Functional annotation of Lablab purpureus genome using tissue‑specific RNA‑Seq data

This genome annotation work aims to annotate the complete chromosome level genome assembly of Lablab purpureus for exploring structural and functional genes based on the transcriptome profiles of different tissue of this multipurpose crop, also known by names Indian bean or hyacinth bean. Recently, chromosome level complete assembly of Lablab purpureus (variety Linghu), has been published as primary reference genome assembly (GCA_051403735.1) from Institute of Virology and Biotechnology, China and need proper annotation of genome for identifying functional genes in this crop. The utilization of genome assembly information for genetic experiments needs annotation of genome with RNA-Seq evidence. For this purpose, the reference genome sequence was downloaded from NCBI and used for mapping and annotation after normalization of sequence headers and softmasking. The primary RNA-Seq evidence were obtained from BioProject PRJNA1260078 and BioSample SAMN48386564 and additional transcript evidences from Lablab purpureus cultivars were sourced from publicly available NCBI BioProjects (PRJNA474418, PRJNA1008422, PRJNA273585, PRJNA601532, and PRJNA1153959) and mapped to the reference genome assembly (GCA_051403735.1) using RNA Star tool v2.7.11b. The primary RNA-Seq reads from SAMN48386564 were used as direct RNA-Seq evidence as those were from the same cultivar, Linghu, whereas other RNA-Seq reads from diverse bioprojects and cultivars were used as merged Stringtie GTF transcript gene model evidences to overcome the data size constraints in Funannotate. For annotation, the mapped reads from different bioprojects and hyacinth bean cultivars were assembled into denovo transcript assembly and merged into a single GTF file using StringTie v 2.2.3 and those assembled transcripts were used as additional transcript evidence in Funannotate v1.8.15 for predicting gene models and functional annotation. These processed sequences were used for structural and functional genome annotation of Lablab purpureus complete genome assembly (GCA_051403735.1). This study will help researchers in gene-based expression or association studies for improving valuable genetic traits in Lablab purpureus or similar crops supporting plant breeding and crop improvement efforts for global food security.