gclink: Gene-Cluster Discovery, Annotation and Visualization

Overview

gclink performs end-to-end analysis of gene clusters (e.g., photosynthesis, carbon/nitrogen/sulfur cycling, carotenoid, antibiotic, or viral genes) from (meta)genomes. It provides:

• Parsing of Basic Local Alignment Search Tool (BLAST) results in tab-delimited format produced by tools like NCBI BLAST+ and Diamond BLASTp
• Contiguous cluster detection
• Publication-ready visualization

Key Features

Adaptive Workflow

• Works with or without coding sequences input
• Skips plotting when functional grouping is absent
• Supports custom gene lists for universal cluster detection

Cluster Detection

• Density-based identification via AllGeneNum and MinConSeq parameters
• Handles incomplete gene annotation coverage
• Optional insertion of hypothetical ORFs at cluster boundaries

Visualization

• Publication-ready arrow plots with customizable based on gggenes:
  • Color themes
  • Functional group levels
  • Genome subsets

Installation

# Install from CRAN
install.packages("gclink")

# Install from GitHub
if (!require("devtools")) install.packages("devtools")
devtools::install_github("LiuyangLee/gclink")

Case 1: Using blastp result

# Case 1: Using blastp result with Full pipeline (Find Cluster + Extract FASTA + Plot Cluster)
library(gclink)
data(blastp_df)
data(seq_data)
data(photosynthesis_gene_list)
data(PGC_group)
gc_list <- gclink(in_blastp_df = blastp_df,
                  in_seq_data = seq_data,
                  in_gene_list = photosynthesis_gene_list,
                  in_GC_group  = PGC_group,
                  AllGeneNum = 50,
                  MinConSeq  = 25,
                  apply_length_filter = TRUE,
                  down_IQR   = 10,
                  up_IQR     = 10,
                  orf_before_first = 0,
                  orf_after_last = 0,
                  levels_gene_group = c('bch','puh','puf','crt','acsF','assembly','regulator',
                                        'hypothetical ORF'),
                  color_theme = c('#3BAA51','#6495ED','#DD2421','#EF9320','#F8EB00',
                                  '#FF0683','#956548','grey'),
                  genome_subset = NULL)
gc_meta = gc_list[["GC_meta"]]
gc_seq = gc_list[["GC_seq"]]
gc_plot = gc_list[["GC_plot"]]
head(gc_meta)   # Cluster metadata
head(gc_seq)    # FASTA sequences
print(gc_plot)  # Visualization

1 Input Data Preview

1.1 A dataframe of Diamond BLASTp output (e.g., head(blastp_df))

1.2 (Optional) A dataframe with SeqName (ORF identifier, Prodigal format: ⁠ORF_id # start # end # strand # ...⁠) and Sequence (e.g., head(seq_data))

1.3 (Optional) Gene group (e.g., head(PGC_group))

1.4 (Optional) Candidate gene list (e.g., head(photosynthesis_gene_list))

