scholarly journals Phylogenomics reveals the evolutionary origin of lichenization in chlorophyte algae

2022 ◽  
Author(s):  
Jean Keller ◽  
Camille Puginier ◽  
Cyril Libourel ◽  
Juergen Otte ◽  
Pavel Skaloud ◽  
...  
Keyword(s):  
Green Algae ◽  
Cell Walls ◽  
De Novo ◽  
Glycosyl Hydrolase ◽  
Gene Families ◽  
Major Transitions ◽  
Genome Wide ◽  
Evolution Of Life ◽  
Terrestrial Habitats ◽  
And Function

Mutualistic symbioses, such as lichens formed between fungi and green algae or cyanobacteria, have contributed to major transitions in the evolution of life and are at the center of extant ecosystems. However, our understanding of their evolution and function remains elusive in most cases. Here, we investigated the evolutionary history and the molecular innovations at the origin of lichens in green algae. We de novo sequenced the genomes or transcriptomes of 15 lichen-forming and closely-related non-lichen-forming algae and performed comparative phylogenomics with 22 genomes previously generated. We identified more than 350 functional categories significantly enriched in chlorophyte green algae able to form lichens. Among them, functions such as light perception or resistance to dehydration were shared between lichenizing and other terrestrial algae but lost in non-terrestrial ones, indicating that the ability to live in terrestrial habitats is a prerequisite for lichens to evolve. We detected lichen-specific expansions of glycosyl hydrolase gene families known to remodel cell walls, including the glycosyl hydrolase 8 which was acquired in lichenizing Trebouxiophyceae by horizontal gene transfer from bacteria, concomitantly with the ability to form lichens. Mining genome-wide orthogroups, we found additional evidence supporting at least two independent origins of lichen-forming ability in chlorophyte green algae. We conclude that the lichen-forming ability evolved multiple times in chlorophyte green algae, following a two-step mechanism which involves an ancestral adaptation to terrestrial lifestyle and molecular innovations to modify the partners cell walls.

scholarly journals Genome-wide analysis of the lignin toolbox for morus and the roles of lignin related genes in response to zinc stress

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11964
Author(s):  
Nan Chao ◽  
Ting Yu ◽  
Chong Hou ◽  
Li Liu ◽  
Lin Zhang
Keyword(s):  
De Novo ◽  
Expression Profiles ◽  
Lignin Biosynthesis ◽  
Gene Families ◽  
Phenylpropanoid Pathway ◽  
Economic Plant ◽  
Systematic Analysis ◽  
Zinc Stress ◽  
Genome Wide ◽  
Bona Fide

Mulberry (Morus, Moraceae) is an important economic plant with nutritional, medicinal, and ecological values. Lignin in mulberry can affect the quality of forage and the saccharification efficiency of mulberry twigs. The availability of the Morus notabilis genome makes it possible to perform a systematic analysis of the genes encoding the 11 protein families specific to the lignin branch of the phenylpropanoid pathway, providing the core genes for the lignin toolbox in mulberry. We performed genome-wide screening, which was combined with de novo transcriptome data for Morus notabilis and Morus alba variety Fengchi, to identify putative members of the lignin gene families followed by phylogenetic and expression profile analyses. We focused on bona fide clade genes and their response to zinc stress were further distinguished based on expression profiles using RNA-seq and RT-qPCR. We finally identified 31 bona fide genes in Morus notabilis and 25 bona fide genes in Fengchi. The putative function of these bona fide genes was proposed, and a lignin toolbox that comprised 19 genes in mulberry was provided, which will be convenient for researchers to explore and modify the monolignol biosynthesis pathway in mulberry. We also observed changes in the expression of some of these lignin biosynthetic genes in response to stress caused by excess zinc in Fengchi and proposed that the enhanced lignin biosynthesis in lignified organs and inhibition of lignin biosynthesis in leaf is an important response to zinc stress in mulberry.

scholarly journals Genome-wide identification, phylogeny and expression analysis of the PME and PMEI gene families in maize

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Panpan Zhang ◽  
Hao Wang ◽  
Xiner Qin ◽  
Kuan Chen ◽  
Jiuran Zhao ◽  
...  
Keyword(s):  
Gene Structure ◽  
Cell Walls ◽  
Pectin Methylesterase ◽  
Gene Families ◽  
Motif Analysis ◽  
Cell Wall Modification ◽  
Genome Wide ◽  
Common Motif ◽  
Structure Patterns ◽  
Catabolic Process

