A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants

Most published genome sequences are drafts, and most are dominated by computational gene prediction. Draft genomes typically incorporate considerable sequence data that are not assigned to chromosomes, and predicted genes without quality confidence measures. The current Actinidia chinensis (kiwifruit) 'Hongyang' draft genome has 164\ua0Mb of sequences unassigned to pseudo-chromosomes, and omissions have been identified in the gene models

Radarsat Constellation Mission Derived Winter Glacier Velocities for the St. Elias Icefield, Yukon/Alaska: 2022 and 2023

Here we use high resolution (5 m) Radarsat Constellation Mission (RCM) imagery acquired in winters 2022 and 2023 to determine motion across glaciers of the St. Elias Icefield in Yukon/Alaska. Our regional velocity mapping largely conforms with previous studies, with faster motion (>600 m/yr) for the glaciers originating in the Yukon that drain southward and westward to the coast of Alaska and relatively slower motion (100–400 m/yr) for the land terminating glaciers that drain eastward and northeastward and stay within the Yukon. We also identify two new glacier surges within the icefields: the surge of Nàłùdäy (Lowell) Glacier in Winter 2022, and Chitina Glacier in Winter 2023, and track the progression of each surge from January to March utilizing ∼4-day repeat RCM imagery. To evaluate the quality of RCM-derived velocities, we compare our results with 50 simultaneous measurements at three on-ice dGPS stations located on two Yukon glaciers and find the average absolute difference between measurements to be 6.6 m/yr. Our results demonstrate the utility of RCM data to determine glacier motion across large regions with complex topography, to support process-based studies of fast flowing and surge-type glaciers and continue the legacy of velocity products derived from the Radarsat-2 mission

Additional file 3: of A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants

Comparison of predicted paired end distance to genome.Heatmaps of alignment distance scores for the alignment of the read pairs from the 9Kb long-insert mate-paired-end (LIMP) library to each of the 29 chromosomes within the Red5 whole genome assembly and. Individual chromosome plots were prepared using hagfish_blockplot from the software program ‘hagfish’ ( https://github.com/mfiers/hagfish/ ). Individual images were cropped for height (not length) then cut and pasted into a table format for easier viewing. Each image depicted the entire length of the chromosome but all images are of standard length irrespective of chromosome length. Green regions indicate mate pairs aligning to the whole genome sequence within the expected distance of the library. Black indicates regions without mate pair alignment. Pinkish-red indicates regions where the distance between mated paired end reads is shorter (assembly compression relative to physical genome) or longer (assembly expansion relative to physical genome). (PPTX 432 kb

Additional file 7: of A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants

Details of sequenced cDNA’s generated. Fasta formatted sequences of 812 bidirectionally sequenced expressed sequence tag clones from A. chinensis var. chinensis used in evaluating manually annotated gene models of Red5. (FASTA 1204 kb

Additional file 4: of A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants

BLASTP comparison of manually edited gene models to the revised ‘Hongyang’ gene models. List of best reciprocal BLASTp matches between the revised Actinidia chinensis ‘Hongyang’ genes [18]and the Red5 gene set (XLSX 436 kb

Additional file 8: of A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants

Sequenced cDNA’s used to verify the gene models.Fasta formatted predicted protein sequences of 550 bidirectionally sequenced expressed sequence tag clones from A. chinensis var. chinensis used in evaluating manually annotated gene models of Red5. (FASTA 220 kb

Additional file 10: of A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants

The manual annotation process.Flow diagram of manual annotation process. A. Timeline showing the manual annotation process. *see materials and methods. B. Annotation followed a 5 step process. The annotator training was completed in the form of both workshops and YouTube training videos. ** https://www.youtube.com/playlist?list=PLcBe8nhQVgUg1zqOsdeRuVq9QVsLfj_Y9 . (PPTX 47 kb

Additional file 6: of A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants

Revised ‘Hongyang’ genes omitted from the manually edited gene set. Average RNA-Seq read coverage of the 1069 KIR V2 models perfectly aligned to the Red5 genome without a protein match in the Red5 gene set. (XLSX 114 kb

Additional file 1: of A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants

Map back rates to the Red5 genome sequence.Summary of the numbers of input reads reads that align to the RED5 genome construction (XLSX 10 kb