acropora, which lacks them, revealed that most gene families continuously expressed in Montipora, but not expressed in Acropora do not have orthologs in Acropora. Among the 30 Montipora-specific gene families under positive selection, 27 are expressed in early life stages. Conclusions: Lineage-specific gene families were important to establish the genus Montipora, particularly genes expressed throughout early life stages, which under positive selection, gave rise to biological traits unique to Montipora. Our findings highlight evolutionarily acquired genomic bases that may support symbiosis in these stony corals and provide novel insights into mechanisms of coral-algal symbiosis, the physiological foundation of coral reefs.

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Haplotype-resolved genome of diploid ginger (Zingiber officinale) and its unique gingerol biosynthetic pathway

Horticulture Research ◽

10.1038/s41438-021-00627-7 ◽

2021 ◽

Vol 8 (1) ◽

Author(s):

Hong-Lei Li ◽

Lin Wu ◽

Zhaoming Dong ◽

Yusong Jiang ◽

Sanjie Jiang ◽

...

Keyword(s):

Biosynthetic Pathway ◽

Southwest China ◽

Reference Genome ◽

Zingiber Officinale ◽

Gene Families ◽

Chromosome Conformation ◽

Long Reads ◽

Transcription Factor Networks ◽

Species Specific ◽

Haplotype 1

AbstractGinger (Zingiber officinale), the type species of Zingiberaceae, is one of the most widespread medicinal plants and spices. Here, we report a high-quality, chromosome-scale reference genome of ginger ‘Zhugen’, a traditionally cultivated ginger in Southwest China used as a fresh vegetable, assembled from PacBio long reads, Illumina short reads, and high-throughput chromosome conformation capture (Hi-C) reads. The ginger genome was phased into two haplotypes, haplotype 1 (1.53 Gb with a contig N50 of 4.68 M) and haplotype 0 (1.51 Gb with a contig N50 of 5.28 M). Homologous ginger chromosomes maintained excellent gene pair collinearity. In 17,226 pairs of allelic genes, 11.9% exhibited differential expression between alleles. Based on the results of ginger genome sequencing, transcriptome analysis, and metabolomic analysis, we proposed a backbone biosynthetic pathway of gingerol analogs, which consists of 12 enzymatic gene families, PAL, C4H, 4CL, CST, C3’H, C3OMT, CCOMT, CSE, PKS, AOR, DHN, and DHT. These analyses also identified the likely transcription factor networks that regulate the synthesis of gingerol analogs. Overall, this study serves as an excellent resource for further research on ginger biology and breeding, lays a foundation for a better understanding of ginger evolution, and presents an intact biosynthetic pathway for species-specific gingerol biosynthesis.

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Comparative genomic analyses of Streptococcus mutans provide insights into chromosomal shuffling and species-specific content

BMC Genomics ◽

10.1186/1471-2164-10-358 ◽

2009 ◽

Vol 10 (1) ◽

pp. 358 ◽

Cited By ~ 52

Author(s):

Fumito Maruyama ◽

Mitsuhiko Kobata ◽

Ken Kurokawa ◽

Keishin Nishida ◽

Atsuo Sakurai ◽

...

Keyword(s):

Streptococcus Mutans ◽

Comparative Genomic ◽

Specific Content ◽

Genomic Analyses ◽

Species Specific

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The genome of the blind soil-dwelling and ancestrally wingless dipluran Campodea augens, a key reference hexapod for studying the emergence of insect innovations

10.1101/585695 ◽

2019 ◽

Cited By ~ 1

Author(s):

Mosè Manni ◽

Felipe A. Simao ◽

Hugh M. Robertson ◽

Marco A. Gabaglio ◽

Robert M. Waterhouse ◽

...

Keyword(s):

Draft Genome ◽

Gene Families ◽

Sister Group ◽

Sensu Stricto ◽

Comparative Genomic ◽

Gene Repertoire ◽

Animal Group ◽

Origin And Evolution ◽

Genomic Analyses ◽

Metabolism Gene

AbstractThe dipluran two-pronged bristletail Campodea augens is a blind ancestrally wingless hexapod with the remarkable capacity to regenerate lost body appendages such as its long antennae. As sister group to Insecta (sensu stricto), Diplura are key to understanding the early evolution of hexapods and the origin and evolution of insects. Here we report the 1.2-Gbp draft genome of C. augens and results from comparative genomic analyses with other arthropods. In C. augens we uncovered the largest chemosensory gene repertoire of ionotropic receptors in the animal kingdom, a massive expansion which might compensate for the loss of vision. We found a paucity of photoreceptor genes mirroring at the genomic level the secondary loss of an ancestral external photoreceptor organ. Expansions of detoxification and carbohydrate metabolism gene families might reflect adaptations for foraging behaviour, and duplicated apoptotic genes might underlie its high regenerative potential.The C. augens genome represents one of the key references for studying the emergence of genomic innovations in insects, the most diverse animal group, and opens up novel opportunities to study the under-explored biology of diplurans.