bciE bchB bchC bchD bchE

2 Output Data Preview

2.1 Gene cluster information (GC_meta)

2.2 Gene cluster sequence (GC_seq)

>pufC_Houyibacteriaceae--LLY-WYZ-15_3---k141_102864---1
GTGAAGAAGATCGCCATCGCCTTCGTGAGCACCTGGCTCCTCATCGGGGCCGTCTACGCCTACGAGCCGACCGAGACCTCGCAGATCGGCGCCGACGGCGTCGCCATGCAGGTCACGCAGACCGAGGACGAGCTCGCCGCGCGCGTGGAGGCGAACACCGTCCCGCCGGCCATCCCGATGCCCCAGAGCAGCGGCGTGCTGGCGGCCGAGGAGTACGAGAACGTGCAGGTCCTCGGCCACCTCAACACGGCCCAGTTCACCCGGCTGATGACCTCCATCACGCTCTGGGTCGCGCCGGAGCAGGGCTGCGCCTACTGCCACAACACGAACAACCTGGCCTCCGACGAGCTCTACACGAAGCGCGTGGCGCGTCGGATGATCCAGATGACCTGGCACATCAACGAGAACTGGCAGTCGCACGTCCAGGAGACCGGCGTGACCTGCTACACGTGCCACCGCGGCAACAACGTGCCCCAGCACATCTGGTTCGAGACGCCGCCCGACGACCACGGCATGGTGGGCTGGCGTGGCTCGCAGAACGCCCCGAACGACCGGACGGGGATCAGCTCCCTGCCGAACGACGTGTTCGAGGTGTTCCTCGAGGAGGACGCGAGCATCCGGGTCCAGTCGGCCGGGGAGGCCTTCCCGAACGAGAACCGCGCGTCCATCAAGCAGGCCGAGTGGACCTATGGGCTGATGATGCACTTCTCCGAGTCGCTCGGGGTGAACTGCACGGCTTGCCACAACTCGCGCTCCTGGAACGACTGGAGCCAGAGCCCGGCCCGCCGCGGGACGGCCTGGCACGGCATCCGGATGGCGCGAAACCTCAACAACCACTGGCTGACGCCGCTGCGCGATCAGTTCCCGCCGAACCGGCTCGGCGAGCTGGGTGACGCCCCGAAGGCCAACTGCGCGACGTGCCACCAGGGCGCGTACCGCCCCCTGCTCGGGCACCGCATGCTCGAGGACTTCCCGTCCCTCGTACGGGCGATGCCGCAGCCCGAGATCGAGCCGGAGCCGGAGCCGGAGCCCGAGCTGGAAGGCGAGGGCGAGGCCGGCGGGCAGCTCGAGCCGGAGGGGGAGGCGCCCGCCGCCGAAGCCCCCGAGGGCACGAACGCTGCGCCGACGGCGATGGCTGCGCCGGCGGCGATGGCCGCTCCGACGGGGATGGCCGCGCCGGCGGCGATGGCTGCGCCGGCGGCGATGGCTGCTCCGGCGGTGGCCGAGCCGACGCCCATGGCCGCGCCGGCGGCGATGGCGGCCCCGGCACCGAACTGA
>pufM_Houyibacteriaceae--LLY-WYZ-15_3---k141_102864---1
ATGGCCCGCTACCAGAACATCTTCACGCAGATCCAAGTCGTCGGTCCGCCGGACACGCCGCCGCCGATCGACCCGGACTTCCGTACGAAGAAGACGCGCATGTCGCGGCTCCTCGGGTGGTTCGGCAACCCGCAGATCGGCCCCGTCTACCTGGGCTACACCGGCCTGGCGTCCGCGATCAGCTTCTTCATCGCTTTCGAGATCATCGGGCTCAACATGCTGGCCTCGGTGGACTGGGACGTCGTTCAGTTCATCCGCCAGCTCCCCTGGCTCGCGCTCGAACCGCCCCCGCCCTCTGCCGGGCTCTCCATCCCGACGCTTCAGGAGGGCGGCTGGTGGCTCATGGCCGGCTTCTTCCTCACGGCGTCGGTCATTCTCTGGTGGATTCGCACCTATCGGCGCGCACGCGCCCTGAAGATGGGCACGCACGTCGCGTGGGCCTTCGCCTCGGCGATCTGGCTCTACCTCGTCCTCGGCTTCATTCGCCCCTTGCTGATGGGGAGCTGGGGGGAGGCGGTGCCCTTCGGCATCTTCCCGCACCTCGACTGGACCGCCGCCTTCTCCGTTCGCTACGGCAACCTCTTCTACAACCCCTTCCACTGCCTCTCGATCGTCTTCCTCTACGGGTCGACGCTCCTCTTCGCCATGCACGGCGCGACGGTGCTCGCGCTCGGGCACGTGGGCGGTGAGCGTGAGGTGAGCCAGGTGGTCGACCGCGGCACGGCGGCCGAGCGCGGGGCGCTCTTCTGGCGCTGGACGATGGGCTTCAACGCGACCTTCGAGTCCATCCACCGCTGGGCCTGGTGGTTCGCGGTGCTCACGCCGCTCACCGGAGGCATCGGCATCCTCCTGACCGGCACCGCCGTCGACAACTGGTATCAGTGGGCCGTCGAGCACGACTTCGCGCCGGCCTATGAGGAGTCCTACGAGGTCGTCCCCGACCCGGTCGACGACCCGGCGAACGAGGACCTGCCCGGTATGCGCGGTGAGTCCACCGCGCAGTGGGAGCCGACCCCCTACGTGCCCGCCGAGGAGCCGGAGGCGCCCGAGGATGGTGCGGACGGCGCGGCCGCGGTCGAAGGCGTCGACGCCGAGGGCGGCGAGGATGCCGCCGCGGATCCCGCGAGCGAGGGCACGAGCGGCCAGCCGGAGACCGGCGCCGCGGCCCCGGAGAGCGAGCGCCTTCCGGACGAAGCGGCGGCGGCCGAGCCCGAAGGGGCTGCGCCGGAGCCCGAACCCCCCGCGCCGTCCGAGACGGCTGCCCCGAGCGAACCCGAGGCGCCCAGCGCGATGACCCCGGAGCAACCGTGA
>pufL_Houyibacteriaceae--LLY-WYZ-15_3---k141_102864---1
ATGGGCCTACTGAGCTTCGAGCGGCGATATCGAGTCCGAGGAGGCACGCTCCTCGGGGGCGACCTATTCGATTTCTGGGTCGGGCCCTTCTACGTGGGGCTCTTCGGCGTCACGACGATCTTCTTCACGATCGTCGGCACCGCGCTGATCCTCTGGGAGGCCTCCCGGGGTGACACCTGGAACCCCTGGCTGATCAACATCCAGCCGCCTCCAATCGAGTACGGGCTCGCCTTCGCGCCCCTCGATCAGGGGGGCATCTGGCAGCTGGTCACCATCTGCGCCATCGGCGCCTTCGGATCCTGGGCGCTCCGACAGGCGGAGATCAGCCGCAAGCTCGGCATGGGCTACCACGTGCCCATCGCCTACGGCGTCGCGGTCTTCGCCTACGTCACGCTCGTGGTGATTCGCCCGGTGATGCTGGGCGCCTGGGGCCACGGCTTCCCCTACGGCATCTTCAGCCACCTCGATTGGGTGTCGAACGTCGGGTACCAGTACCTGCACTTCCACTACAACCCGGCCCACATGATCGCGGTGAGCTTCTTCTTCACCACGACGCTCGCGCTCTCCCTCCACGGCGGTTTGATCCTCTCCGCCGTGAATCCGCCGAAGGGAGAGAAGGTGAAGACCGCCGAGTACGAGGACGGGTTCTTCCGTGACCACATCGGCTACTCGATCGGCGCCCTGGGCATTCATCGACTCGGCCTCTTCCTGGCGCTGAGCGCCGGGATCTGGAGCGCGATCTGCATTCTCATCAGCGGCCCGATGTGGACCAAGGGGTGGCCCGAGTGGTGGGACTGGTGGCTCAACCTCCCCGTGTGGAGCTGA
>bchO_Houyibacteriaceae--LLY-WYZ-15_3---k141_102864---1
