scholarly journals Targeted Enrichment of Large Gene Families for Phylogenetic Inference: Phylogeny and Molecular Evolution of Photosynthesis Genes in the Portullugo Clade (Caryophyllales)

2017 ◽  
Vol 67 (3) ◽  
pp. 367-383 ◽  
Author(s):  
Abigail J Moore ◽  
Jurriaan M De Vos ◽  
Lillian P Hancock ◽  
Eric Goolsby ◽  
Erika J Edwards
Keyword(s):  
Molecular Evolution ◽  
Gene Families ◽  
Phylogenetic Inference ◽  
Large Gene ◽  
Photosynthesis Genes ◽  
Evolution Of Photosynthesis ◽  
Targeted Enrichment

scholarly journals Targeted Enrichment of Large Gene Families for Phylogenetic Inference: Phylogeny and Molecular Evolution of Photosynthesis Genes in the Portullugo (Caryophyllales)

2017 ◽  
Author(s):  
Abigail J. Moore ◽  
Jurriaan M. de Vos ◽  
Lillian P. Hancock ◽  
Eric Goolsby ◽  
Erika J. Edwards
Keyword(s):  
Molecular Evolution ◽  
Phylogenetic Analyses ◽  
Strong Support ◽  
Gene Families ◽  
Sister Group ◽  
Single Copy ◽  
Gene Trees ◽  
Evolutionary Transitions ◽  
Large Gene ◽  
Cam Photosynthesis

ABSTRACTHybrid enrichment is an increasingly popular approach for obtaining hundreds of loci for phylogenetic analysis across many taxa quickly and cheaply. The genes targeted for sequencing are typically single-copy loci, which facilitate a more straightforward sequence assembly and homology assignment process. However, single copy loci are relatively uncommon elements of most genomes, and as such may provide a biased evolutionary history. Furthermore, this approach limits the inclusion of most genes of functional interest, which often belong to multi-gene families. Here we demonstrate the feasibility of including large gene families in hybrid enrichment protocols for phylogeny reconstruction and subsequent analyses of molecular evolution, using a new set of bait sequences designed for the “portullugo” (Caryophyllales), a moderately sized lineage of flowering plants (~2200 species) that includes the cacti and harbors many evolutionary transitions to C4 and CAM photosynthesis. Including multi-gene families allowed us to simultaneously infer a robust phylogeny and construct a dense sampling of sequences for a major enzyme of C4 and CAM photosynthesis, which revealed the accumulation of adaptive amino acid substitutions associated with C4 and CAM origins in particular paralogs. Our final set of matrices for phylogenetic analyses included 75–218 loci across 74 taxa, with ~50% matrix completeness across datasets. Phylogenetic resolution was greatly improved across the tree, at both shallow and deep levels. Concatenation and coalescent-based approaches both resolve with strong support the sister lineage of the cacti: Anacampserotaceae + Portulacaceae, two lineages of mostly diminutive succulent herbs of warm, arid regions. In spite of this congruence, BUCKy concordance analyses demonstrated strong and conflicting signals across gene trees for the resolution of the sister group of the cacti. Our results add to the growing number of examples illustrating the complexity of phylogenetic signals in genomic-scale data.

scholarly journals Ultra Large Gene Families: A Matter of Adaptation or Genomic Parasites?

Life ◽  
2016 ◽  
Vol 6 (3) ◽  
pp. 32 ◽  
Author(s):  
Philipp Schiffer ◽  
Jan Gravemeyer ◽  
Martina Rauscher ◽  
Thomas Wiehe
Keyword(s):  
Gene Families ◽  
Large Gene

Ribosomal DNA: Molecular Evolution and Phylogenetic Inference

1991 ◽  
Vol 66 (4) ◽  
pp. 411-453 ◽  
Author(s):  
David M. Hillis ◽  
Michael T. Dixon
Keyword(s):  
Molecular Evolution ◽  
Ribosomal Dna ◽  
Phylogenetic Inference

scholarly journals Complex Molecular Evolution and Expression of Expansin Gene Families in Three Basic Diploid Species of Brassica