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Phylogenetic analysis of fungal aquaporins provides insight into their possible role in water transport of mycorrhizal associations

Botany ◽

10.1139/cjb-2013-0041 ◽

2013 ◽

Vol 91 (8) ◽

pp. 495-504 ◽

Cited By ~ 21

Author(s):

Hao Xu ◽

Janice E.K. Cooke ◽

Janusz J. Zwiazek

Keyword(s):

Water Transport ◽

Mycorrhizal Fungi ◽

Functional Characterization ◽

Arbuscular Mycorrhizal ◽

Gene Families ◽

Fungal Species ◽

Comparative Genomic ◽

Mycorrhizal Associations ◽

Insight Into

In mycorrhizal associations, water transport properties of the fungal hyphae may have a profound effect on water transport of the host plant. The importance of aquaporins, water-transporting members of the major intrinsic protein (MIP) family, in facilitating water transport has been widely acknowledged and extensively studied in plants. However, until recently, relatively little was known about the structure, function, and regulation of fungal MIPs. The rapid increase in the number of sequenced fungal genomes, including Laccaria bicolor and other mycorrhizal fungi, has enabled functional and comparative genomic investigations to delineate the role that fungal MIPs play in mycorrhizal-facilitated plant water transport. Phylogenic analysis of 229 fungal MIPs from 88 species revealed that MIPs of mycorrhizal fungal species fall into four clusters delineated by functionally characterized fungal MIPs: the orthodox aquaporins, the aquaglyceroporins, the facultative fungal aquaporins, and the X intrinsic proteins. This comparative genomics analysis, together with in silico structural characterization of predicted MIPs and recently published functional characterization of MIPs from a small number of ectomycorrhizal and arbuscular mycorrhizal species, provide new insight into MIP gene families of mycorrhizal fungi and possible roles for fungal aquaporins in water relations of mycorrhizal plant–fungus symbioses.

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The Genome of the Great Gerbil Reveals Species-Specific Duplication of an MHCII Gene

Genome Biology and Evolution ◽

10.1093/gbe/evaa008 ◽

2020 ◽

Vol 12 (2) ◽

pp. 3832-3849 ◽

Cited By ~ 1

Author(s):

Pernille Nilsson ◽

Monica H Solbakken ◽

Boris V Schmid ◽

Russell J S Orr ◽

Ruichen Lv ◽

...

Keyword(s):

Gene Families ◽

Meriones Unguiculatus ◽

Comparative Genomic ◽

Great Gerbil ◽

Main Host ◽

Rhombomys Opimus ◽

Vector Borne ◽

Species Specific ◽

Close Relatives ◽

Genome Assemblies

Abstract The great gerbil (Rhombomys opimus) is a social rodent living in permanent, complex burrow systems distributed throughout Central Asia, where it serves as the main host of several important vector-borne infectious pathogens including the well-known plague bacterium (Yersinia pestis). Here, we present a continuous annotated genome assembly of the great gerbil, covering over 96% of the estimated 2.47-Gb genome. Taking advantage of the recent genome assemblies of the sand rat (Psammomys obesus) and the Mongolian gerbil (Meriones unguiculatus), comparative immunogenomic analyses reveal shared gene losses within TLR gene families (i.e., TLR8, TLR10, and the entire TLR11-subfamily) for Gerbillinae, accompanied with signs of diversifying selection of TLR7 and TLR9. Most notably, we find a great gerbil-specific duplication of the MHCII DRB locus. In silico analyses suggest that the duplicated gene provides high peptide binding affinity for Yersiniae epitopes as well as Leishmania and Leptospira epitopes, putatively leading to increased capability to withstand infections by these pathogens. Our study demonstrates the power of whole-genome sequencing combined with comparative genomic analyses to gain deeper insight into the immunogenomic landscape of the great gerbil and its close relatives.

