scholarly journals Phylogenomic Analysis of the PEBP Gene Family from Kalanchoë

Agronomy ◽  
2019 ◽  
Vol 9 (4) ◽  
pp. 171 ◽  
Author(s):  
Kathryn Kuligowska Mackenzie ◽  
Lívia Lopes Coelho ◽  
Henrik Lütken ◽  
Renate Müller
Keyword(s):  
Gene Family ◽  
Plant Architecture ◽  
Amino Acid Sequences ◽  
Phylogenomic Analysis ◽  
Flowering Locus T ◽  
Molecular Control ◽  
Protein Functions ◽  
Flowering Control ◽  
Conserved Gene ◽  
Insight Into

The PEBP family comprises proteins that function as key regulators of flowering time throughout the plant kingdom and they also regulate growth and plant architecture. Within the PEBP protein family, three subfamilies can be distinguished in angiosperms: MOTHER OF FT AND TFL1-like (MFT), FLOWERING LOCUS T-like (FT-like), and TERMINAL FLOWER1-like (TFL1-like). Taking advantage of the genome sequences available from K. fedtschenkoi and K. laxiflora, we performed computational analysis to identify the members of the PEBP gene family in these species. The analyses revealed the existence of 11 PEBP genes in K. fedtschenkoi and 18 in K. laxiflora, which are clustered in two clades: FT-like and TFL1-like. The PEBP genes had conserved gene structure and the proteins had highly conserved amino acid sequences in the positions crucial for the protein functions. The analysis of Ka/Ks ratio revealed that most recently duplicated genes are under positive selection. Despite being an economically important genus, the genetics underlying the regulation of flowering in Kalanchoë is poorly understood. The results of this study may provide a new insight into the molecular control of flowering that will allow further studies on flowering control in Kalanchoë.

scholarly journals The Dynein Gene Family in Chlamydomonas reinhardtii

Genetics ◽  
1996 ◽  
Vol 144 (2) ◽  
pp. 569-585 ◽  
Author(s):  
Mary E Porter ◽  
Julie A Knott ◽  
Steven H Myster ◽  
Samuel J Farlow
Keyword(s):  
Gene Family ◽  
Genetic Map ◽  
Single Copy ◽  
Amino Acid Sequences ◽  
Single Copy Gene ◽  
Heavy Chains ◽  
Length Polymorphisms ◽  
Copy Gene ◽  
Genes Encoding ◽  
Insight Into

Abstract To correlate dynein heavy chain (Dhc) genes with flagellar mutations and gain insight into the function of specific dynein isoforms, we placed eight members of the Dhc gene family on the genetic map of Chlamydomonas. Using a PCR-based strategy, we cloned 11 Dhc genes from Chlamydomonas. Comparisons with other Dhc genes indicate that two clones correspond to genes encoding the alpha and beta heavy chains of the outer dynein arm. Alignment of the predicted amino acid sequences spanning the nucleotide binding site indicates that the remaining nine clones can be subdivided into three groups that are likely to include representatives of the inner-arm Dhc isoforms. Gene-specific probes reveal that each clone represents a single-copy gene that is expressed as a transcript of the appropriate size (>13 kb) sufficient to encode a high molecular weight Dhc polypeptide. The expression of all nine genes is upregulated in response to deflagellation, suggesting a role in axoneme assembly or motility. Restriction fragment length polymorphisms between divergent C. reinhardtii strains have been used to place each Dhr gene on the genetic map of Chlamydomonas. These studies lay the groundwork for correlating defects in different Dhc genes with specific flagellar mutations.

scholarly journals FIND: Identifying Functionally and Structurally Important Features in Protein Sequences with Deep Neural Networks

2019 ◽  
Author(s):  
Ranjani Murali ◽  
James Hemp ◽  
Victoria Orphan ◽  
Yonatan Bisk
Keyword(s):  
Neural Networks ◽  
Amino Acid ◽  
Hidden Markov Models ◽  
Markov Models ◽  
Genomic Sequence ◽  
Hidden Markov ◽  
Amino Acid Sequences ◽  
Homologous Proteins ◽  
Biological Studies ◽  
Insight Into

AbstractThe ability to correctly predict the functional role of proteins from their amino acid sequences would significantly advance biological studies at the molecular level by improving our ability to understand the biochemical capability of biological organisms from their genomic sequence. Existing methods that are geared towards protein function prediction or annotation mostly use alignment-based approaches and probabilistic models such as Hidden-Markov Models. In this work we introduce a deep learning architecture (FunctionIdentification withNeuralDescriptions orFIND) which performs protein annotation from primary sequence. The accuracy of our methods matches state of the art techniques, such as protein classifiers based on Hidden Markov Models. Further, our approach allows for model introspection via a neural attention mechanism, which weights parts of the amino acid sequence proportionally to their relevance for functional assignment. In this way, the attention weights automatically uncover structurally and functionally relevant features of the classified protein and find novel functional motifs in previously uncharacterized proteins. While this model is applicable to any database of proteins, we chose to apply this model to superfamilies of homologous proteins, with the aim of extracting features inherent to divergent protein families within a larger superfamily. This provided insight into the functional diversification of an enzyme superfamily and its adaptation to different physiological contexts. We tested our approach on three families (nitrogenases, cytochromebd-type oxygen reductases and heme-copper oxygen reductases) and present a detailed analysis of the sequence characteristics identified in previously characterized proteins in the heme-copper oxygen reductase (HCO) superfamily. These are correlated with their catalytic relevance and evolutionary history. FIND was then applied to discover features in previously uncharacterized members of the HCO superfamily, providing insight into their unique sequence features. This modeling approach demonstrates the power of neural networks to recognize patterns in large datasets and can be utilized to discover biochemically and structurally important features in proteins from their amino acid sequences.Author summary