2020 ◽  
Vol 21 (10) ◽  
pp. 3424 ◽  
Author(s):  
Weimiao Liu ◽  
Tianqi Lyu ◽  
Liai Xu ◽  
Ziwei Hu ◽  
Xingpeng Xiong ◽  
...  
Keyword(s):  
Molecular Evolution ◽  
Cell Walls ◽  
Plant Cell Wall ◽  
Diploid Species ◽  
Brassica Species ◽  
Gene Families ◽  
Structural Proteins ◽  
Development Processes ◽  
Positive Correlations ◽  
Complete Genomic

Expansins are a kind of structural proteins of the plant cell wall, and they enlarge cells by loosening the cell walls. Therefore, expansins are involved in many growth and development processes. The complete genomic sequences of Brassica rapa, Brassica oleracea and Brassica nigra provide effective platforms for researchers to study expansin genes, and can be compared with analogues in Arabidopsis thaliana. This study identified and characterized expansin families in B. rapa, B. oleracea, and B. nigra. Through the comparative analysis of phylogeny, gene structure, and physicochemical properties, the expansin families were divided into four subfamilies, and then their expansion patterns and evolution details were explored accordingly. Results showed that after the three species underwent independent evolution following their separation from A. thaliana, the expansin families in the three species had increased similarities but fewer divergences. By searching divergences of promoters and coding sequences, significant positive correlations were revealed among orthologs in A. thaliana and the three basic species. Subsequently, differential expressions indicated extensive functional divergences in the expansin families of the three species, especially in reproductive development. Hence, these results support the molecular evolution of basic Brassica species, potential functions of these genes, and genetic improvement of related crops.

scholarly journals A Genome-Wide Analysis of the Pentatricopeptide Repeat (PPR) Gene Family and PPR-Derived Markers for Flesh Color in Watermelon (Citrullus lanatus)

Genes ◽  
2020 ◽  
Vol 11 (10) ◽  
pp. 1125
Author(s):  
Saminathan Subburaj ◽  
Luhua Tu ◽  
Kayoun Lee ◽  
Gwang-Soo Park ◽  
Hyunbae Lee ◽  
...  
Keyword(s):  
Gene Family ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Citrullus Lanatus ◽  
Gene Families ◽  
Nucleotide Polymorphisms ◽  
Pentatricopeptide Repeat ◽  
Flesh Color ◽  
Large Gene ◽  
A Genome

Watermelon (Citrullus lanatus) is an economically important fruit crop grown for consumption of its large edible fruit flesh. Pentatricopeptide-repeat (PPR) encoding genes, one of the large gene families in plants, are important RNA-binding proteins involved in the regulation of plant growth and development by influencing the expression of organellar mRNA transcripts. However, systematic information regarding the PPR gene family in watermelon remains largely unknown. In this comprehensive study, we identified and characterized a total of 422 C. lanatus PPR (ClaPPR) genes in the watermelon genome. Most ClaPPRs were intronless and were mapped across 12 chromosomes. Phylogenetic analysis showed that ClaPPR proteins could be divided into P and PLS subfamilies. Gene duplication analysis suggested that 11 pairs of segmentally duplicated genes existed. In-silico expression pattern analysis demonstrated that ClaPPRs may participate in the regulation of fruit development and ripening processes. Genotyping of 70 lines using 4 single nucleotide polymorphisms (SNPs) from 4 ClaPPRs resulted in match rates of over 0.87 for each validated SNPs in correlation with the unique phenotypes of flesh color, and could be used in differentiating red, yellow, or orange watermelons in breeding programs. Our results provide significant insights for a comprehensive understanding of PPR genes and recommend further studies on their roles in watermelon fruit growth and ripening, which could be utilized for cultivar development of watermelon.

scholarly journals Exploration of the Germline Genome of the Ciliate Chilodonella uncinata through Single-Cell Omics (Transcriptomics and Genomics)

mBio ◽  
2018 ◽  
Vol 9 (1) ◽  
Author(s):  
Xyrus X. Maurer-Alcalá ◽  
Rob Knight ◽  
Laura A. Katz
Keyword(s):  
Single Cell ◽  
Large Scale ◽  
Gc Content ◽  
Gene Families ◽  
Genome Rearrangements ◽  
Paramecium Tetraurelia ◽  
Protein Coding ◽  
Genome Data ◽  
Large Gene ◽  
Disproportionate Number

