dorsal/arxiv
View SchemaGenome-wide EST data mining approaches to resolving incongruence of molecular phylogenies
| Authors | Yunfeng Shan |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0609004 |
| URL | https://arxiv.org/abs/q-bio/0609004 |
Abstract
36 single genes of six plants inferred 18 unique trees using maximum parsimony. Such incongruence is an important issue and how to reconstruct the congruent tree still is one of the most challenges in molecular phylogenetics. For resolving this problem, a genome-wide EST data mining approach was systematically investigated by retrieving a large size of EST data of 144 shared genes of six green plants from GenBank. The results show that the concatenated alignments approach overcame incongruence among single-gene phylogenies and successfully reconstructed the congruent tree of six species with 100% jackknife support across each branch when 144 genes was used. Jackknife supports of correct branches increased with number of genes linearly, but those of wrong branches also increased linearly. For inferring the congruent tree, the minimum 30 genes were required. This approach may provide potential power in resolving conflictions of phylogenies. Keywords: Genome-wide; Data mining; EST; Phylogeny; Congruent tree; Jackknife support; Plants.
{
"annotation_id": "bdde00be-3481-44ae-8883-068c84d617b1",
"date_created": "2026-03-02T18:01:35.333000Z",
"date_modified": "2026-03-02T18:01:35.333000Z",
"file_hash": "3567d856803e1063c5dcf9a7d85ca0b742e7e2f32cc3f49fe1aca69bf12fafb2",
"private": false,
"record": {
"abstract": "36 single genes of six plants inferred 18 unique trees using maximum\nparsimony. Such incongruence is an important issue and how to reconstruct the\ncongruent tree still is one of the most challenges in molecular phylogenetics.\nFor resolving this problem, a genome-wide EST data mining approach was\nsystematically investigated by retrieving a large size of EST data of 144\nshared genes of six green plants from GenBank. The results show that the\nconcatenated alignments approach overcame incongruence among single-gene\nphylogenies and successfully reconstructed the congruent tree of six species\nwith 100% jackknife support across each branch when 144 genes was used.\nJackknife supports of correct branches increased with number of genes linearly,\nbut those of wrong branches also increased linearly. For inferring the\ncongruent tree, the minimum 30 genes were required. This approach may provide\npotential power in resolving conflictions of phylogenies.\n Keywords: Genome-wide; Data mining; EST; Phylogeny; Congruent tree; Jackknife\nsupport; Plants.",
"arxiv_id": "q-bio/0609004",
"authors": [
"Yunfeng Shan"
],
"categories": [
"q-bio.GN"
],
"title": "Genome-wide EST data mining approaches to resolving incongruence of molecular phylogenies",
"url": "https://arxiv.org/abs/q-bio/0609004"
},
"schema_id": "dorsal/arxiv",
"source": {
"execution_id": "6b5f5f8d-e956-4a24-97af-12e8a4ea40ca",
"id": "arXiv Dataset IDs",
"type": "Model",
"variant": "snapshot-2026-03-01",
"version": "0.1.0"
},
"user_id": 1000002
}