Plant Pan-Genomics Comes of Age

2021 ◽  
Vol 72 (1) ◽  
Author(s):  
Li Lei ◽  
Eugene Goltsman ◽  
David Goodstein ◽  
Guohong Albert Wu ◽  
Daniel S. Rokhsar ◽  
...  
Keyword(s):  
High Resolution ◽  
Dna Sequences ◽  
Repetitive Sequences ◽  
Plant Biology ◽  
Annual Review ◽  
Publication Date ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Large Size ◽  
Sizable Fraction

A pan-genome is the nonredundant collection of genes and/or DNA sequences in a species. Numerous studies have shown that plant pan-genomes are typically much larger than the genome of any individual and that a sizable fraction of the genes in any individual are present in only some genomes. The construction and interpretation of plant pan-genomes are challenging due to the large size and repetitive content of plant genomes. Most pan-genomes are largely focused on nontransposable element protein coding genes because they are more easily analyzed and defined than noncoding and repetitive sequences. Nevertheless, noncoding and repetitive DNA play important roles in determining the phenotype and genome evolution. Fortunately, it is now feasible to make multiple high-quality genomes that can be used to construct high-resolution pan-genomes that capture all the variation. However, assembling, displaying, and interacting with such high-resolution pan-genomes will require the development of new tools. Expected final online publication date for the Annual Review of Plant Biology, Volume 72 is May 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Long Noncoding RNAs in Plants

2021 ◽  
Vol 72 (1) ◽  
Author(s):  
Andrzej T. Wierzbicki ◽  
Todd Blevins ◽  
Szymon Swiezewski
Keyword(s):  
Gene Expression ◽  
Nuclear Dna ◽  
Noncoding Rnas ◽  
Chromatin Accessibility ◽  
Long Noncoding Rnas ◽  
Annual Review ◽  
Publication Date ◽  
Protein Coding ◽  
Ribonucleic Acids ◽  
Coding Potential

Plants have an extraordinary diversity of transcription machineries, including five nuclear DNA-dependent RNA polymerases. Four of these enzymes are dedicated to the production of long noncoding RNAs (lncRNAs), which are ribonucleic acids with functions independent of their protein-coding potential. lncRNAs display a broad range of lengths and structures, but they are distinct from the small RNA guides of RNA interference (RNAi) pathways. lncRNAs frequently serve as structural, catalytic, or regulatory molecules for gene expression. They can affect all elements of genes, including promoters, untranslated regions, exons, introns, and terminators, controlling gene expression at various levels, including modifying chromatin accessibility, transcription, splicing, and translation. Certain lncRNAs protect genome integrity, while others respond to environmental cues like temperature, drought, nutrients, and pathogens. In this review, we explain the challenge of defining lncRNAs, introduce the machineries responsible for their production, and organize this knowledge by viewing the functions of lncRNAs throughout the structure of a typical plant gene. Expected final online publication date for the Annual Review of Plant Biology, Volume 72 is May 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

A Comparative Overview of the Intracellular Guardians of Plants and Animals: NLRs in Innate Immunity and Beyond

2021 ◽  
Vol 72 (1) ◽  
Author(s):  
Zane Duxbury ◽  
Chih-hang Wu ◽  
Pingtao Ding
Keyword(s):  
Immune Responses ◽  
Genetic Architecture ◽  
Pathogen Detection ◽  
Current Knowledge ◽  
Plant Immunity ◽  
Innate Immune ◽  
Plant Biology ◽  
Annual Review ◽  
Publication Date ◽  
Nucleotide Binding Domain