AbstractPectins, the major components of cell walls in plants, are synthesized and secreted to cell walls as highly methyl-esterified polymers and then demethyl-esterified by pectin methylesterases (PMEs). The PMEs are spatially regulated by pectin methylesterase inhibitors (PMEIs). In this study, 43 and 49 putative PME and PMEI genes were identified in maize, respectively. Gene structure and motif analysis revealed that members in the same paralogous pairs or in the same subgroup generally had common motif compositions and gene structure patterns, which indicates functional similarity between the closely related ZmPME/PMEI genes. Gene ontology annotation analysis showed that most of the ZmPME/PMEI genes are involved in cell wall modification and pectin catabolic process with molecular functions of pectinesterase or pectinesterase inhibitor activities. There are 35 ZmPME/PMEI genes expressed higher in anthers than in other tissues from the NimbleGen maize microarray data, and the semiq-RT-PCR assay revealed most of these ZmPME/PMEIs specially expressed in anthers and pollens, indicating they possibly had role in anther and pollen development. In addition, these ZmPME/PMEI genes were highly expressed in the fertile anthers, while lowly or no expressed in sterile anthers. This further indicated these genes might be involved in the development of anther and pollen.

scholarly journals Identification of chromatin loops from Hi-C interaction matrices by CTCF-CTCF topology classification

2020 ◽  
Author(s):  
Silvia Galan ◽  
François Serra ◽  
Marc A. Marti-Renom
Keyword(s):  
De Novo ◽  
Topological Classification ◽  
Feature Maps ◽  
Chromatin Loops ◽  
Chromatin Interactions ◽  
Pairwise Interactions ◽  
Genome Wide ◽  
Long Range Interactions ◽  
And Function ◽  
Interaction Matrices

ABSTRACTGenome-wide profiling of long-range interactions has revealed that the CCCTC-Binding factor (CTCF) often anchors chromatin loops and is enriched at boundaries of the so-called Topologically Associating Domains or TADs, which suggests that CTCF is essential in the 3D organization of chromatin. However, the systematic topological classification of pairwise CTCF-CTCF interactions has not been yet explored.Here, we developed a computational pipeline able to classify all CTCF-CTCF pairs according to their chromatin interactions from Hi-C experiments. The interaction profiles of all CTCF-CTCF pairs were further structurally clustered using Self-Organizing Feature Maps (SOFM) and their functionality characterized by their epigenetic states. The resulting cluster were then input to a convolutional neural network aiming at the de novo detecting chromatin loops from Hi-C interaction matrices.Our new method, called LOOPbit, is able to automatically detect higher number of pairwise interactions with functional significance compared to other loop callers highlighting the link between chromatin structure and function.

scholarly journals Plant cell walls: the skeleton of the plant world

2010 ◽  
Vol 37 (5) ◽  
pp. 357 ◽  
Author(s):  
Monika S. Doblin ◽  
Filomena Pettolino ◽  
Antony Bacic
Keyword(s):  
Cell Walls ◽  
Growth Regulation ◽  
Raw Materials ◽  
Gene Families ◽  
Building Blocks ◽  
Plant Production ◽  
Wall Structure ◽  
Renewable Biomass ◽  
Signal Perception ◽  
And Function

Plants are our major source of renewable biomass. Since cell walls represent some 50% of this biomass, they are major targets for biotechnology. Major drivers are their potential as a renewable source of energy as transport fuels (biofuels), functional foods to improve human health and as a source of raw materials to generate building blocks for industrial processes (biobased industries). To achieve sustainable development, we must optimise plant production and utilisation and this will require a complete understanding of wall structure and function at the molecular/biochemical level. This overview summarises the current state of knowledge in relation to the synthesis and assembly of the wall polysaccharides (i.e. the genes and gene families encoding the polysaccharide synthases and glycosyltransferases (GlyTs)), the predominant macromolecular components. We also touch on an exciting emerging role of the cell wall–plasma membrane–cytoskeleton continuum as a signal perception and transduction pathway allowing plant growth regulation in response to endogenous and exogenous cues.

scholarly journals Dissecting the chromosome-level genome of the Asian Clam (Corbicula fluminea)

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Tongqing Zhang ◽  
Jiawen Yin ◽  
Shengkai Tang ◽  
Daming Li ◽  
Xiankun Gu ◽  
...  
Keyword(s):  
De Novo ◽  
Corbicula Fluminea ◽  
Gene Families ◽  
Ruditapes Philippinarum ◽  
Genomic Sequences ◽  
Future Research ◽  
Asian Clam ◽  
Sequencing Technologies ◽  
East And Southeast Asia ◽  
Clam Corbicula