scholarly journals Molecular cloning of RBCS genes in Selaginella and the evolution of the rbcS gene family

2015 ◽  
Vol 67 (2) ◽  
pp. 373-383
Author(s):  
Bo Wang ◽  
Su Yingjuan ◽  
Ting Wang
Keyword(s):  
Gene Family ◽  
Physcomitrella Patens ◽  
Higher Plants ◽  
Genome Wide ◽  
A Genome ◽  
Rbcs Gene ◽  
Rbcs Genes ◽  
Selaginella Moellendorffii ◽  
Insight Into ◽  
Major Domain

Rubisco small subunits (RBCS) are encoded by a nuclear rbcS multigene family in higher plants and green algae. However, owing to the lack of rbcS sequences in lycophytes, the characteristics of rbcS genes in lycophytes is unclear. Recently, the complete genome sequence of the lycophyte Selaginella moellendorffii provided the first insight into the rbcS gene family in lycophytes. To understand further the characteristics of rbcS genes in other Selaginella, the full length of rbcS genes (rbcS1 and rbcS2) from two other Selaginella species were isolated. Both rbcS1 and rbcS2 genes shared more than 97% identity among three Selaginella species. RBCS proteins from Selaginella contained the Pfam RBCS domain F00101, which was a major domain of other plant RBCS proteins. To explore the evolution of the rbcS gene family across Selaginella and other plants, we identified and performed comparative analysis of the rbcS gene family among 16 model plants based on a genome-wide analysis. The results showed that (i) two rbcS genes were obtained in Selaginella, which is the second fewest number of rbcS genes among the 16 representative plants; (ii) an expansion of rbcS genes occurred in the moss Physcomitrella patens; (iii) only RBCS proteins from angiosperms contained the Pfam PF12338 domains, and (iv) a pattern of concerted evolution existed in the rbcS gene family. Our study provides new insights into the evolution of the rbcS gene family in Selaginella and other plants.

scholarly journals A Comprehensive Survey on the Terpene Synthase Gene Family Provides New Insight into Its Evolutionary Patterns

2019 ◽  
Vol 11 (8) ◽  
pp. 2078-2098 ◽  
Author(s):  
Shu-Ye Jiang ◽  
Jingjing Jin ◽  
Rajani Sarojam ◽  
Srinivasan Ramachandran
Keyword(s):  
Gene Family ◽  
Large Scale ◽  
Family Members ◽  
Terpene Synthase ◽  
Limited Information ◽  
Terpene Synthases ◽  
Genome Wide ◽  
A Genome ◽  
Family Expansion ◽  
Insight Into

Abstract Terpenes are organic compounds and play important roles in plant growth and development as well as in mediating interactions of plants with the environment. Terpene synthases (TPSs) are the key enzymes responsible for the biosynthesis of terpenes. Although some species were employed for the genome-wide identification and characterization of the TPS family, limited information is available regarding the evolution, expansion, and retention mechanisms occurring in this gene family. We performed a genome-wide identification of the TPS family members in 50 sequenced genomes. Additionally, we also characterized the TPS family from aromatic spearmint and basil plants using RNA-Seq data. No TPSs were identified in algae genomes but the remaining plant species encoded various numbers of the family members ranging from 2 to 79 full-length TPSs. Some species showed lineage-specific expansion of certain subfamilies, which might have contributed toward species or ecotype divergence or environmental adaptation. A large-scale family expansion was observed mainly in dicot and monocot plants, which was accompanied by frequent domain loss. Both tandem and segmental duplication significantly contributed toward family expansion and expression divergence and played important roles in the survival of these expanded genes. Our data provide new insight into the TPS family expansion and evolution and suggest that TPSs might have originated from isoprenyl diphosphate synthase genes.

scholarly journals An evolutionarily conserved gene family encodes proton-selective ion channels

Science ◽  
2018 ◽  
Vol 359 (6379) ◽  
pp. 1047-1050 ◽  
Author(s):  
Yu-Hsiang Tu ◽  
Alexander J. Cooper ◽  
Bochuan Teng ◽  
Rui B. Chang ◽  
Daniel J. Artiga ◽  
...  
Keyword(s):  
Ion Channels ◽  
Gene Family ◽  
Evolutionarily Conserved ◽  
Conserved Gene

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

2019 ◽  
Vol 10 (1) ◽  
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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