Nucleotide-binding domain leucine-rich repeat receptors (NLRs) play important roles in the innate immune systems of both plants and animals. Recent breakthroughs in NLR biochemistry and biophysics have revolutionized our understanding of how NLR proteins function in plant immunity. In this review, we summarize the latest findings in plant NLR biology and draw direct comparisons to NLRs of animals. We discuss different mechanisms by which NLRs recognize their ligands in plants and animals. The discovery of plant NLR resistosomes that assemble in a comparable way to animal inflammasomes reinforces the striking similarities between the formation of plant and animal NLR complexes. Furthermore, we discuss the mechanisms by which plant NLRs mediate immune responses and draw comparisons to similar mechanisms identified in animals. Finally, we summarize the current knowledge of the complex genetic architecture formed by NLRs in plants and animals and the roles of NLRs beyond pathogen detection. Expected final online publication date for the Annual Review of Plant Biology, Volume 72 is May 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals Analyzing and characterization of the chloroplast genome of Salix suchowensis

2016 ◽  
Author(s):  
Congrui Sun ◽  
Jie Li ◽  
Xiaogang Dai ◽  
Yingnan Chen
Keyword(s):  
Tandem Repeats ◽  
Gene Annotation ◽  
Repetitive Sequences ◽  
Single Copy ◽  
Phylogenetic Position ◽  
Shrub Willow ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Cp Genome ◽  
Rna Genes

By screening sequence reads from the chloroplast (cp) genome of S. suchowensis that generated by the next generation sequencing platforms, we built the complete circular pseudomolecule for its cp genome. This pseudomolecule is 155,508 bp in length, which has a typical quadripartite structure containing two single copy regions, a large single copy region (LSC 84,385 bp), and a small single copy region (SSC 16,209 bp) separated by inverted repeat regions (IRs 27,457 bp). Gene annotation revealed that the cp genome of S. suchowensis encoded 119 unique genes, including 4 ribosome RNA genes, 30 transfer RNA genes, 82 protein-coding genes and 3 pseudogenes. Analyzing the repetitive sequences detected 15 tandem repeats, 16 forward repeats and 5 palindromic repeats. In addition, a total of 188 perfect microsatellites were detected, which were characterized as A/T predominance in nucleotide compositions. Significant shifting of the IR/SSC boundaries was revealed by comparing this cp genome with that of other rosids plants. We also built phylogenetic trees to demonstrate the phylogenetic position of S. suchowensis in Rosidae, with 66 orthologous protein-coding genes presented in the cp genomes of 32 species. By sequencing 30 amplicons based on the pseudomolecule, experimental verification achieved accuracy up to 99.84% for the cp genome assembly of S. suchowensis. In conclusion, this study built a high quality pseudomolecule for the cp genome of S. suchowensis, which is a useful resource for facilitating the development of this shrub willow into a more productive bioenergy crop.

scholarly journals Phylogeny of water birds inferred from mitochondrial DNA sequences of nine protein coding genes

2014 ◽  
Author(s):  
Tsendsesmee Lkhagvajav Treutlein ◽  
Javier Gonzalez ◽  
Michael Wink
Keyword(s):  
Mitochondrial Dna ◽  
Dna Sequences ◽  
Mitochondrial Protein ◽  
Sister Relationship ◽  
Protein Coding ◽  
Water Bird ◽  
Protein Coding Genes ◽  
Reconstruction Methods ◽  
Mtdna Sequence ◽  
Water Birds

Background: The phylogeny of birds which are adapted to aquatic environments is controversial because of convergent evolution. Methods: To understand water bird evolution in more detail, we sequenced the majority of mitochondrial protein coding genes (6699 nucleotides in length) of 14 water birds, and reconstructed their phylogeny in the context of other taxa across the whole class of birds for which complete mitochondrial DNA (mtDNA) sequences were available. Results: The water bird clade, as defined by Hackett et al. (2008) based on nuclear DNA (ncDNA) sequences, was also found in our study by Bayesian Inference (BI) and Maximum Likelihood (ML) analyses. In both reconstruction methods, genera belonging to the same family generally clustered together with moderate to high statistical support. Above the family level, we identified three monophyletic groups: one clade consisting of Procellariidae, Hydrobatidae and Diomedeidae, and a second clade consisting of Sulidae, Anhingidae and Phalacrocoracidae, and a third clade consisting of Ardeidae and Threskiornithidae. Discussion: Based on our mtDNA sequence data, we recovered a robust direct sister relationship between Ardeidae and Threskiornithidae for the first time for mtDNA. Our comprehensive phylogenetic reconstructions contribute to the knowledge of higher level relationships within the water birds and provide evolutionary hypotheses for further studies.

