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      On the origin of the widespread self-compatible allotetraploid Capsella bursa-pastoris (Brassicaceae)

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          Abstract

          Polyploidy, or whole-genome duplication, is a common speciation mechanism in plants. An important barrier to polyploid establishment is a lack of compatible mates. Because self-compatibility alleviates this problem, it has long been hypothesized that there should be an association between polyploidy and self-compatibility (SC), but empirical support for this prediction is mixed. Here, we investigate whether the molecular makeup of the Brassicaceae self-incompatibility (SI) system, and specifically dominance relationships among S-haplotypes mediated by small RNAs, could facilitate loss of SI in allopolyploid crucifers. We focus on the allotetraploid species Capsella bursa-pastoris, which formed ~300 kya by hybridization and whole-genome duplication involving progenitors from the lineages of Capsella orientalis and Capsella grandiflora. We conduct targeted long-read sequencing to assemble and analyze eight full-length S-locus haplotypes, representing both homeologous subgenomes of C. bursa-pastoris. We further analyze small RNA (sRNA) sequencing data from flower buds to identify candidate dominance modifiers. We find that C. orientalis-derived S-haplotypes of C. bursa-pastoris harbor truncated versions of the male SI specificity gene SCR and express a conserved sRNA-based candidate dominance modifier with a target in the C. grandiflora-derived S-haplotype. These results suggest that pollen-level dominance may have facilitated loss of SI in C. bursa-pastoris. Finally, we demonstrate that spontaneous somatic tetraploidization after a wide cross between C. orientalis and C. grandiflora can result in production of self-compatible tetraploid offspring. We discuss the implications of this finding on the mode of formation of this widespread weed.

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          The Sequence Alignment/Map format and SAMtools

          Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments. Availability: http://samtools.sourceforge.net Contact: rd@sanger.ac.uk
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            STAR: ultrafast universal RNA-seq aligner.

            Accurate alignment of high-throughput RNA-seq data is a challenging and yet unsolved problem because of the non-contiguous transcript structure, relatively short read lengths and constantly increasing throughput of the sequencing technologies. Currently available RNA-seq aligners suffer from high mapping error rates, low mapping speed, read length limitation and mapping biases. To align our large (>80 billon reads) ENCODE Transcriptome RNA-seq dataset, we developed the Spliced Transcripts Alignment to a Reference (STAR) software based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. STAR outperforms other aligners by a factor of >50 in mapping speed, aligning to the human genome 550 million 2 × 76 bp paired-end reads per hour on a modest 12-core server, while at the same time improving alignment sensitivity and precision. In addition to unbiased de novo detection of canonical junctions, STAR can discover non-canonical splices and chimeric (fusion) transcripts, and is also capable of mapping full-length RNA sequences. Using Roche 454 sequencing of reverse transcription polymerase chain reaction amplicons, we experimentally validated 1960 novel intergenic splice junctions with an 80-90% success rate, corroborating the high precision of the STAR mapping strategy. STAR is implemented as a standalone C++ code. STAR is free open source software distributed under GPLv3 license and can be downloaded from http://code.google.com/p/rna-star/.
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              Basic local alignment search tool.

              A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score. Recent mathematical results on the stochastic properties of MSP scores allow an analysis of the performance of this method as well as the statistical significance of alignments it generates. The basic algorithm is simple and robust; it can be implemented in a number of ways and applied in a variety of contexts including straightforward DNA and protein sequence database searches, motif searches, gene identification searches, and in the analysis of multiple regions of similarity in long DNA sequences. In addition to its flexibility and tractability to mathematical analysis, BLAST is an order of magnitude faster than existing sequence comparison tools of comparable sensitivity.
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                Author and article information

                Contributors
                tanja.slotte@su.se
                Journal
                Heredity (Edinb)
                Heredity (Edinb)
                Heredity
                Springer International Publishing (Cham )
                0018-067X
                1365-2540
                19 April 2021
                19 April 2021
                July 2021
                : 127
                : 1
                : 124-134
                Affiliations
                [1 ]GRID grid.10548.38, ISNI 0000 0004 1936 9377, Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, , Stockholm University, ; Stockholm, Sweden
                [2 ]GRID grid.6341.0, ISNI 0000 0000 8578 2742, Department of Plant Biology, , Swedish University of Agricultural Sciences & Linnean Center for Plant Biology, ; Uppsala, Sweden
                [3 ]GRID grid.6268.a, ISNI 0000 0004 0379 5283, Present Address: School of Chemistry and Biosciences, Faculty of Life Sciences, , University of Bradford, ; Bradford, UK
                [4 ]GRID grid.6190.e, ISNI 0000 0000 8580 3777, Present Address: Institute of Botany, Biozentrum, , University of Cologne, ; Cologne, Germany
                [5 ]GRID grid.4491.8, ISNI 0000 0004 1937 116X, Present Address: Department of Botany, Faculty of Science, , Charles University, ; Prague, Czech Republic
                Author information
                http://orcid.org/0000-0002-7212-813X
                http://orcid.org/0000-0002-7378-4673
                http://orcid.org/0000-0002-2962-2669
                http://orcid.org/0000-0002-2619-4857
                Article
                434
                10.1038/s41437-021-00434-9
                8249383
                33875831
                4f766bbb-f65c-4e39-8b75-ecf5be6cb9b7
                © The Author(s) 2021

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 17 June 2020
                : 2 April 2021
                : 2 April 2021
                Funding
                Funded by: FundRef https://doi.org/10.13039/501100004359, Vetenskapsrådet (Swedish Research Council);
                Award ID: 621-2013-4320
                Award Recipient :
                Funded by: Science for Life Laboratory, Swedish Biodiversity Program
                Funded by: FundRef https://doi.org/10.13039/501100001725, Royal Swedish Academy of Sciences (Kungl. Vetenskapsakademien);
                Funded by: FundRef https://doi.org/10.13039/501100005753, Kungliga Fysiografiska Sällskapet i Lund (Royal Physiographic Society in Lund);
                Categories
                Article
                Custom metadata
                © The Genetics Society 2021

                Human biology
                evolution,polyploidy in plants,plant evolution,haplotypes
                Human biology
                evolution, polyploidy in plants, plant evolution, haplotypes

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