ABSTRACTSeparate germline and somatic genomes are found in numerous lineages across the eukaryotic tree of life, often separated into distinct tissues (e.g., in plants, animals, and fungi) or distinct nuclei sharing a common cytoplasm (e.g., in ciliates and some foraminifera). In ciliates, germline-limited (i.e., micronuclear-specific) DNA is eliminated during the development of a new somatic (i.e., macronuclear) genome in a process that is tightly linked to large-scale genome rearrangements, such as deletions and reordering of protein-coding sequences. Most studies of germline genome architecture in ciliates have focused on the model ciliatesOxytricha trifallax,Paramecium tetraurelia, andTetrahymena thermophila, for which the complete germline genome sequences are known. Outside of these model taxa, only a few dozen germline loci have been characterized from a limited number of cultivable species, which is likely due to difficulties in obtaining sufficient quantities of “purified” germline DNA in these taxa. Combining single-cell transcriptomics and genomics, we have overcome these limitations and provide the first insights into the structure of the germline genome of the ciliateChilodonella uncinata, a member of the understudied classPhyllopharyngea. Our analyses reveal the following: (i) large gene families contain a disproportionate number of genes from scrambled germline loci; (ii) germline-soma boundaries in the germline genome are demarcated by substantial shifts in GC content; (iii) single-cell omics techniques provide large-scale quality germline genome data with limited effort, at least for ciliates with extensively fragmented somatic genomes. Our approach provides an efficient means to understand better the evolution of genome rearrangements between germline and soma in ciliates.IMPORTANCEOur understanding of the distinctions between germline and somatic genomes in ciliates has largely relied on studies of a few model genera (e.g.,Oxytricha,Paramecium,Tetrahymena). We have used single-cell omics to explore germline-soma distinctions in the ciliateChilodonella uncinata, which likely diverged from the better-studied ciliates ~700 million years ago. The analyses presented here indicate that developmentally regulated genome rearrangements between germline and soma are demarcated by rapid transitions in local GC composition and lead to diversification of protein families. The approaches used here provide the basis for future work aimed at discerning the evolutionary impacts of germline-soma distinctions among diverse ciliates.

Diversification of the Histone Fold Motif in Plants: Evolution of New Functional Roles

2016 ◽  
Vol 1 (1) ◽  
pp. 63 ◽  
Author(s):  
Amish Kumar ◽  
Gitanjali Yadav
Keyword(s):  
Gene Families ◽  
Chromatin Accessibility ◽  
Core Histone ◽  
Alpha Helices ◽  
Functional Roles ◽  
Histone Fold ◽  
Nuclear Factor Y ◽  
The Core ◽  
Large Gene ◽  
Core Histones

<p>The Histone fold motif (HFM) is one of the most conserved structural motifs in biology, mainly found in the core histone sub-units of all eukaryotes. The HFM represents a helix-strand-helix motif having three alpha helices connected by two loops/beta strands. This helix-strand-helix motif has the unique property of binding strongly with proteins as well as with DNA. Apart from core histones, the HFM has been reported in a variety of other proteins in all forms of life. In this work, we review the various classes of proteins that contain the HFM, as well as the diverse roles played by these proteins in the plant kingdom. As will be clear from this review, formation of the core histones through multi-merisation is not the only role played by this conserved fold, although the characteristic ability of the HFM to dimerize with suitable partner proteins has been used by nature to perform several non-core-histone functions. Most of the information about plant HFM containing proteins, such as identification and classification, has been done based on homology with yeast and animal counterparts. However, the ability of plants genomes to duplicate extensively has led to the existence of large gene families of the HFM containing proteins, unlike other eukaryotes. Plant HFM containing proteins can broadly be classified under the following major categories; TBP-associated factors (TAF), Nuclear Factor Y (NF-Y), Dr1/DrAp1 proteins and the chromatin accessibility complex (CHRAC). These proteins families are known to be involved in transcriptional regulation, co-activation and chromosome maintenance. Partner recognition through dimer formation remains a major conserved feature of these groups when compared with core histone sub-units.</p>

scholarly journals Duplication of chickendefensin7gene generated by gene conversion and homologous recombination

