With the change of to type bigBed 12 + the gene models are appearing as expected in UCSC.

Note on the E_unicornis example file. It is a bed detail (12 + 2 columns), but note that there are no introns, so the gene models will appear as rectangles in UCSC/IGB.

One additional issue with the type parameter in the trackDb.txt. The type parameter should be set to bigBed 12 + as this specifies that the file is bed 12 plus additional columns (the bigbed file is a bed detail with 14 columns). Unfortunately this means that we may have to make assumptions about how many columns are present in a user's bigBed file as this information is not required for an IGB QuickLoad.
From: https://genome.ucsc.edu/goldenpath/help/hgTrackHubHelp.html

type - the format of the file specified by bigDataUrl. Must be either bigWig, bigBed, bigBarChart, bigGenePred, bigInteract, bigNarrowPeak, bigChain, bigPsl, bigMaf, hic, bam, halSnake or vcfTabix (Note: use type bam for CRAM files). If the type is bigBed, it may be followed by an optional number denoting the number of fields in the bigBed file (e.g., "type bigBed 12" for a file with 12 fields or "type bigBed 12 +" for a file that contains additional non-standard columns). If no number is given, a default value of 3 is assumed (a very limited display that omits names, strand information, and exon boundaries).

Dr.Nowlan Freese, Could you please check now? It is working.

I made below changes in genomes.txt:

Before :
genome tair9
trackDb tair9/trackDb.txt
organism araTha
*defaultPos chrI:0-30427671
twoBitPath http://igbquickload.org/quickload/A_thaliana_Jun_2009/A_thaliana_Jun_2009.2bit

Now:
genome tair9
trackDb tair9/trackDb.txt
organism araTha
*defaultPos Chr1:0-30427671
twoBitPath http://igbquickload.org/quickload/A_thaliana_Jun_2009/A_thaliana_Jun_2009.2bit

Bitbucket : https://bitbucket.org/lorainelab_udaya/testquickload/src/main/trackHub2/

When I add the hub to UCSC and then click GO I see the following error:
Can't find description for hub_6367087_tair9

The above papaya example is not working since there is an issue with that genome in igb.
So created another POC.

Trackhub : https://api.bitbucket.org/2.0/repositories/lorainelab_udaya/testquickload/src/main/trackHub2/hub.txt
UCSC connect hub : https://genome.ucsc.edu/cgi-bin/hgHubConnect

To test if the above hub is working, add the provided track hub in ucsc connected hubs

Created an example for POC from existing quickload:

• hub.txt:

1. hub IGBQuickLoad
2. shortLabel IGB QUICK LOAD
3. longLabel Generated from IGB QuickLoad
4. genomesFile genomes.txt
5. email myEmail@address

• genomes.txt

1. genome C_papaya_Aug_2010
   C_papaya_Aug_2010 is igb quickload name but we need to assign ucsc genome name. To get ucsc genome name we need to check in synomyns.txt. If it is not in synomyns.txt then we assign same igb quickload name.
2. trackDb C_papaya_Aug_2010/trackDb.txt
3. organism Carica papaya
   (we get the organism from species.txt by checking with C_papaya i.e we split the genome name with "_ " an combine first two words in list with "_ " an dchcek if it is present in species.txt. If it is present we get the first column name as organism name)
4. defaultPos chrI:0-6239266
   From <http://igbquickload.org/quickload/C_papaya_Aug_2010/genome.txt>
5. twoBitPath http://igbquickload.org/quickload/C_papaya_Aug_2010/C_papaya_Aug_2010.2bit

we can get directly from annots.xml when reference = true or we can fetch from genome version folder
http://igbquickload.org/quickload/C_papaya_Aug_2010/

1. Organism, defaultPos and 2 bit file are not mandatory
   It is required only when ucsc genome name is not matched with igbquickload name

• trackDb.txt

1. track Caricapapaya
2. bigDataUrl C_papaya_Aug_2010.bed.gz
   From <http://igbquickload.org/quickload/C_papaya_Aug_2010/annots.xml> (name)
3. shortLabel Carica papaya gene models from Phytozome v7
   From <http://igbquickload.org/quickload/C_papaya_Aug_2010/annots.xml>
4. longLabel protein-coding gene models
   From <http://igbquickload.org/quickload/C_papaya_Aug_2010/annots.xml>
5. type bed
6. visibility dense (hard coded)

track hub : https://api.bitbucket.org/2.0/repositories/lorainelab_udaya/testquickload/src/main/trackHub1/hub.txt

The above track hub did not work since i need to convert bigdataurl to bed