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Novel Sequence Discovery by Subtractive Genomics
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Towards a higher-level Ensifera phylogeny inferred from mitogenome sequences
Zhijun Zhou1, Ling Zhao2, Nian Liu3
1Key Laboratory of Invertebrate Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding, Hebei 071002, China.
Molecular Phylogenetics and Evolution
|February 12, 2017
Summary
This study sequenced 32 ensiferan mitogenomes, revealing novel gene arrangements and base composition biases. Phylogenetic analyses clarified evolutionary relationships within Ensifera, confirming Grylloidea and Gryllotalpoidea as sister groups.
Area of Science:
- * Evolutionary Biology
- * Genomics
- * Molecular Phylogenetics
Background:
- * Mitogenomes are crucial for understanding evolutionary history, but data for many Ensifera lineages remain scarce.
- * Previous studies have been limited by the availability of representative mitogenome sequences.
Purpose of the Study:
- * To determine and analyze 32 ensiferan mitogenomes to expand the genomic resources for this insect group.
- * To investigate patterns of gene arrangement and identify potential evolutionary markers.
- * To infer the higher-level phylogeny of Ensifera using both site-heterogeneous and site-homogeneous analytical methods.
Main Methods:
- * Sequencing of 32 ensiferan mitogenomes using ABI Sanger sequencing and Illumina® HiSeq2000.
- * Analysis of gene arrangements across 59 ensiferan mitogenomes, identifying six distinct patterns.
- * Phylogenetic inference using Bayesian inference (BI) and maximum likelihood (ML) analyses, with both site-heterogeneous and site-homogeneous models.
Main Results:
- * Identification of six gene arrangement patterns, including a novel arrangement in Lipotactes tripyrga.
- * Discovery of potential shared derived characters in gene rearrangements for Pseudophyllinae and Gryllidae.
- * Phylogenetic analyses resolved superfamilies as monophyletic, with Grylloidea and Gryllotalpoidea confirmed as sister groups. Site-heterogeneous BI analysis provided a more robust topology, placing Schizodactyloidea as the basal lineage.
Conclusions:
- * The study significantly expands the available ensiferan mitogenomic data and provides insights into gene arrangement evolution.
- * Base composition biases can complicate phylogenetic inference, highlighting the importance of appropriate analytical methods.
- * The resolved phylogeny clarifies the evolutionary relationships among Ensifera superfamilies, particularly the basal position of Schizodactyloidea and the sister relationship of Grylloidea and Gryllotalpoidea.
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