scholarly journals Chromosome-level genome assembly of a butterflyfish, Chelmon rostratus

2019 ◽  
Author(s):  
Xiaoyun Huang ◽  
Yue Song ◽  
Suyu Zhang ◽  
A Yunga ◽  
Mengqi Zhang ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Repetitive Sequences ◽  
Ecological Environment ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
A Genome ◽  
Genome Information ◽  
Adaptation Evolution ◽  
Core Genes ◽  
Chromosome Level

AbstractChelmon rostratus (Teleostei, Perciformes, Chaetodontidae) is a copperband butterflyfish. As an ornamental fish, the genome information for this species might help understanding the genome evolution of Chaetodontidae and adaptation/evolution of coral reef fish.In this study, using the stLFR co-Barcode reads data, we assembled a genome of 638.70 Mb in size with contig and scaffold N50 sizes of 294.41 kb and 2.61 Mb, respectively. 94.40% of scaffold sequences were assigned to 24 chromosomes using Hi-C data and BUSCO analysis showed that 97.3% (2,579) of core genes were found in our assembly. Up to 21.47 % of the genome was found to be repetitive sequences and 21,375 protein-coding genes were annotated. Among these annotated protein-coding genes, 20,163 (94.33%) proteins were assigned with possible functions.As the first genome for Chaetodontidae family, the information of these data helpfully to improve the essential to the further understanding and exploration of marine ecological environment symbiosis with coral and the genomic innovations and molecular mechanisms contributing to its unique morphology and physiological features.

scholarly journals Assembly and Annotation of an Ashkenazi Human Reference Genome

2020 ◽  
Author(s):  
Alaina Shumate ◽  
Aleksey V. Zimin ◽  
Rachel M. Sherman ◽  
Daniela Puiu ◽  
Justin M. Wagner ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Reference Genome ◽  
Gene Families ◽  
Gene Content ◽  
Specific Reference ◽  
Protein Coding ◽  
Human Reference Genome ◽  
Protein Coding Genes ◽  
Reference Genomes ◽  
Similar Gene

AbstractHere we describe the assembly and annotation of the genome of an Ashkenazi individual and the creation of a new, population-specific human reference genome. This genome is more contiguous and more complete than GRCh38, the latest version of the human reference genome, and is annotated with highly similar gene content. The Ashkenazi reference genome, Ash1, contains 2,973,118,650 nucleotides as compared to 2,937,639,212 in GRCh38. Annotation identified 20,157 protein-coding genes, of which 19,563 are >99% identical to their counterparts on GRCh38. Most of the remaining genes have small differences. 40 of the protein-coding genes in GRCh38 are missing from Ash1; however, all of these genes are members of multi-gene families for which Ash1 contains other copies. 11 genes appear on different chromosomes from their homologs in GRCh38. Alignment of DNA sequences from an unrelated Ashkenazi individual to Ash1 identified ~1 million fewer homozygous SNPs than alignment of those same sequences to the more-distant GRCh38 genome, illustrating one of the benefits of population-specific reference genomes.

scholarly journals Complete Mitochondrial and Plastid DNA Sequences of the Freshwater Green Microalga Medakamo hakoo

2021 ◽  
Author(s):  
Mari Takusagawa ◽  
Shoichi Kato ◽  
Sachihiro Matsunaga ◽  
Shinichiro Maruyama ◽  
Yayoi Tsujimoto-Inui ◽  
...  
Keyword(s):  
Green Alga ◽  
Dna Sequences ◽  
Plastid Dna ◽  
Mitochondrial Genomes ◽  
Genome Sequences ◽  
Protein Coding ◽  
Putative Protein ◽  
Protein Coding Genes ◽  
Organellar Genome ◽  
Green Microalga

Here we report the complete organellar genome sequences of Medakamo hakoo, a green alga identified in freshwater in Japan. It has 90.8-kb plastid and 36.5-kb mitochondrial genomes containing 80 and 33 putative protein coding genes, respectively, representing the smallest organellar genome among currently known core Trebouxiophyceae.