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A high-quality chromosome-level genome assembly reveals genetics for important traits in eggplant

Horticulture Research ◽

10.1038/s41438-020-00391-0 ◽

2020 ◽

Vol 7 (1) ◽

Author(s):

Qingzhen Wei ◽

Jinglei Wang ◽

Wuhong Wang ◽

Tianhua Hu ◽

Haijiao Hu ◽

...

Keyword(s):

Genome Assembly ◽

Reference Genome ◽

Repetitive Sequences ◽

Gene Families ◽

Specific Gene ◽

High Quality ◽

Total Size ◽

Protein Coding ◽

Fruit Length ◽

Protein Coding Genes

Abstract Eggplant (Solanum melongena L.) is an economically important vegetable crop in the Solanaceae family, with extensive diversity among landraces and close relatives. Here, we report a high-quality reference genome for the eggplant inbred line HQ-1315 (S. melongena-HQ) using a combination of Illumina, Nanopore and 10X genomics sequencing technologies and Hi-C technology for genome assembly. The assembled genome has a total size of ~1.17 Gb and 12 chromosomes, with a contig N50 of 5.26 Mb, consisting of 36,582 protein-coding genes. Repetitive sequences comprise 70.09% (811.14 Mb) of the eggplant genome, most of which are long terminal repeat (LTR) retrotransposons (65.80%), followed by long interspersed nuclear elements (LINEs, 1.54%) and DNA transposons (0.85%). The S. melongena-HQ eggplant genome carries a total of 563 accession-specific gene families containing 1009 genes. In total, 73 expanded gene families (892 genes) and 34 contraction gene families (114 genes) were functionally annotated. Comparative analysis of different eggplant genomes identified three types of variations, including single-nucleotide polymorphisms (SNPs), insertions/deletions (indels) and structural variants (SVs). Asymmetric SV accumulation was found in potential regulatory regions of protein-coding genes among the different eggplant genomes. Furthermore, we performed QTL-seq for eggplant fruit length using the S. melongena-HQ reference genome and detected a QTL interval of 71.29–78.26 Mb on chromosome E03. The gene Smechr0301963, which belongs to the SUN gene family, is predicted to be a key candidate gene for eggplant fruit length regulation. Moreover, we anchored a total of 210 linkage markers associated with 71 traits to the eggplant chromosomes and finally obtained 26 QTL hotspots. The eggplant HQ-1315 genome assembly can be accessed at http://eggplant-hq.cn. In conclusion, the eggplant genome presented herein provides a global view of genomic divergence at the whole-genome level and powerful tools for the identification of candidate genes for important traits in eggplant.

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A chromosome-scale reference genome of Lobularia maritima, an ornamental plant with high stress tolerance

Horticulture Research ◽

10.1038/s41438-020-00422-w ◽

2020 ◽

Vol 7 (1) ◽

Author(s):

Li Huang ◽

Yazhen Ma ◽

Jiebei Jiang ◽

Ting Li ◽

Wenjie Yang ◽

...

Keyword(s):

Stress Tolerance ◽

Repetitive Sequences ◽

High Stress ◽

Genomic Analysis ◽

Gene Families ◽

Ornamental Plant ◽

Comparative Genomic ◽

Chromosome Conformation ◽

Lobularia Maritima ◽

Species Specific

AbstractLobularia maritima (L.) Desv. is an ornamental plant cultivated across the world. It belongs to the family Brassicaceae and can tolerate dry, poor and contaminated habitats. Here, we present a chromosome-scale, high-quality genome assembly of L. maritima based on integrated approaches combining Illumina short reads and Hi–C chromosome conformation data. The genome was assembled into 12 pseudochromosomes with a 197.70 Mb length, and it includes 25,813 protein-coding genes. Approximately 41.94% of the genome consists of repetitive sequences, with abundant long terminal repeat transposable elements. Comparative genomic analysis confirmed that L. maritima underwent a species-specific whole-genome duplication (WGD) event ~22.99 million years ago. We identified ~1900 species-specific genes, 25 expanded gene families, and 50 positively selected genes in L. maritima. Functional annotations of these genes indicated that they are mainly related to stress tolerance. These results provide new insights into the stress tolerance of L. maritima, and this genomic resource will be valuable for further genetic improvement of this important ornamental plant.

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