design: Two HiFi SMRTbell libraries were constructed based on the DNA availability.  The first regular HiFi SMRTbell library was constructed using the SMRTbell Express Template Prep Kit v2.0 (Pacific Biosciences, Menlo Park, CA; Cat. #100-938-900) according to the manufacturer's instructions. HMW gDNA was sheared to a target DNA size distribution between 12 - 20 kb using Diagenodes Megaruptor 3 system (Diagenode, Belgium; cat. B06010003). The sheared gDNA was concentrated using 1.8X of AMPure PB beads (Pacific Biosciences, Menlo Park, CA; Cat. #100-265-900) for the removal of single-strand overhangs at 37C for 15 minutes, followed by further enzymatic steps of DNA damage repair at 37C for 30 minutes, end repair and A-tailing at 20C for 10 minutes and 65C for 30 minutes, and ligation of overhang adapters v3 at 20C for 60 minutes. The SMRTbell library was purified and concentrated with 0.45X AMPure PB beads for size selection with 2.2X of 40% v/v diluted AMPure PB beads to remove short SMRTbell templates.  The remaining limited DNA was used to construct a second library called ultra-low HiFi SMRTbell library using the SMRTbell gDNA Sample Amplification Kit (Pacific Biosciences, Menlo Park, CA; Cat. #101-980-000) and the SMRTbell Express Template Prep Kit 2.0 (Pacific Biosciences; Cat. #100-938-900) according to the manufacturer's instructions. Approximately 10 kb sheared DNA by the Megaruptor 3 system (Diagenode, Belgium; Cat. #B06010003) was used for removal of single-strand overhangs at 37C for 15 minutes, DNA damage repair at 37C for 30 minutes, end repair and A-tailing at 20C for 30 minutes and 65C for 30 minutes, and ligation of overhang adapters at 20C for 60 minutes. To prepare for library amplification by PCR, the library was purified with ProNex beads (Promega, Madison, WI; Cat. # NG2002) for two PCR amplification conditions at 15 cycles each then another ProNex beads purification.  Purified amplified DNA from both reactions were pooled in equal mass quantities for another round of enzymatic steps that included DNA repair, end repair/A-tailing, overhang adapter ligation, and purification with ProNex Beads. The PippinHT system (Sage Science, Beverly, MA; Cat # HPE7510) was used for SMRTbell library size selection to remove fragments < 6-10 kb. The 10  11 kb average.  Both libraries were sequenced across three SMRT cells at UC Davis DNA Technologies Core (Davis, CA) using one 8M SMRT cell for the low-input 17 kb average HiFi library and using two 8M SMRT cells for the ultra-low 12 kb average HiFi library with Sequel II sequencing chemistry 2.0, and 30-hour movies each on a PacBio Sequel IIe sequencer.