2016 ◽  
Vol 113 (48) ◽  
pp. 13815-13820 ◽  
Author(s):  
Mi Ok Lee ◽  
Susanne Bornelöv ◽  
Leif Andersson ◽  
Susan J. Lamont ◽  
Junfeng Chen ◽  
...  
Keyword(s):  
Homologous Recombination ◽  
Copy Number Variation ◽  
Gene Conversion ◽  
Copy Number ◽  
Computational Prediction ◽  
Gene Families ◽  
Duplication Event ◽  
Promoter Regions ◽  
Large Gene ◽  
Number Variation

Defensins constitute an evolutionary conserved family of cationic antimicrobial peptides that play a key role in host innate immune responses to infection. Defensin genes generally reside in complex genomic regions that are prone to structural variation, and defensin genes exhibit extensive copy number variation in humans and in other species. Copy number variation of defensin genes was examined in inbred lines of Leghorn and Fayoumi chickens, and a duplication ofdefensin7was discovered in the Fayoumi breed. Analysis of junction sequences confirmed the occurrence of a simple tandem duplication ofdefensin7with sequence identity at the junction, suggesting nonallelic homologous recombination betweendefensin7anddefensin6. The duplication event generated two chimeric promoters that are best explained by gene conversion followed by homologous recombination. Expression ofdefensin7was not elevated in animals with two genes despite both genes being transcribed in the tissues examined. Computational prediction of promoter regions revealed the presence of several putative transcription factor binding sites generated by the duplication event. These data provide insight into the evolution and possible function of large gene families and specifically, the defensins.

scholarly journals Conversion between 100-million-year-old duplicated genes contributes to rice subspecies divergence

2020 ◽  
Author(s):  
Chendan Wei ◽  
Zhenyi Wang ◽  
Jianyu Wang ◽  
Jia Teng ◽  
Shaoqi Shen ◽  
...  
Keyword(s):  
Gene Conversion ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Chromosome Rearrangement ◽  
Gene Families ◽  
Single Pair ◽  
Duplicated Genes ◽  
Cultivated Rice ◽  
Large Gene ◽  
Conversion Rates

AbstractExtensive sequence similarity between duplicated gene pairs produced by paleo-polyploidization may result from illegitimate recombination between homologous chromosomes. The genomes of Asian cultivated rice Xian/indica (XI) and Geng/japonica (GJ) have recently been updated, providing new opportunities for investigating on-going gene conversion events. Using comparative genomics and phylogenetic analyses, we evaluated gene conversion rates between duplicated genes produced by polyploidization 100 million years ago (mya) in GJ and XI. At least 5.19%–5.77% of genes duplicated across three genomes were affected by whole-gene conversion after the divergence of GJ and XI at ~0.4 mya, with more (7.77%–9.53%) showing conversion of only gene portions. Independently converted duplicates surviving in genomes of different subspecies often used the same donor genes. On-going gene conversion frequency was higher near chromosome termini, with a single pair of homoeologous chromosomes 11 and 12 in each genome most affected. Notably, on-going gene conversion has maintained similarity between very ancient duplicates, provided opportunities for further gene conversion, and accelerated rice divergence. Chromosome rearrangement after polyploidization may result in gene loss, providing a basis for on-going gene conversion, and may have contributed directly to restricted recombination/conversion between homoeologous regions. Gene conversion affected biological functions associated with multiple genes, such as catalytic activity, implying opportunities for interaction among members of large gene families, such as NBS-LRR disease-resistance genes, resulting in gene conversion. Duplicated genes in rice subspecies generated by grass polyploidization ~100 mya remain affected by gene conversion at high frequency, with important implications for the divergence of rice subspecies.One-sentence summaryOn-going gene conversion between duplicated genes produced by 100 mya polyploidization contributes to rice subspecies divergence, often involving the same donor genes at chromosome termini.

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