AbstractThe Asian Clam (Corbicula fluminea) is a valuable commercial and medicinal bivalve, which is widely distributed in East and Southeast Asia. As a natural nutrient source, the clam is rich in protein, amino acids, and microelements. The genome of C. fluminea has not yet been characterized; therefore, genome-assisted breeding and improvements cannot yet be implemented. In this work, we present a de novo chromosome-scale genome assembly of C. fluminea using PacBio and Hi-C sequencing technologies. The assembled genome comprised 4728 contigs, with a contig N50 of 521.06 Kb, and 1,215 scaffolds with a scaffold N50 of 70.62 Mb. More than 1.51 Gb (99.17%) of genomic sequences were anchored to 18 chromosomes, of which 1.40 Gb (92.81%) of genomic sequences were ordered and oriented. The genome contains 38,841 coding genes, 32,591 (83.91%) of which were annotated in at least one functional database. Compared with related species, C. fluminea had 851 expanded gene families and 191 contracted gene families. The phylogenetic tree showed that C. fluminea diverged from Ruditapes philippinarum, ~ 228.89 million years ago (Mya), and the genomes of C. fluminea and R. philippinarum shared 244 syntenic blocks. Additionally, we identified 2 MITF members and 99 NLRP members in C. fluminea genome. The high-quality and chromosomal Asian Clam genome will be a valuable resource for a range of development and breeding studies of C. fluminea in future research.

scholarly journals Genome-wide search and structural and functional analyses for late embryogenesis-abundant (LEA) gene family in poplar

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Zihan Cheng ◽  
Xuemei Zhang ◽  
Wenjing Yao ◽  
Kai Zhao ◽  
Lin Liu ◽  
...  
Keyword(s):  
Gene Family ◽  
Higher Plants ◽  
Abiotic Stress Tolerance ◽  
Gene Families ◽  
Regulatory Elements ◽  
Late Embryogenesis Abundant ◽  
Genome Wide ◽  
Lea Gene ◽  
Late Embryogenesis ◽  
Genome Wide Search

Abstract Background The Late Embryogenesis-Abundant (LEA) gene families, which play significant roles in regulation of tolerance to abiotic stresses, widely exist in higher plants. Poplar is a tree species that has important ecological and economic values. But systematic studies on the gene family have not been reported yet in poplar. Results On the basis of genome-wide search, we identified 88 LEA genes from Populus trichocarpa and renamed them as PtrLEA. The PtrLEA genes have fewer introns, and their promoters contain more cis-regulatory elements related to abiotic stress tolerance. Our results from comparative genomics indicated that the PtrLEA genes are conserved and homologous to related genes in other species, such as Eucalyptus robusta, Solanum lycopersicum and Arabidopsis. Using RNA-Seq data collected from poplar under two conditions (with and without salt treatment), we detected 24, 22 and 19 differentially expressed genes (DEGs) in roots, stems and leaves, respectively. Then we performed spatiotemporal expression analysis of the four up-regulated DEGs shared by the tissues, constructed gene co-expression-based networks, and investigated gene function annotations. Conclusion Lines of evidence indicated that the PtrLEA genes play significant roles in poplar growth and development, as well as in responses to salt stress.

scholarly journals Identification and Expression Analysis of the Genes Involved in the Raffinose Family Oligosaccharides Pathway of Phaseolus vulgaris and Glycine max

Plants ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 1465
Author(s):  
Ramon de Koning ◽  
Raphaël Kiekens ◽  
Mary Esther Muyoka Toili ◽  
Geert Angenon
Keyword(s):  
Common Bean ◽  
Seed Development ◽  
Expression Analysis ◽  
De Novo ◽  
Expression Patterns ◽  
Gene Families ◽  
Rna Seq ◽  
Raffinose Family Oligosaccharides ◽  
Specific Expression ◽  
Raffinose Synthase

Raffinose family oligosaccharides (RFO) play an important role in plants but are also considered to be antinutritional factors. A profound understanding of the galactinol and RFO biosynthetic gene families and the expression patterns of the individual genes is a prerequisite for the sustainable reduction of the RFO content in the seeds, without compromising normal plant development and functioning. In this paper, an overview of the annotation and genetic structure of all galactinol- and RFO biosynthesis genes is given for soybean and common bean. In common bean, three galactinol synthase genes, two raffinose synthase genes and one stachyose synthase gene were identified for the first time. To discover the expression patterns of these genes in different tissues, two expression atlases have been created through re-analysis of publicly available RNA-seq data. De novo expression analysis through an RNA-seq study during seed development of three varieties of common bean gave more insight into the expression patterns of these genes during the seed development. The results of the expression analysis suggest that different classes of galactinol- and RFO synthase genes have tissue-specific expression patterns in soybean and common bean. With the obtained knowledge, important galactinol- and RFO synthase genes that specifically play a key role in the accumulation of RFOs in the seeds are identified. These candidate genes may play a pivotal role in reducing the RFO content in the seeds of important legumes which could improve the nutritional quality of these beans and would solve the discomforts associated with their consumption.

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