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

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.

The Making of Plant Armor: The Periderm

2022 ◽  
Vol 73 (1) ◽  
Author(s):  
Olga Serra ◽  
Ari Pekka Mähönen ◽  
Alexander J. Hetherington ◽  
Laura Ragni
Keyword(s):  
Regulatory Networks ◽  
Plant Biology ◽  
Raw Material ◽  
Industrial Processes ◽  
Annual Review ◽  
Publication Date ◽  
Biotic And Abiotic Stress ◽  
Meristematic Tissue ◽  
Future Challenges ◽  
Periderm Formation

The periderm acts as armor protecting the plant's inner tissues from biotic and abiotic stress. It forms during the radial thickening of plant organs such as stems and roots and replaces the function of primary protective tissues such as the epidermis and the endodermis. A wound periderm also forms to heal and protect injured tissues. The periderm comprises a meristematic tissue called the phellogen, or cork cambium, and its derivatives: the lignosuberized phellem and the phelloderm. Research on the periderm has mainly focused on the chemical composition of the phellem due to its relevance as a raw material for industrial processes. Today, there is increasing interest in the regulatory network underlying periderm development as a novel breeding trait to improve plant resilience and to sequester CO2. Here, we discuss our current understanding of periderm formation, focusing on aspects of periderm evolution, mechanisms of periderm ontogenesis, regulatory networks underlying phellogen initiation and cork differentiation, and future challenges of periderm research. Expected final online publication date for the Annual Review of Plant Biology, Volume 73 is May 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

The Complete Mitochondrial Genomes of two Flying Fishes, Cheilopogon pinnatibarbatus japonicus and Hirundichthys rondeletii

2020 ◽  
Author(s):  
Liyan Qu ◽  
Heng Zhang ◽  
Fengying Zhang ◽  
Wei Wang ◽  
Fenghua Tang ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Dna Sequences ◽  
Rrna Genes ◽  
Phylogenetic Position ◽  
Mitochondrial Genomes ◽  
Trna Genes ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Flying Fishes ◽  
Complete Mitochondrial Genomes

Background: Genome-scale approaches have played a significant role in the analysis of evolutionary relationships. Because of rich polymorphisms, high evolutionary rate and rare recombination, mitochondrial DNA sequences are commonly considered as effective markers for estimating population genetics, evolutionary and phylogenetic relationships. Flying fishes are important components of epipelagic ecosystems. Up to now, only few complete mitochondrial genomes of flying fishes have been reported. In the present study, the complete mitochondrial DNA sequences of the Cheilopogon pinnatibarbatus japonicus and Hirundichthys rondeletii had been determined. Methods: Based on the published mitogenome of Cheilopogon atrisignis (GenBank: KU360729), fifteen pairs of primers were designed by the software Primer Premier 5.0 to get the complete mitochondrial genomes of two flying fishes. According to the reported data, the phylogenetic position of two flying fishes were detected using the conserved 12 protein-coding genes. Result: The complete mitochondrial genomes of Cheilopogon pinnatibarbatus japonicus and Hirundichthys rondeletii are determined. They are 16532bp and 16525bp in length, respectively. And they both consists of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and a control region. The OL regions are conserved in these two flying fishes and might have no function. From the tree topologies, we found C.p. japonicus and H. rondeletii clustered in a group. The findings of the study would contribute to the phylogenetic classification and the genetic conservation management of C.p. japonicus and H. rondeletii.

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