Whole Genome Assembly and Annotation of M. troglodytarum

The repeats and protein-coding genes in the genome were annotated by MAKER2 (v3.01.02). The MAKER2 pipeline was processed twice to obtain high-quality gene annotations. The RNA-seq reads of the leaves, stems, roots and fruits were imported to Trinity to generate genome-guided and de novo assemblies, with the default parameters used.

Then, the assemblies were imported into the PASA pipeline (v2.3.3) to construct a comprehensive transcript database. The comprehensive transcripts were used to train the predictors embedded in the MAKER2 pipeline, including AUGUSTUS (v3.3.1), GENEMARK (v3.5.2) and SNAP (version 2006-07-28).

After filtering out proteins produced by MAKER2 that had low AED values, the ab initio predictors AUGUSTUS, GENEMARK and SNAP were trained again.

Then, utilizing high-confidence and high-sensitivity transcripts produced by StringTie (v2.1.1) as inputs, the MAKER2 pipeline was run again. Using eggNOG-mapper (v2) and its default database, genes were assigned functional annotations.

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Friday, August 26, 2022 - 15:57
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Li Z, Wang J, Fu Y, Jing Y, Huang B, Chen Y, Wang Q, Wang XB, Meng C, Yang Q, Xu L. The Musa troglodytarum L. genome provides insights into the mechanism of non-climacteric behaviour and enrichment of carotenoids.. BMC biology. 2022 Aug 24; 20(1):186.