Comparative phylogenetic analysis of aquaporins provides insight into the gene family expansion and evolution in plants and their role in drought tolerant and susceptible chickpea cultivars

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.

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The Evolution, Gene Expression Profile, and Secretion of Digestive Peptidases in Lepidoptera Species

Catalysts ◽

10.3390/catal10020217 ◽

2020 ◽

Vol 10 (2) ◽

pp. 217

Author(s):

Lucas R. Lima ◽

Renata O. Dias ◽

Felipe Jun Fuzita ◽

Clélia Ferreira ◽

Walter R. Terra ◽

...

Keyword(s):

Gene Family ◽

Expression Profile ◽

Catalytic Triad ◽

Rna Seq ◽

Anterior Portion ◽

Gene Family Expansion ◽

Genes Encoding ◽

Peptidase Inhibitor ◽

Family Expansion ◽

Midgut Lumen

Serine peptidases (SPs) are responsible for most primary protein digestion in Lepidoptera species. An expansion of the number of genes encoding trypsin and chymotrypsin enzymes and the ability to upregulate the expression of some of these genes in response to peptidase inhibitor (PI) ingestion have been associated with the adaptation of Noctuidae moths to herbivory. To investigate whether these gene family expansion events are common to other Lepidoptera groups, we searched for all genes encoding putative trypsin and chymotrypsin enzymes in 23 publicly available genomes from this taxon. Phylogenetic analysis showed that several gene family expansion events may have occurred in the taxon’s evolutionary history and that these events gave rise to a very diverse group of enzymes, including proteins lacking the canonical SP catalytic triad. The expression profile of these enzymes along the midgut and the secretion mechanisms by which these enzymes enter the luminal content were also analyzed in Spodoptera frugiperda larvae using RNA-seq and proteomics. These results support the proposal of a midgut countercurrent flux responsible for the direction of these proteins to the anterior portion of the midgut and show that these enzymes reach the midgut lumen via both exocytosis and microapocrine secretion mechanisms.

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Comparative phylogenetic analysis and transcriptional profiling of MADS-box gene family identified DAM and FLC-like genes in apple (Malusx domestica)

Scientific Reports ◽

10.1038/srep20695 ◽

2016 ◽

Vol 6 (1) ◽

Cited By ~ 38

Author(s):

Gulshan Kumar ◽

Preeti Arya ◽

Khushboo Gupta ◽

Vinay Randhawa ◽

Vishal Acharya ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Gene Family ◽

Transcriptional Profiling ◽

Mads Box ◽

Mads Box Gene ◽

Comparative Phylogenetic Analysis

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The roles of LINEs, LTRs and SINEs in lineage-specific gene family expansions in the human and mouse genomes

10.1101/042309 ◽

2016 ◽

Cited By ~ 1

Author(s):

Václav Janoušek ◽

Christina M Laukaitis ◽

Alexey Yanchukov ◽

Robert Karn

Keyword(s):

Gene Family ◽

Gene Families ◽

Specific Gene ◽

Second Phase ◽

Open Chromatin ◽

Gene Family Expansion ◽

Family Expansion ◽

Human And Mouse ◽

Lineage Specific Gene ◽

Runaway Process

We explored genome-wide patterns of RT content surrounding lineage-specific gene family expansions in the human and mouse genomes. Our results suggest that the size of a gene family is an important predictor of the RT distribution in close proximity to the family members. The distribution differs considerably between the three most common RT classes (LINEs, LTRs and SINEs). LINEs and LTRs tend to be more abundant around genes of multi-copy gene families, whereas SINEs tend to be depleted around such genes. Detailed analysis of the distribution and diversity of LINEs and LTRs with respect to gene family size suggests that each has a distinct involvement in gene family expansion. LTRs are associated with open chromatin sites surrounding the gene families, supporting their involvement in gene regulation, whereas LINEs may play a structural role, promoting gene duplication. This suggests that gene family expansions, especially in the mouse genome, might undergo two phases, the first is characterized by elevated deposition of LTRs and their utilization in reshaping gene regulatory networks. The second phase is characterized by rapid gene family expansion due to continuous accumulation of LINEs and it appears that, in some instances at least, this could become a runaway process. We provide an example in which this has happened and we present a simulation supporting the possibility of the runaway process. Our observations also suggest that specific differences exist in this gene family expansion process between human and mouse genomes.

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