ATGAGCTCGGCCGTCGAAGAGCAGCGCGTCGAGCACCCGCGGGTCGAGCAGCAGCCCATCGAGCAGCAGCGCGTCGAGCACCAGCGCGTCGAGCGTTCGGGCGTGCGGTGGAACGTCGCCCGCCGCGGCGCCGGACCCACGCTCCTGGCGCTCCACGGGACCGGCAGCTCGAGCCGCTCCTTCTGCGCCCTCGCGGCCACGCTCGGTGCTCGCTTCACCGTCGTGGCGCCCGATCTACCCGGCCACGCCGGGAGCCGGATCGATCGCCGCTTCCGCCTCTCGCTCCCCTCGATCGCCGCCGCCCTCGGCGAGCTCATCGAGGCGCTCGCCGTCCAGCCGGCGCTGGTCCTCGCTCACTCCGCGGGCGCGGCGGTGGCGGCGCGCGCCATGCTCGACGGGGCTCTCCGCCCGGCGCTCTTCGTCGGGCTCGGCGCGGCCCTGACGCCCCTCGAGGGGCTCGCCCGGCTCGGCGCGCGCCCGGCGGCCGCGATGCTCGCCCGCTCGCCCATCACGCGGCGGGTGGCGCGCCGGGCTGGAGGCGCCCTCGTCGGACCGATCCTGCGCAGCGTCGGATCCACCGTCGGCCCCGAGGCCACACAGCGCTATCGGGAGCTCGCCCGCGATCCCGCCCACGTCGGGGCGGTCTTCTCGATGCTCGCCCAGTGGGATCTCGACGGGCTCCACGCGGCGCTACCACGCCTGGACGTACCGACCCTGCTCCTCGGCGGCGCCCGCGACGGCGCCACCCCGATCGCCCAGCAGCGCGCCCTCGCACGTCGCCTCCCGGCCGCGCGCGCGCACGTCGTCCTCGGCGCCGGGCACCTGCTCCACGAGGAGCGACCCGCCGAGATCGCGCGCCTCGTCGAGGCCGAGTGGAACAGATTGGACGGCGGTCGTGTCAAAAATGCTTGA
>bchD_Houyibacteriaceae--LLY-WYZ-15_3---k141_102864---1
ATGAGCGGCTGGCCCGACGTGGCGCGCGTCGCCGAGCTCCTGAGCGTCGACCCGGACGGCCTCGGAGGCGTGCGCCTGCGGGGTCGCCCGGGGCCGCACCGGCGCCGGGTGCTCGAGTGGGTGCGCGAGAGGCTGGCCCCGGAGGCGCCCTTCCGGCGCCTGCCCGCGCACGTGACCGAGGATCGGCTCCTCGGGGGCCTCGCGCTCGCGGAGACCTTGCGTTCGGGGCGGGCCGTCATGGAGCAGGGCGTGCTCGCGCGGAGCGACGGCGGCCTGCTCGTCGTGGCCATGGCCGAGCGGGCCGAGCGGGAGGTCGTGGCGCACCTCTGCGCGGCCCTCGACCGCGGCGCGATCACCGTCGAACGCGACGGCATGAGCGCCGAGGCGTCCTGCCGCGTGGGCCTCATCGCGCTCGACGAGGGCATCGACGAGGAGCACGTCGACCCGGCGCTCGCCGACCGGCTCGCCTTCGCGCTGGACCTCGACGCGCTCGATCCGCGGGGAGGGGCGGCGCCGGAACACGGACCCGAGGAGGTCGCGCGAGCCCGCGCCCGCCTCCCGCACGTGAGCCTCGGCGACGACATCATCGCGGCCCTCTCGGAGGCGGCCCAGGCCCTCGGCGTGGAGGCGCTCCGGCCGCTCCTGCTCGCGGCGAAGGCGGCCCGCGCGCACGCGGCGCTCCTCGGCCGGACCCGCGTCGAGGAGGAAGACGCCGGGATGGCGGCGCGCCTCGTCCTCGGCCCGAGGGCGACGCGAGCGCCGAGCGCCGAGCCCGAAGAGGCGGCCGAGCGCGAGGCCGAAGAGGGCGACCCCGACCCGGGAGGCGCCGGCGCGGCTGCAGCCGGCGAACGGGCGGACGGCGCCGACGAGGCCCCGCCGGGCGAGGTCCCGCTCGGCGATCTCGTCTTGGCGGCGGCCGAGAGCGGCATCCCGGCGGGGCTGCTCGACGCCCTCGACGTCGGGACCACCCGGCGGGCCGGCGCGACCGGTCGGAGCGGGGCGACGCGCATCGGCCCGAGCGGCGGCCGCCCGGCGGGGACGCGCGCCGCGCCGCCCACCCGAGGCCAGCGCCTGAACGTCGTCGAGACCCTCCGCGCCGCCGCGCCCTGGCAGCGGCTCCGCGGGGGCGGCTTCGGCGCGGGCGTGCGCGTCCGGCCGGAGGACTTCCGTGTCACCCGTCACCGGCAGCCGATCGAGAGCTGCGTGATCTTCGCCGTCGACGCGTCCGGCTCCGCCGCGCTTCGACGCCTGGCCGAGGCGAAGGGCGCCGTCGAGCGCGTGCTCGGCGACTGCTACGTGCGGCGCGACCACGTCGCCCTCGTCGCGTTCCGCCAGGACGGCGCCGAGCTGCTCCTGCCCCCGACGCGCTCCCTCGCCCGCGTGCGTCGCAGCCTGGCTGCCCTCGCCGGCGGCGGCGCGACCCCCCTCGCCGCGGGGATCGACGCCGCCCATCGGCTCGCCCTCGACGCCCGCGGGCGCGGCCGCGAGCCCATCGTGGTCGTCATGACCGACGGGCGGGCGAACGTGACCCGGGACGGCCGCCGGGACCCCGCGGTCGCCACCACGGACGCCCTCGAGAGCGCGCGCGGGCTCCAGCGAGCCGCCGTGCCGACCCTCTTCCTCGACACGGCCCCACGCCCCCGGCGCCGTGCCCGCGAGCTCGCCGAGGCCATGGACGCCCGCTACCTGCCGCTGCCCTACCTCGACGCGGCGGGGATCTCACGCCACGTCCAAGCGCTCGCCCGCGAGGGAGCCCGATGA
>bchI_Houyibacteriaceae--LLY-WYZ-15_3---k141_102864---1
ATGACGCCCTATCCCTTCACCGCCATCGTCGCGCAGGACGAGCTCAAGCTCGCCCTGCAGATCGCCACCGTCGACCGCAGCATCGGCGGGGTCCTCGCCTTCGGCGACCGCGGCACCGGCAAGTCGACCACCATCCGCGCGCTCGCCCGGCTCCTGCCGCCGATGCGCGTCGTCGCCAGCTGCCCGTACCACTGTGATCCGGCCGACGCGCGCGCTCGCTGTCCGCACTGTGCCGAAGCCGCAGGGGAGCGGGAGGCGATCGAGACGCCCGTGCCGGTCGTGGACCTGCCCCTCGGCGCCACCGAGGATCGCGTCGTCGGCGCGCTCGATCTCGAGGCGGCCCTCACGCGCGGGGAGCGCCGCTTCTCACCGGGCCTGCTCGCCGCGGCGCATCGAGGCTTCCTCTACATCGACGAGGTCAACCTCCTCCCCGATCACCTCGTGGATCTGCTGCTCGACGTCGCGGCCTCGGGCGAGAACGTGGTCGAGCGCGAGGGCCTGAGCGTGCGCCACCCCGCGCGCTTCGTGCTGATCGGCAGCGGAAACCCGGAGGAGGGCGAGCTGCGCCCCCAGCTGCTCGATCGCTTCGGCCTCTCGCTCGAGGTCCGCACGCCGGACGAGGTCGCGACGCGCGTCGAGGTCGTCAAGCGGCGCATGCGCTACGATCAGGACCCGGAGGCCTTCGCGGCCGCCTGGGCGGAGGACGAGGCGGCCCTCATCGTTCGCCTCCGGGACGCGCGGGCGCGCTTGCCCGAGGTGGCCGTCAGCGACGCCGTGATCGAGCGCGCGAGCCGGCTCTGCCAGGCGCTCGGCACCGACGGGCTCCGGGGGGAGCTGACCTTGATCCGCGCCGCGCGCGCGGCCGCCAGCCTCGACGCGCAGCGGGAGGTCGCCGACGTGCACCTCGCCCAGGTCGCCCCCCTCGCGCTCCGCCACCGGCTGCGACGCGCCCCCCTGGACGACGTCGGCTCGGGCGCGCGCGTGCAGAAGGCCGTCGAGGACGTGCTCGGGGGCTGA

