microsynteny_networks — Microsynteny networks of mammal and plant genomes (2019, 2021)

Description

Networks of microsynteny (conserved gene order) between the genes of many genomes, built by T. Zhao, M. E. Schranz and collaborators to study the evolution of genome structure in mammals and flowering plants. The protein-coding genes of the pairs of genomes were compared (with the best hits of each gene in the other genomes), and collinear blocks of homologous genes (syntenic blocks) were detected with MCScanX (for the networks of 2019, with the 5 best hits per gene, at least 5 anchor gene pairs per block, and at most 15 (mammals) or 25 (plants) genes between anchors); the anchor pairs of all the blocks form the network.

Nodes are genes, and an edge connects two genes that are anchors of the same syntenic block (one edge per block, so that a pair of genes in several blocks is connected by several edges).

mammals: 87 mammalian genomes (Zhao and Schranz, 2019).
mammals_busco: the subnetwork of the BUSCO genes (near-universal single-copy orthologs) of the 87 mammals, built separately with other gene identifiers (NCBI), as given by the authors (two columns, without blocks).
plants_107: 107 genomes of flowering plants and other plants (Zhao and Schranz, 2019).
plants_107_busco: the subnetwork of the BUSCO genes of the 107 plants (without blocks).
plants_123: 123 plant genomes, mostly flowering plants (Zhao et al., 2021).

The networks have the following properties:

(Node) name: the identifier of the gene, prefixed by the code of its genome (e.g. Hsap... for mammals, ath_... for plants).
(Node) genome: the code of the genome of the gene.
(Node) species: the species of the genome (from the tables of the genomes of the studies; empty if the code is not in the tables).
(Node) cluster: the cluster of the gene in the clustering of the network with Infomap by the authors (-1 if the gene is not in the clustering).
(Node) chromosome (plants_123): the chromosome (or scaffold) of the gene.
(Edge) block, anchor (except the BUSCO networks): the syntenic block of the anchor pair, identified in the data as <genome 1>_<genome 2><n>-<k>b, where n (block) numbers the blocks of the pair of genomes (those of the two genes of the edge) and k (anchor) the anchor pairs of the block.
(Edge) block_score (except the BUSCO networks): the score of the block computed by MCScanX.
(Edge) evalue, block_evalue, block_size (plants_123): the E-value of the anchor pair, and the E-value and the number of anchor pairs of the block.

Tags

Biological Genetic Unweighted Multigraph Metadata

Added

2026-10-31

Citation

T. Zhao, M. E. Schranz, "Network-based microsynteny analysis identifies major differences and genomic outliers in mammalian and angiosperm genomes." Proceedings of the National Academy of Sciences 116, 2165-2174 (2019) 10.1073/pnas.1801757116 Sci-Hub
T. Zhao, A. Zwaenepoel, J.-Y. Xue, S.-M. Kao, Z. Li, M. E. Schranz, Y. Van de Peer, "Whole-genome microsynteny-based phylogeny of angiosperms." Nature Communications 12, 3498 (2021) 10.1038/s41467-021-23665-0 Sci-Hub

Upstream URL OK

https://doi.org/10.7910/DVN/BDMA7A
https://doi.org/10.7910/DVN/7ZZWIH

Upstream license

Creative Commons CC0 1.0 Universal (CC0 1.0), https://creativecommons.org/publicdomain/zero/1.0/

Networks

Tip: click on a column header to sort the list, or hover over it for a description.

Column legend

$\left<k\right>$: Mean degree
$\sigma_k$: Standard deviation of the degrees
$\lambda_h$: Largest eigenvalue of the Hashimoto (non-backtracking) matrix
$\tau$: Random walk mixing time
$r$: Degree assortativity
$c$: Global clustering coefficient
$\oslash$: (Pseudo-) diameter
$S$: Relative size of the largest component
NPs: Node properties
EPs: Edge properties

Name	Nodes	Edges	$\left<k\right>$	$\sigma_k$	$\lambda_h$	$\tau$	$r$	$c$	$\oslash$	$S$	Kind	Mode	NPs	EPs	gt	GraphML	GML	csv
mammals	1,476,838	50,962,561	69.02	27.17	303.17	500452.44	0.78	0.93	47	0.06	Undirected	Unipartite	name genome species cluster	block anchor block_score	109.6 MiB	341.5 MiB	332.1 MiB	400.8 MiB
mammals_busco	330,152	12,248,803	74.20	14.85	131.44	6216.71	0.66	0.98	8	0.00	Undirected	Unipartite	name genome species cluster		3.5 MiB	43.9 MiB	43.1 MiB	47.9 MiB
plants_107	2,221,461	47,846,137	43.08	41.87	211.46	49102.77	0.56	0.69	49	0.83	Undirected	Unipartite	name genome species cluster	block anchor block_score	196.2 MiB	445.7 MiB	436.0 MiB	436.3 MiB
plants_107_busco	128,024	2,094,024	32.71	22.75	84.62	22337.64	0.55	0.80	37	0.07	Undirected	Unipartite	name genome species cluster		3.8 MiB	10.8 MiB	10.6 MiB	11.0 MiB
plants_123	3,098,333	94,980,088	61.31	60.98	308.12	110591.31	0.58	0.69	50	0.86	Undirected	Unipartite	name genome species cluster chromosome	block anchor block_score evalue block_evalue block_size	700.0 MiB	1.357 GiB	1.280 GiB	1.312 GiB