High-quality genome assembly of the endemic threatened White-bellied Sholakili Sholicola albiventris (Muscicapidae: Blanford, 1868) from the Shola Sky Islands, India.

Overview

This repo contains scripts and a pipeline for the Reference genome assembly for the White-bellied Sholakili Sholicola albiventris, an endemic vulnerable species from the Western Ghats of India. Assembly has numerous steps, and each of them is numbered and can be found in respective subdirectories.

Repo Structure

• 00_scripts : All scripts used in the manuscript with subdirectories of each process.

  • 00-RAW_DATA : Contains QC and adapter trimming scripts.

  • 01-CLEAN-READS : K-mer count and assembly size estimation using meryl.

  • 02-ASSEMBLY : Script for draft assembly using Flye.

  • 02-MITO-ASSEMBLY : Contains scripts for identifying the closest sister species mitogenome and de-novo assembly of the mito genome.

  • 00-NCBI : Screening for adapter and alien species contamination using NCBI-FCS suit.

  • 04-QC : Compleasm scripts for genome completeness assessment after each step of assembly, polishing, and scaffolding.

  • 05-POLISHING : Five rounds of polishing scripts of two types of reads and three different tools.

  • 06-PURGE-DUPS : Scripts for removing any redundant haplotypes.

  • 07b-SCAFFOLDING : Minimizer map-based assembly scaffolding using long reads.

  • 07c-PSEUDOMOLECULE : Reference assisted assembly scaffolding to generate pseudomolecule/pseudochromosomes using Zebra Finch reference genome.

  • 08-FINAL : Custom python scripts to rename the scaffolds of nuclear and mitogenome assemblies.

  • 09-ANNOTATE

    • 01_repeat_masking : Scripts to build species-specific repeat library and soft masking the genome using RepeatMasker.

    • 02_gene_prediction : ab initio gene prediction and annotation based on the multiple gene annotations tools.

  • 10-UCEs : Scripts to isolate Ultra Conserved Elements as a measure of QC for genome completeness following Phyluce Tutorial III.

  • 11-GENOME-SYNTENY : Genome-genome alignment using the Nucmer module and visualization of the scaffold synteny using R.

  • 12-JOH-REVIEW-REVISION : Post first round review re-scaffolding and synteny scripts.

• 01_Figures : Contains the final figures as displayed in the manuscript. Figure_{i}.jpg are main text figures and Figure_S{i}.png are supplemental figures.

• bShoAlb1.1_Pipeline_Flowchart.pdf : Contains the step-by-step flowchart depicting the process of assembly and subsequent analysis.

Data Availability

This Whole Genome Shotgun project has been deposited at GenBank under the accession JBDGPF000000000. The version described in this repo is version JBDGPF010000000. Raw reads with accession numbers SRR28564530 and SRR28558515 under the BioProject PRJNA1096119 are available from NCBI. Additional supporting data are available from the Open Science Framework

Attribution

To cite the publication: K L Vinay, Chiti Arvind, Naman Goyal, V V Robin, High-quality genome assembly of the endemic, threatened, White-bellied Sholakili Sholicola albiventris (Muscicapidae: Blanford, 1868) from the Shola Sky Islands, India, Journal of Heredity, Volume 117, Issue 1, January 2026, Pages 151–158, https://doi.org/10.1093/jhered/esaf049

Contact information

Please contact the following in case of interest.

Vinay K L vkl1@lsu.edu
PhD student, Louisiana State University