2.3 Gene cluster plot (GC_plot)

Case 2: Using eggNOG (evolutionary gene genealogy Nonsupervised Orthologous Groups) format result

# Case 2: Using eggNOG result with Full pipeline (Find Cluster + Extract FASTA + Plot Cluster)
library(gclink)
data(eggnog_df)
data(seq_data)
data(KO_group)
KOs = c("K02291","K09844","K20611","K13789",
        "K09846","K08926","K08927","K08928",
        "K08929","K13991","K04035","K04039",
        "K11337","K03404","K11336","K04040",
        "K03403","K03405","K04037","K03428",
        "K04038","K06049","K10960","K11333",
        "K11334","K11335","K08226","K08226",
        "K09773")
rename_KOs = paste0("ko:", KOs)
eggnog_df$qaccver = eggnog_df$`#query`
eggnog_df$saccver = eggnog_df$KEGG_ko
eggnog_df$evalue = eggnog_df$evalue
eggnog_df$bitscore = eggnog_df$score
eggnog_df$gene = eggnog_df$KEGG_ko
gc_list_2 = gclink(in_blastp_df = eggnog_df,
                  in_seq_data = seq_data,
                  in_gene_list = rename_KOs,
                  in_GC_group  = KO_group,
                  AllGeneNum = 50,
                  MinConSeq  = 25,
                  apply_evalue_filter = FALSE,
                  min_evalue = 1,
                  apply_score_filter = TRUE,
                  min_score = 10,
                  orf_before_first = 1,
                  orf_after_last = 1,
                  levels_gene_group = c('bch','puh','puf','crt',
                                        'acsF','assembly','hypothetical ORF'),
                  color_theme = c('#3BAA51','#6495ED','#DD2421','#EF9320',
                                  '#F8EB00','#FF0683','grey'))
gc_meta_2 = gc_list_2[["GC_meta"]]
gc_seq_2 = gc_list_2[["GC_seq"]]
gc_plot_2 = gc_list_2[["GC_plot"]]
head(gc_meta_2)   # Cluster metadata
head(gc_seq_2)    # FASTA sequences
print(gc_plot_2)  # Visualization

1 Input Data Preview

1.1 A dataframe of Diamond BLASTp output from eggNOG (e.g., head(eggnog_df))

1.2 (Optional) A dataframe with SeqName (ORF identifier, Prodigal format: ⁠ORF_id # start # end # strand # ...⁠) and Sequence (e.g., head(seq_data))

Same with Case 1

1.3 (Optional) KO/gene group (e.g., head(KO_group))

1.4 (Optional) Candidate KO/gene list

ko:K04035 ko:K08226 ko:K04039 ko:K11337 ko:K03404 ko:K11336

2 Output Data Preview

2.1 Gene cluster information (GC_meta)

Similar with Case 1

2.2 Gene cluster sequence (GC_seq)

Similar with Case 1

2.3 Gene cluster plot (GC_plot)

Documentation

Full function reference:

?gclink::gclink

Citation

If you use gclink in your research, please cite:

Li, L., Huang, D., Hu, Y., Rudling, N. M., Canniffe, D. P., Wang, F., & Wang, Y. "Globally distributed Myxococcota with photosynthesis gene clusters illuminate the origin and evolution of a potentially chimeric lifestyle." Nature Communications (2023), 14, 6450. https://doi.org/10.1038/s41467-023-42193-7

Dependencies

• R (≥ 3.5)
• dplyr (≥ 1.1.4)
• gggenes (≥ 0.5.1)
• ggplot2 (≥ 3.5.2)

License

GPL-3 © Liuyang Li

Contact

• Maintainer: Liuyang Li cyanobacteria@yeah.net
• Bug reports: https://github.com/LiuyangLee/gclink/issues